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Merkouris E, Mavroudi T, Miliotas D, Tsiptsios D, Serdari A, Christidi F, Doskas TK, Mueller C, Tsamakis K. Probiotics' Effects in the Treatment of Anxiety and Depression: A Comprehensive Review of 2014-2023 Clinical Trials. Microorganisms 2024; 12:411. [PMID: 38399815 PMCID: PMC10893170 DOI: 10.3390/microorganisms12020411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/11/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Changes in the gut microbiome can affect cognitive and psychological functions via the microbiota-gut-brain (MGB) axis. Probiotic supplements are thought to have largely positive effects on mental health when taken in sufficient amounts; however, despite extensive research having been conducted, there is a lack of consistent findings on the effects of probiotics on anxiety and depression and the associated microbiome alterations. The aim of our study is to systematically review the most recent literature of the last 10 years in order to clarify whether probiotics could actually improve depression and anxiety symptoms. Our results indicate that the majority of the most recent literature suggests a beneficial role of probiotics in the treatment of depression and anxiety, despite the existence of a substantial number of less positive findings. Given probiotics' potential to offer novel, personalized treatment options for mood disorders, further, better targeted research in psychiatric populations is needed to address concerns about the exact mechanisms of probiotics, dosing, timing of treatment, and possible differences in outcomes depending on the severity of anxiety and depression.
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Affiliation(s)
- Ermis Merkouris
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
| | - Theodora Mavroudi
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
| | - Daniil Miliotas
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
| | - Dimitrios Tsiptsios
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
- 3rd Neurology Department, Aristotle University, 54124 Thessaloniki, Greece
| | - Aspasia Serdari
- Department of Child and Adolescent Psychiatry, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Foteini Christidi
- Neurology Department, Democritus University of Thrace, 68100 Alexandroupoli, Greece; (E.M.); (T.M.); (D.M.); (D.T.); (F.C.)
| | | | - Christoph Mueller
- Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London SE5 8AB, UK;
- Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, London SE5 8AF, UK
| | - Konstantinos Tsamakis
- Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London SE5 8AB, UK;
- Institute of Medical and Biomedical Education, St George’s, University of London, London SW17 0RE, UK
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Higher white-nose syndrome fungal isolate yields from UV-guided wing biopsies compared with skin swabs and optimal culture media. BMC Vet Res 2023; 19:40. [PMID: 36759833 PMCID: PMC9912490 DOI: 10.1186/s12917-023-03603-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 10/17/2022] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND North American bat populations have suffered severe declines over the last decade due to the Pseudogymnoascus destructans fungus infection. The skin disease associated with this causative agent, known as white-nose syndrome (WNS), is specific to bats hibernating in temperate regions. As cultured fungal isolates are required for epidemiological and phylogeographical studies, the purpose of the present work was to compare the efficacy and reliability of different culture approaches based on either skin swabs or wing membrane tissue biopsies for obtaining viable fungal isolates of P. destructans. RESULTS In total, we collected and analysed 69 fungal and 65 bacterial skin swabs and 51 wing membrane tissue biopsies from three bat species in the Czech Republic, Poland and the Republic of Armenia. From these, we obtained 12 viable P. destructans culture isolates. CONCLUSIONS Our results indicated that the efficacy of cultures based on wing membrane biopsies were significantly higher. Cultivable samples tended to be based on collections from bats with lower body surface temperature and higher counts of UV-visualised lesions. While cultures based on both skin swabs and wing membrane tissue biopsies can be utilised for monitoring and surveillance of P. destructans in bat populations, wing membrane biopsies guided by UV light for skin lesions proved higher efficacy. Interactions between bacteria on the host's skin also appear to play an important role.
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Epiphytic and Endophytic Fungi Colonizing Seeds of Two Poaceae Weed Species and Fusarium spp. Seed Degradation Potential In Vitro. Microorganisms 2023; 11:microorganisms11010184. [PMID: 36677476 PMCID: PMC9863844 DOI: 10.3390/microorganisms11010184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Fungi colonizing the surface and endosphere of two widespread Poaceae weed species, Avena fatua and Echinochloa crus-galli, were isolated to compare the taxonomic composition between the plant species, location, and year of the seed collection. The seed-degrading potential of Fusarium isolated from the seeds was tested by inoculating seeds of E. crus-galli with spore suspension. Molecular identification of epiphytic and endophytic fungal genera was performed by sequencing the ITS region of rDNA. Endophytes comprised of significantly lower fungal richness compared to epiphytes. A significant taxonomic overlap was observed between the endosphere and seed surface. The most abundant genera were Alternaria, Fusarium, Cladosporium, and Sarocladium. Analysis of similarities and hierarchical clustering showed that microbial communities were more dissimilar between the two plant species than between the years. Fusarium isolates with a high potential to infect and degrade E. crus-galli seeds in laboratory conditions belong to F. sporotrichioides and F. culmorum.
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Visagie CM, Boekhout T, Theelen B, Dijksterhuis J, Yilmaz N, Seifert KA. Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov. Yeast 2023; 40:7-31. [PMID: 36168284 PMCID: PMC10108157 DOI: 10.1002/yea.3816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 01/18/2023] Open
Abstract
A new species of the yeast genus Blastobotrys was discovered during a worldwide survey of culturable xerophilic fungi in house dust. Several culture-dependent and independent studies from around the world detected the same species from a wide range of substrates including indoor air, cave wall paintings, bats, mummies, and the iconic self-portrait of Leonardo da Vinci from ca 1512. However, none of these studies identified their strains, clones, or OTUs as Blastobotrys. We introduce the new species as Blastobotrys davincii f.a., sp. nov. (holotype CBS H-24879) and delineate it from other species using morphological, phylogenetic, and physiological characters. The new species of asexually (anamorphic) budding yeast is classified in Trichomonascaceae and forms a clade along with its associated sexual state genus Trichomonascus. Despite the decade-old requirement to use a single generic name for fungi, both names are still used. Selection of the preferred name awaits a formal nomenclatural proposal. We present arguments for adopting Blastobotrys over Trichomonascus and introduce four new combinations as Blastobotrys allociferrii (≡ Candida allociferrii), B. fungorum (≡ Sporothrix fungorum), B. mucifer (≡ Candida mucifera), and Blastobotrys vanleenenianus (≡ Trichomonascus vanleenenianus). We provide a nomenclatural review and an accepted species list for the 37 accepted species in the Blastobotrys/Trichomonascus clade. Finally, we discuss the identity of the DNA clones detected on the da Vinci portrait, and the importance of using appropriate media to isolate xerophilic or halophilic fungi.
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Affiliation(s)
- Cobus M Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.,Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Neriman Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.,Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada
| | - Keith A Seifert
- Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, Ontario, Canada.,Department of Biology, Carleton University, Ottawa, Ontario, Canada
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Nasif SO, Siddique AB, Siddique AB, Islam MM, Hassan O, Deepo DM, Hossain A. Prospects of endophytic fungi as a natural resource for the sustainability of crop production in the modern era of changing climate. Symbiosis 2022. [DOI: 10.1007/s13199-022-00879-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Fungicolous Fungi on Pseudosclerotial Plates and Apothecia of Hymenoscyphus fraxineus and Their Biocontrol Potential. Microorganisms 2022; 10:microorganisms10112250. [DOI: 10.3390/microorganisms10112250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/28/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2022] Open
Abstract
In the present work, research tasks were carried out in the search for fungi with potential biocontrol possibilities in relation to the ash dieback pathogen, Hymenoscyphus fraxineus. In the years 2012–2021, dead petioles of F. excelsior and F. mandshurica were collected, on which morphological structures of H. fraxineus showed unusual symptoms of dying (apothecia) and signs of colonization by other fungi (pseudosclerotial plates). Based on morphological and molecular phylogenetic data, 18 fungal taxa were identified. Thirteen of them belong to Ascomycota: Clonostachys rosea, Cl. solani, Cordyceps sp., Minimidochium sp., Nemania diffusa, Fusarium sp., Pestalotiopsis sp., Trichoderma atroviride, T. harzianum, T. polysporum, T. rodmanii, T. tomentosum, Trichoderma sp., and five other taxa are represented by Basidiomycota: Corticiales sp., Cyathus olla, Efibula sp., Gymnopus sp. and Polyporales sp. In 108 dual cultures in vitro, three different types of interactions were distinguished: (i) physical colony contact (5.6%), (ii) presence of an inhibition zone between the colonies (0.9%), and (iii) copartner overgrowth of H. fraxineus colonies and partial or complete replacement of the pathogen (93.5%). In the dual cultures, various morphological deformations of H. fraxineus hyphae were observed: the development of apical or intercalary cytoplasmic extrusions, development of internal hyphae of the test fungi in pathogens’ hyphae, the deformation and disruption of significant sections of H. fraxineus hyphae via lysis and mycoparasitism, complete desolation of H. fraxineus cells and breakdown of hyphae into short fragments, and disappearing of pigment in the affected hyphae of H. fraxineus. The inoculation tests performed in vivo or in glass Petrie dishes showed that all the identified taxa were able to lead to pathological changes in H. fraxineus apothecia, and the mycelium of some of them completely covered pseudosclerotial plates of H. fraxineus. It was emphasized in the discussion that such activity of these fungi in forest stands may contribute to the reduction in the H. fraxineus inoculum reservoir.
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Hagh-Doust N, Färkkilä SM, Hosseyni Moghaddam MS, Tedersoo L. Symbiotic fungi as biotechnological tools: Methodological challenges and relative benefits in agriculture and forestry. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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8
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Witty M. Examples of potato epidermis endophytes and rhizosphere microbes that may be human pathogens contributing to potato peel colic. ACTA ALIMENTARIA 2022. [DOI: 10.1556/066.2021.00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Potato tubers defend themselves against herbivores with endogenous secondary compounds such as solanine and scopolamine. They also recruit endophytes and members of the tuberosphere to repel herbivores. Many of these endophyte defence features are overcome by cooking, with some notable exceptions that have been identified by rDNA analysis of potato peel samples and may account for some previously unrecognised features of potato peel colic. This is relevant regarding the rather modern way of cooking, where the potato peel is left intact in food and consumed.
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Affiliation(s)
- M. Witty
- Math and Science Department, School of Pure and Applied Sciences, Florida SouthWestern State College, 8099 College Parkway, Fort Myers, Florida 33919, USA
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9
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Bilański P, Kowalski T. Fungal endophytes in Fraxinus excelsior petioles and their in vitro antagonistic potential against the ash dieback pathogen Hymenoscyphus fraxineus. Microbiol Res 2022; 257:126961. [PMID: 35042053 DOI: 10.1016/j.micres.2022.126961] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 12/05/2021] [Accepted: 01/02/2022] [Indexed: 02/08/2023]
Abstract
Fungal endophytes were isolated from 250 asymptomatic leaf petioles of Fraxinus excelsior collected from trees showing symptoms of ash dieback in five forest sites in southern Poland. Fungal isolations yielded 1646 colonies representing 97 taxa, including 92 Ascomycota and 5 Basidiomycota species. The most common Ascomycota comprised Nemania serpens (38.0 % of colonized petioles), Diaporthe eres (33.6 %), Venturia fraxini (26.4 %), Diaporthe sp. 1 (20.4 %), Alternaria sp. 1 (14.8 %), Colletotrichum acutatum (14.8 %), Nemania diffusa (14.0 %), Colletotrichum gloeosporioides (12.4 %) and Colletotrichum sp. (12.4 %). The occurrence of all these taxa except Alternaria sp. 1 was significantly different between the studied forest sites. Two yeast species, Vishniacozyma foliicola (4.8 %) and Cystobasidium pinicola (2.8 %), dominated among the Basidiomycota endophytes detected. All the fungal endophytes were tested in dual culture antagonistic assays against two strains of Hymenoscyphus fraxineus, resulting in the development of four interaction types. The interactions included the physical contact of co-partners' mycelia (41.8 %), development of an inhibition zone (47.4 %), growth of endophyte mycelia over H. fraxineus colonies (9.3 %) and growth of H. fraxineus mycelia over endophyte colonies (1.5 %). The strongest antibiotic activity against H. fraxineus, measured by the width of the inhibition zone, was observed for Cytospora pruinosa, Fusarium lateritium, Phoma sp. 2, Pleosporales sp. 2 and Thielavia basicola. A variety of morphophysiological deformations of H. fraxineus hyphae were observed under endophyte pressure: spiral twist of the hyphae, formation of cytoplasmic extrusions, development of torulose hyphae and excessive lateral branching of the hyphae. The strongest antagonistic effects, coupled with the potential to overgrow H. fraxineus colonies, was shown by Clonostachys rosea, Nemania diffusa, N. serpens, Peniophora cinerea, Rosellinia corticium and Xylaria polymorpha. Some of these species were able to attack H. fraxineus hyphae in a mycoparasitic manner. The antagonistic activities included the physical penetration of H. fraxineus hyphae, dissolution of hyphal cell walls, disappearance of pigmentation, disintegration of hyphae and degradation of other fungal structures. In contrast, one of the most commonly detected endophytes in ash leaves, Venturia fraxini, did not show in vitro antagonistic potential against H. fraxineus. Finally, we discuss the potential of the detected fungal endophytes to combat H. fraxineus invasion, the cause of ash decline in Europe.
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Affiliation(s)
- Piotr Bilański
- Department of Forest Ecosystem Protection, Faculty of Forestry, University of Agriculture in Cracow, 31-425 Cracow, Al. 29-Listopada 46, Poland
| | - Tadeusz Kowalski
- Department of Forest Ecosystem Protection, Faculty of Forestry, University of Agriculture in Cracow, 31-425 Cracow, Al. 29-Listopada 46, Poland.
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10
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Abstract
AbstractYeasts, usually defined as unicellular fungi, occur in various fungal lineages. Hence, they are not a taxonomic unit, but rather represent a fungal lifestyle shared by several unrelated lineages. Although the discovery of new yeast species occurs at an increasing speed, at the current rate it will likely take hundreds of years, if ever, before they will all be documented. Many parts of the earth, including many threatened habitats, remain unsampled for yeasts and many others are only superficially studied. Cold habitats, such as glaciers, are home to a specific community of cold-adapted yeasts, and, hence, there is some urgency to study such environments at locations where they might disappear soon due to anthropogenic climate change. The same is true for yeast communities in various natural forests that are impacted by deforestation and forest conversion. Many countries of the so-called Global South have not been sampled for yeasts, despite their economic promise. However, extensive research activity in Asia, especially China, has yielded many taxonomic novelties. Comparative genomics studies have demonstrated the presence of yeast species with a hybrid origin, many of them isolated from clinical or industrial environments. DNA-metabarcoding studies have demonstrated the prevalence, and in some cases dominance, of yeast species in soils and marine waters worldwide, including some surprising distributions, such as the unexpected and likely common presence of Malassezia yeasts in marine habitats.
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11
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Fungi Detected in the Previous Year’s Leaf Petioles of Fraxinus excelsior and Their Antagonistic Potential against Hymenoscyphus fraxineus. FORESTS 2021. [DOI: 10.3390/f12101412] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Studies on fungal communities in the previous year’s leaf petioles of Fraxinus excelsior found in litter in five ash stands in southern Poland were made in 2017. Fungi were identified on the basis of isolation from 300 surface sterilized leaf petioles and by in situ inventory of fruit bodies (on 600 petioles, in spring and autumn). Identification was based on morphology of colonies and fruit bodies, and sequencing of ITS region of the rRNA gene cluster. In total, 2832 isolates from 117 taxa (Ascomycota—100; Basidiomycota—15; Mucoromycota—2 taxa) were obtained with the isolation method. The most frequent taxa (with frequency >10%) were: Nemania serpens, Hymenoscyphus fraxineus, Alternaria sp. 1, Boeremia sp., Helotiales sp. 1, Epicoccum nigrum, Venturia fraxini, Fusarium sp., Fusarium lateritium, Nemania diffusa, Typhula sp. 2 (in descending order). In total, 45 taxa were detected with the in situ inventory method. Eleven taxa were classified as dominant: Hymenoscyphus fraxineus, Venturia fraxini, Leptosphaeria sp. 2, Cyathicula fraxinophila, Typhula sp. 2, Hypoderma rubi, Pyrenopeziza petiolaris, Cyathicula coronata, Hymenoscyphus scutula, Leptosphaeria sclerotioides and Hymenoscyphus caudatus. Among 202 leaf petioles colonized by H. fraxineus, 177 petioles also showed fructification of 26 other fungi. All the isolated saprotrophs were tested in dual-culture assay for antagonism to two strains of H. fraxineus. Three interaction types were observed: type A, mutual direct contact, when the two fungi meet along the contact line (occurred with 43.3% of test fungi); type B, with inhibition zone between colonies (with 46.9% of test fungi); type C, when the test fungus overgrows the colony of H. fraxineus (with 9.8% of test fungi). The possible contribution of the fungal saprotrophs in limiting of the expansion of H. fraxineus in ash leaf petioles, which may result in reduction in the inoculum of ash dieback causal agent, is discussed.
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12
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Rämä T, Quandt CA. Improving Fungal Cultivability for Natural Products Discovery. Front Microbiol 2021; 12:706044. [PMID: 34603232 PMCID: PMC8481835 DOI: 10.3389/fmicb.2021.706044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
The pool of fungal secondary metabolites can be extended by activating silent gene clusters of cultured strains or by using sensitive biological assays that detect metabolites missed by analytical methods. Alternatively, or in parallel with the first approach, one can increase the diversity of existing culture collections to improve the access to new natural products. This review focuses on the latter approach of screening previously uncultured fungi for chemodiversity. Both strategies have been practiced since the early days of fungal biodiscovery, yet relatively little has been done to overcome the challenge of cultivability of as-yet-uncultivated fungi. Whereas earlier cultivability studies using media formulations and biological assays to scrutinize fungal growth and associated factors were actively conducted, the application of modern omics methods remains limited to test how to culture the fungal dark matter and recalcitrant groups of described fungi. This review discusses the development of techniques to increase the cultivability of filamentous fungi that include culture media formulations and the utilization of known chemical growth factors, in situ culturing and current synthetic biology approaches that build upon knowledge from sequenced genomes. We list more than 100 growth factors, i.e., molecules, biological or physical factors that have been demonstrated to induce spore germination as well as tens of inducers of mycelial growth. We review culturing conditions that can be successfully manipulated for growth of fungi and visit recent information from omics methods to discuss the metabolic basis of cultivability. Earlier work has demonstrated the power of co-culturing fungi with their host, other microorganisms or their exudates to increase their cultivability. Co-culturing of two or more organisms is also a strategy used today for increasing cultivability. However, fungi possess an increased risk for cross-contaminations between isolates in existing in situ or microfluidics culturing devices. Technological improvements for culturing fungi are discussed in the review. We emphasize that improving the cultivability of fungi remains a relevant strategy in drug discovery and underline the importance of ecological and taxonomic knowledge in culture-dependent drug discovery. Combining traditional and omics techniques such as single cell or metagenome sequencing opens up a new era in the study of growth factors of hundreds of thousands of fungal species with high drug discovery potential.
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Affiliation(s)
- Teppo Rämä
- Marbio, Norwegian College of Fishery Science, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
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Smercina DN, Bailey VL, Hofmockel KS. Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function. FEMS Microbiol Ecol 2021; 97:6315324. [PMID: 34223869 DOI: 10.1093/femsec/fiab091] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/01/2021] [Indexed: 11/13/2022] Open
Abstract
Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.
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Affiliation(s)
- Darian N Smercina
- Biological Sciences Division, Earth and Biological Sciences Directorate, 3335 Innovation Blvd, Richland, WA, 99354, USA
| | - Vanessa L Bailey
- Biological Sciences Division, Earth and Biological Sciences Directorate, 3335 Innovation Blvd, Richland, WA, 99354, USA
| | - Kirsten S Hofmockel
- Biological Sciences Division, Earth and Biological Sciences Directorate, 3335 Innovation Blvd, Richland, WA, 99354, USA.,Department of Agronomy, Iowa State University, 716 Farm House Ln, Ames, IA 50011, USA
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Réblová M, Nekvindová J, Kolařík M, Hernández-Restrepo M. Delimitation and phylogeny of Dictyochaeta, and introduction of Achrochaeta and Tubulicolla, genera nova. Mycologia 2021; 113:390-433. [PMID: 33595417 DOI: 10.1080/00275514.2020.1822095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dictyochaeta (Chaetosphaeriaceae) is a phialidic dematiaceous hyphomycete with teleomorphs classified in Chaetosphaeria. It is associated with significant variability of asexual morphological traits, which led to its broad delimitation. In the present study, six loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), nuc 18S rDNA (18S), nuc 28S rDNA (28S), DNA-directed RNA polymerase II second largest subunit gene (RPB2), translation elongation factor 1-α (TEF1-α), and β-tubulin (TUB2), along with comparative morphological and cultivation studies, are used to reevaluate the concept of Dictyochaeta and establish species boundaries. Based on revised species, morphological characteristics of conidia (shape, septation, absence or presence of setulae), collarettes (shape), and setae (presence or absence) and an extension of the conidiogenous cell proved to be important at the generic level. The dual DNA barcoding using ITS and TEF1-α, together with TUB2, facilitated accurate identification of Dictyochaeta species. Thirteen species are accepted, of which seven are characterized in this study; an identification key is provided. It was revealed that D. fuegiana, the type species, is a complex of three distinct species including D. querna and the newly described D. stratosa. Besides, a new species, D. detriticola, and two new combinations, D. callimorpha and D. montana, are proposed. An epitype of D. montana is selected. Dictyochaeta includes saprobes on decaying wood, bark, woody fruits, and fallen leaves. Dictyochaeta is shown to be distantly related to the morphologically similar Codinaea, which is resolved as paraphyletic. Chaetosphaeria talbotii with a Dictyochaeta anamorph represents a novel lineage in the Chaetosphaeriaceae; it is segregated from Dictyochaeta, and a new genus Achrochaeta is proposed. Multigene phylogenetic analysis revealed that D. cylindrospora belongs to the Vermiculariopsiellales, and a new genus Tubulicolla is introduced.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany, Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
| | - Jana Nekvindová
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, 142 20 Prague 4, Czech Republic
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15
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Abstract
Four new Talaromyces species without any close relatives are reported here, namely, T. aureolinus (ex-type AS3.15865 T), T. bannicus (ex-type AS3.15862 T), T. penicillioides (ex-type AS3.15822 T), and T. sparsus (ex-type AS3.16003 T). Morphologically, T. aureolinus is unique in producing orange-yellow mycelium and gymnothecia, singly borne asci, and ellipsoidal, spiny ascospores. Talaromyces bannicus is characterized by the slow growth rate, polymorphic conidiophores, inconsistent stipe lengths, and pyriform to ellipsoidal, echinulate conidia. Talaromyces penicillioides is distinguished by good growth and sporulation on malt extract agar (MEA) and yeast extract sucrose agar (YES) media, resembling the colony appearances of certain Penicillium species, and appressed biverticillate and occasionally monoverticillate penicilli bearing globose to ellipsoidal, echinulate conidia. Talaromyces sparsus has wide, submerged colony margins with sparse aerial mycelium, and conidial areas overlaid with yellow-green, sterile hyphae on MEA medium. These four new species are well supported by individual phylogenetic trees based on β-tubulin (BENA), calmodulin (CALM), DNA-dependent RNA polymerase II second largest subunit (RPB2), and internal transcribed spacer region (ITS) gene sequences and the tree of the concatenated BENA-CALM-RPB2 sequence.
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Affiliation(s)
- Shangzhu Wei
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, China
| | - Xiuli Xu
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, China
| | - Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Crespo G, Pérez-Victoria I, Ortiz-López FJ, González-Menéndez V, de la Cruz M, Cautain B, Sánchez P, Vicente F, Genilloud O, Reyes F. Structural Elucidation of Antibiotic TKR2999, an Antifungal Lipodepsipeptide Isolated from the Fungus Foliophoma fallens. Antibiotics (Basel) 2020; 9:antibiotics9060278. [PMID: 32466351 PMCID: PMC7345921 DOI: 10.3390/antibiotics9060278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 11/16/2022] Open
Abstract
An antifungal lipodepsipeptide was obtained from cultures of the fungus Foliophoma fallens CF-236885. Its structure, elucidated by HRMS and NMR spectroscopy, contained Gly, Thr, Asn, β-Ala, Orn, Ala, two Ser residues, and 3-hydroxy-4-methylhexadecanoic acid. The absolute configuration of its amino acid residues was determined using Marfey’s analysis and J-based configuration analysis helped to establish the relative configuration of the 3-hydroxy-4-methylhexadecanoic acid moiety. A literature search retrieved a patent describing antibiotic TKR2999 (1), whose non-disclosed structure was confirmed to be identical to that found for our compound, according to its physicochemical properties and NMR spectra. Compound 1 displayed potent antifungal activity against Aspergillus fumigatus and a panel of Candida strains.
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Shirouzu T, Matsuoka S, Doi H, Nagata N, Ushio M, Hosaka K. Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms. Sci Rep 2020; 10:3057. [PMID: 32080243 PMCID: PMC7033186 DOI: 10.1038/s41598-020-59620-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/03/2020] [Indexed: 11/28/2022] Open
Abstract
Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DNA (eDNA) metabarcoding of decaying branches. Among the 28 operational taxonomic units (OTUs) detected during a three-year investigation, 10 each were from fruiting bodies and cultured mycelia and 27 were detected as eDNA sequences. eDNA metabarcoding revealed various lineages across the Dacrymycetes phylogeny. Alternatively, fruiting-body and culture surveys uncovered only ~50% of the OTUs detected through eDNA metabarcoding, suggesting that several inconspicuous or difficult-to-isolate strains are latent in the environment. Further, eDNA and culture surveys revealed early-diverging clades that were not identified in the fruiting-body survey. Thus, eDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations.
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Affiliation(s)
- Takashi Shirouzu
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan.
| | - Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Nobuaki Nagata
- Collection Center, National Museum of Nature and Science, 4-1-1 Amakubo, Ibaraki, 305-0005, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, 606-8501, Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
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19
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Masumoto H, Degawa Y. The effect of surface sterilization and the type of sterilizer on the genus composition of lichen-inhabiting fungi with notes on some frequently isolated genera. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Ren F, Dong W, Yan DH. Organs, Cultivars, Soil, and Fruit Properties Affect Structure of Endophytic Mycobiota of Pinggu Peach Trees. Microorganisms 2019; 7:E322. [PMID: 31492017 PMCID: PMC6780621 DOI: 10.3390/microorganisms7090322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 11/16/2022] Open
Abstract
Pinggu peach (Prunus persica (L.)) has great economic and ecological value in north China. As a plant, the peach is naturally colonized by a variety of endophytic fungi, which are very important for tree growth and health. However, the mycobiota composition and their affecting factors of the peach trees are still unknown. In our study, the fungal communities in flowers, leaves, stems, and roots of the three cultivars (Dajiubao, Qingfeng, and Jingyan) of Pinggu peach trees and in the rhizosphere soils were investigated by both Illumina Miseq sequencing of ITS rDNA and traditional culturing methods. For organs, except for roots, flowers had the highest fungal richness and diversity, while the leaves had the lowest richness and diversity. Ascomycota and Basidiomycota were the most abundant phyla among samples. The fungal assemblage composition of each organ was distinctive. Fungal communities of the three cultivars also differed from each other. The fungal community structure significantly correlated with soil pH, soil K, fruit soluble solid content, and fruit titratable acidity with the redundancy analysis (RDA). Most isolated fungal strains can be found within high-throughput sequencing identified taxa. This study indicates that plant organs, the cultivars, the soil, and fruit properties may have profound effects on the endophytic fungal community structure associated with Pinggu peach trees. With this study, microbiota-mediated pathogen protection and fruit quality promotion associated with peach trees could be further studied.
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Affiliation(s)
- Fei Ren
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing 102300, China.
| | - Wei Dong
- China Electric Power Research Institute, Beijing 100192, China
| | - Dong-Hui Yan
- The Key Laboratory of Forest Protection affiliated to State Forestry Administration of China, Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.
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21
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Rasheed U, Wu H, Wei J, Ou X, Qin P, Yao X, Chen H, Chen AJ, Liu B. A polyphasic study of Aspergillus section Flavi isolated from corn in Guangxi, China- a hot spot of aflatoxin contamination. Int J Food Microbiol 2019; 310:108307. [PMID: 31476582 DOI: 10.1016/j.ijfoodmicro.2019.108307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 01/22/2023]
Abstract
Aspergillus section Flavi is widely known as a potential threat to contaminate agricultural products and food commodities. In this study, a polyphasic approach consisting of micro- and macro-morphological, chemical and molecular features, was applied to survey the Aspergillus section Flavi population in corn collected from Guangxi, China. Based on multigene phylogenies as well as morphological observations, Aspergillus flavus (192/195), A. arachidicola (1/195), A. pseudonomius (1/195) and A. novoparasiticus (1/195) were found to be the predominant section Flavi population. Among them, 31 representative isolates were selected for mycotoxin determination. The results showed that Aspergillus flavus chemotype I was most common, chemotype IV was also detected with low incidence and low CPA amounts, while chemotypes II and III were absent. Other tested species including A. arachidicola, A. pseudonomius, and A. novoparasiticus produced all types of aflatoxins, but none of them produced CPA. The polyphasic approach applied in this study permitted reliable understanding of the prevailing Aspergillus section Flavi population and their mycotoxin profiles. Knowledge of the prevailing section Flavi population will aid in developing a sustainable strategy to mitigate the effects of aflatoxin contamination. This study suggests that CPA contamination of food should be considered while conducting mycotoxigenic surveys of food commodities, and the same should be considered while planning a bio-control strategy to control aflatoxin contamination.
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Affiliation(s)
- Usman Rasheed
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Hao Wu
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Jinfan Wei
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Xiaoyun Ou
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Peisheng Qin
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Xiaohua Yao
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Han Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Amanda Juan Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
| | - Bin Liu
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning 530005, China.
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22
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Cercospora sp. as a source of anti-aging polyketides targeting 26S proteasome and scale-up production in submerged bioreactor. J Biotechnol 2019; 301:88-96. [PMID: 31152756 DOI: 10.1016/j.jbiotec.2019.05.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/14/2019] [Accepted: 05/27/2019] [Indexed: 12/31/2022]
Abstract
From a large screening of microbial extracts for the discovery of proteasome modulating natural products, the fungal strain Cercospora sp. (CF-223709) was selected as the most promising for further investigation. Different liquid cultures of the strain were initially screened for their anti-oxidant activity (DPPH, ABTS) and for their cytotoxicity against the A2058, HepG2 and CCD25sk cell lines. A detailed chemical analysis and evaluation of the capacity to activate 26S-proteasome was followed for the most active extract. Three main polyketides were isolated and characterized by extensive analysis of NMR and HRMS spectra data as penialidine F (1), fulvic acid (2), and SB238569 (3). Fulvic acid showed the most significant anti-oxidant activity. Its IC50 value (8.16 μM) against the ABTS radical resulted 3-fold lower than the standard trolox. Fulvic acid also demonstrated a significant effect on proteasome by enhancing the chymotrypsin- and caspase-like activities of the 26S proteasome of human fibroblasts by 71.43% and 37.5% at 1 μM, respectively. Furthermore by scaling up the culture in a 30 L submerged bioreactor, Cercospora sp. produced up to 162.6 ± 1.3 mg of fulvic acid/L. Our findings suggest that CF-223709 can be a promising source of proteasome activating natural compounds.
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23
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Overy DP, Rämä T, Oosterhuis R, Walker AK, Pang KL. The Neglected Marine Fungi, Sensu stricto, and Their Isolation for Natural Products' Discovery. Mar Drugs 2019; 17:md17010042. [PMID: 30634599 PMCID: PMC6356354 DOI: 10.3390/md17010042] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/20/2018] [Accepted: 12/22/2018] [Indexed: 12/03/2022] Open
Abstract
Despite the rapid development of molecular techniques relevant for natural product research, culture isolates remain the primary source from which natural products chemists discover and obtain new molecules from microbial sources. Techniques for obtaining and identifying microbial isolates (such as filamentous fungi) are thus of crucial importance for a successful natural products’ discovery program. This review is presented as a “best-practices guide” to the collection and isolation of marine fungi for natural products research. Many of these practices are proven techniques used by mycologists for the isolation of a broad diversity of fungi, while others, such as the construction of marine baiting stations and the collection and processing of sea foam using dilution to extinction plating techniques, are methodological adaptations for specialized use in marine/aquatic environments. To this day, marine fungi, Sensu stricto, remain one of the few underexplored resources of natural products. Cultivability is one of the main limitations hindering the discovery of natural products from marine fungi. Through encouraged collaboration with marine mycologists and the sharing of historically proven mycological practices for the isolation of marine fungi, our goal is to provide natural products chemists with the necessary tools to explore this resource in-depth and discover new and potentially novel natural products.
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Affiliation(s)
- David P Overy
- Ottawa Research and Development Centre, Agriculture and AgriFood Canada, Ottawa, ON K1A 0C6, Canada.
| | - Teppo Rämä
- Marbio, Norwegian College of Fishery Science, University of Tromsø-The Arctic University of Norway, 9019 Tromsø, Norway.
| | - Rylee Oosterhuis
- Department of Biology, Acadia University, Wolfville, NS B4P2R6, Canada.
| | - Allison K Walker
- Department of Biology, Acadia University, Wolfville, NS B4P2R6, Canada.
| | - Ka-Lai Pang
- Institute of Marine Biology and Centre of Excellence for the Oceans, National Taiwan Ocean University, 20224 Keelung, Taiwan.
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24
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25
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Lacerda LT, Gusmão LFP, Rodrigues A. Diversity of endophytic fungi in Eucalyptus microcorys assessed by complementary isolation methods. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1385-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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26
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Albrectsen BR, Siddique AB, Decker VHG, Unterseher M, Robinson KM. Both plant genotype and herbivory shape aspen endophyte communities. Oecologia 2018; 187:535-545. [PMID: 29492690 PMCID: PMC5997111 DOI: 10.1007/s00442-018-4097-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/13/2018] [Indexed: 12/29/2022]
Abstract
Salicinoid phenolic glycosides are common defence substances in salicaceous trees and specialist leaf beetles use these compounds for their own defence against predators. Salicinoids vary qualitatively and qualitatively in aspen (Populus tremula) and this variation has a genetic basis. The foliar endophyte mycobiome is plentiful and we hypothesised that it is related to plant genotype, potentially mediated by salicinoid composition, and that interactions with the leaf beetle Chrysomela tremula may alter this relationship. We studied these three-way interactions in controlled greenhouse experiments. Endophytic fungi were isolated from sterilised leaf tissues with and without beetle damage, and from beetles. We confirmed that endophyte composition was influenced by host genotype. Beetle activity added generalist morphs to the mycobiome that overrode the initial host association. Yeast-like genera (Cryptococcus and Rhodotorula) were isolated only from beetle-damaged tissues and from beetles, whereas fast-growing filamentous fungi dominated beetle-free control plants. Competition experiments between filamentous fungi of plant origin and beetle-related yeasts suggested interaction of both stimulating and inhibiting modes of action amongst the fungi. As a result, we detected examples of amensalism, commensalism, parasitism and competition between the morphs tested, but we found no evidence of mutualism, and consequently no co-evolutionary relationship could be demonstrated, between yeasts carried by beetles, host genotype and associated filamentous morphs. Endophyte studies are method-dependent and high-throughput sequencing technology best define the fungal mycobiome, culturing however continues to be a cheap way to provide fundamental ecological insights and it is also required for experimental studies.
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Affiliation(s)
| | - Abu Bakar Siddique
- Ernst-Moritz-Arndt Universität Greifswald, Institut für Botanik und Landschaftsökologie, Soldmannstr. 15, 17487, Greifswald, Germany
| | - Vicki Huizu Guo Decker
- Department of Plant Physiology, Umeå University, Umeå Plant Science Centre, Umeå, Sweden
| | - Martin Unterseher
- Ernst-Moritz-Arndt Universität Greifswald, Institut für Botanik und Landschaftsökologie, Soldmannstr. 15, 17487, Greifswald, Germany.,Evangelisches Schulzentrum Martinschule, Max-Planck- Str. 7, 17491, Greifswald, Germany
| | - Kathryn M Robinson
- Department of Plant Physiology, Umeå University, Umeå Plant Science Centre, Umeå, Sweden
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27
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Zhang Z, Liu F, Zhou X, Liu X, Liu S, Cai L. Culturable mycobiota from Karst caves in China, with descriptions of 20 new species. PERSOONIA 2017; 39:1-31. [PMID: 29503468 PMCID: PMC5832949 DOI: 10.3767/persoonia.2017.39.01] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 01/09/2017] [Indexed: 11/25/2022]
Abstract
Karst caves are distinctly characterised by darkness, low to moderate temperatures, high humidity, and scarcity of organic matter. During the years of 2014-2015, we explored the mycobiota in two unnamed Karst caves in Guizhou province, China, and obtained 563 fungal strains via the dilution plate method. Preliminary ITS analyses of these strains suggested that they belonged to 246 species in 116 genera, while 23.5 % were not identified to species level. Among these species, 85.8 % (211 species) belonged to Ascomycota; 7.3 % (18 species) belonged to Basidiomycota; 6.9 % (17 species) belonged to Mucoromycotina. The majority of these species have been previously known from other environments, mostly from plants or animals as pathogens, endophytes or via a mycorrhizal association. We also found that 59 % of these species were discovered for the first time from Karst caves, including 20 new species that are described in this paper. The phylogenetic tree based on LSU sequences revealed 20 new species were distributed in six different orders. In addition, ITS or multi-locus sequences were employed to infer the phylogenetic relationships of new taxa with closely related allies. We conclude that Karst caves encompass a high fungal diversity, including a number of previously unknown species. Novel species described include: Amphichorda guana, Auxarthronopsis guizhouensis, Biscogniauxia petrensis, Cladorrhinum globisporum, Collariella quadrum, Gymnoascus exasperatus, Humicola limonisporum, Metapochonia variabilis, Microascus anfractus, Microascus globulosus, Microdochium chrysanthemoides, Paracremonium variiforme, Pectinotrichum chinense, Phaeosphaeria fusispora, Ramophialophora globispora, Ramophialophora petraea, Scopulariopsis crassa, Simplicillium calcicola, Volutella aeria, and Wardomycopsis longicatenata.
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Affiliation(s)
- Z.F. Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - F. Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - X. Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - X.Z. Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - S.J. Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
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28
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Johnston PR, Park D, Smissen RD. Comparing diversity of fungi from living leaves using culturing and high-throughput environmental sequencing. Mycologia 2017; 109:643-654. [PMID: 29140754 DOI: 10.1080/00275514.2017.1384712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
High-throughput sequencing technologies using amplicon approaches have changed the way that studies investigating fungal distribution are undertaken. These powerful and time-efficient technologies have the potential for the first time to accurately map fungal distributions across landscapes or changes in diversity across ecological or biological gradients of interest. There is no requirement for a fungus to form a fruiting body to be detected, and both culturable and nonculturable organisms can be detected. Here we use high-throughput amplicon sequencing from bulk DNA extracts to test the impact that biases associated with culture-based methods had on an earlier study that compared the influence of site and host on fungal diversity in Nothofagaceae forests in New Zealand. Both detection methods sampled tissue from the same set of symptomless, living leaves. We found that both the culturing and high-throughput approaches show that host is a stronger driver of fungal community structure than site, but that both methods have some taxonomic biases. We also found that the individual trees selected for high-throughput sampling can impact the alpha-diversity detected and through this could potentially affect subsequent analyses based on a comparison of this diversity.
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Affiliation(s)
- Peter R Johnston
- a Landcare Research , Private Bag 92170 , Auckland 1142, New Zealand
| | - Duckchul Park
- a Landcare Research , Private Bag 92170 , Auckland 1142, New Zealand
| | - Rob D Smissen
- a Landcare Research , Private Bag 92170 , Auckland 1142, New Zealand
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29
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Humphries Z, Seifert KA, Hirooka Y, Visagie CM. A new family and genus in Dothideales for Aureobasidium-like species isolated from house dust. IMA Fungus 2017; 8:299-315. [PMID: 29242777 PMCID: PMC5729714 DOI: 10.5598/imafungus.2017.08.02.05] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/10/2017] [Indexed: 11/01/2022] Open
Abstract
An international survey of house dust collected from eleven countries using a modified dilution-to-extinction method yielded 7904 isolates. Of these, six strains morphologically resembled the asexual morphs of Aureobasidium and Hormonema (sexual morphs ?Sydowia), but were phylogenetically distinct. A 28S rDNA phylogeny resolved strains as a distinct clade in Dothideales with families Aureobasidiaceae and Dothideaceae their closest relatives. Further analyses based on the ITS rDNA region, β-tubulin, 28S rDNA, and RNA polymerase II second largest subunit confirmed the distinct status of this clade and divided strains among two consistent subclades. As a result, we introduce a new genus and two new species as Zalariaalba and Z. obscura, and a new family to accommodate them in Dothideales. Zalaria is a black yeast-like fungus, grows restrictedly and produces conidiogenous cells with holoblastic synchronous or percurrent conidiation. Zalaria microscopically closely resembles Hormonema by having only one to two loci per conidiogenous cell, but species of our new genus generally has more restricted growth. Comparing the two species, Z. obscura grows faster on lower water activity (aw) media and produces much darker colonies than Z. alba after 7 d. Their sexual states, if extant, are unknown.
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Affiliation(s)
- Zoë Humphries
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada, K1A 0C6
| | - Keith A Seifert
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada, K1A 0C6.,Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, ON, Canada, K1N 6N5
| | - Yuuri Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo, Japan
| | - Cobus M Visagie
- Biodiversity (Mycology), Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada, K1A 0C6.,Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, ON, Canada, K1N 6N5.,Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood 0121, Pretoria, South Africa
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30
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Abstract
Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 isolates comprising all currently accepted species and was strongly supported by Maximum likelihood (ML) and Bayesian inferrence (BI) analysis based on β-tubulin (benA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) loci. More than 300 strains belonging to sect. Restricti from various isolation sources and four continents were characterized by DNA sequencing, and 193 isolates were selected for phylogenetic analyses and phenotypic studies. Species delimitation methods based on multispecies coalescent model were employed on DNA sequences from four loci, i.e., ID region of rDNA (ITS + 28S), CaM, benA and RPB2, and supported recognition of 21 species, including 14 new. All these species were also strongly supported in ML and BI analyses. All recognised species can be reliably identified by all four examined genetic loci. Phenotype analysis was performed to support the delimitation of new species and includes colony characteristics on seven cultivation media incubated at several temperatures, growth on an osmotic gradient (six media with NaCl concentration from 0 to 25 %) and analysis of morphology including scanning electron microscopy. The micromorphology of conidial heads, vesicle dimensions, temperature profiles and growth parameters in osmotic gradient were useful criteria for species identification. The vast majority of species in sect. Restricti produce asperglaucide, asperphenamate or both in contrast to species in sect. Aspergillus. Mycophenolic acid was detected for the first time in at least six members of the section. The ascomata of A. halophilicus do not contain auroglaucin, epiheveadride or flavoglaucin which are common in sect. Aspergillus, but shares the echinulins with sect. Aspergillus.
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Key Words
- Aspergillus canadensis Visagie, Yilmaz, F. Sklenar & Seifert
- Aspergillus clavatophorus F. Sklenar, S.W. Peterson & Hubka
- Aspergillus destruens Zalar, F. Sklenar, S.W. Peterson & Hubka
- Aspergillus domesticus F. Sklenar, Houbraken, Zalar & Hubka
- Aspergillus glabripes F. Sklenar, Ž. Jurjević & Hubka
- Aspergillus hordei F. Sklenar, S.W. Peterson & Hubka
- Aspergillus infrequens F. Sklenar, S.W. Peterson & Hubka
- Aspergillus magnivesiculatus F. Sklenar, Zalar, Ž. Jurjević & Hubka
- Aspergillus pachycaulis F. Sklenar, S.W. Peterson, Ž. Jurjević & Hubka
- Aspergillus penicillioides
- Aspergillus pseudogracilis F. Sklenar, Ž. Jurjević & Hubka
- Aspergillus restrictus
- Aspergillus reticulatus F. Sklenar, Ž. Jurjević, S.W. Peterson & Hubka
- Aspergillus salinicola Zalar, F. Sklenar, Visagie & Hubka
- Aspergillus tardicrescens F. Sklenar, Houbraken, Zalar, & Hubka
- Aspergillus villosus F. Sklenar, S.W. Peterson & Hubka
- Eurotium
- food spoilage
- indoor fungi
- linear discriminant analysis
- multigene phylogeny
- multispecies coalescent model
- sick building syndrome
- xerophilic fungi
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Abstract
Xerophilic fungi, especially Aspergillus species, are prevalent in the built environment. In this study, we employed a combined culture-independent (454-pyrosequencing) and culture-dependent (dilution-to-extinction) approach to investigate the mycobiota of indoor dust collected from 93 buildings in 12 countries worldwide. High and low water activity (aw) media were used to capture mesophile and xerophile biodiversity, resulting in the isolation of approximately 9 000 strains. Among these, 340 strains representing seven putative species in Aspergillus subgenus Polypaecilum were isolated, mostly from lowered aw media, and tentatively identified based on colony morphology and internal transcribed spacer rDNA region (ITS) barcodes. Further morphological study and phylogenetic analyses using sequences of ITS, β-tubulin (BenA), calmodulin (CaM), RNA polymerase II second largest subunit (RPB2), DNA topoisomerase 1 (TOP1), and a pre-mRNA processing protein homolog (TSR1) confirmed the isolation of seven species of subgenus Polypaecilum, including five novel species: A. baarnensis, A. keratitidis, A. kalimae sp. nov., A. noonimiae sp. nov., A. thailandensis sp. nov., A. waynelawii sp. nov., and A. whitfieldii sp. nov. Pyrosequencing detected six of the seven species isolated from house dust, as well as one additional species absent from the cultures isolated, and three clades representing potentially undescribed species. Species were typically found in house dust from subtropical and tropical climates, often in close proximity to the ocean or sea. The presence of subgenus Polypaecilum, a recently described clade of xerophilic/xerotolerant, halotolerant/halophilic, and potentially zoopathogenic species, within the built environment is noteworthy.
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Affiliation(s)
- J.B. Tanney
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - C.M. Visagie
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
- Biosystematics Division, ARC-Plant Health and Protection, P/BagX134, Queenswood, 0121 Pretoria, South Africa
| | - N. Yilmaz
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
| | - K.A. Seifert
- Ottawa Research and Development Centre, Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
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Siddique AB, Khokon AM, Unterseher M. What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 2017. [DOI: 10.3897/mycokeys.20.11265] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Bills GF, Platas G, Overy DP, Collado J, Fillola A, Jiménez MR, Martín J, del Val AG, Vicente F, Tormo JR, Peláez F, Calati K, Harris G, Parish C, Xu D, Roemer T. Discovery of the parnafungins, antifungal metabolites that inhibit mRNA polyadenylation, from theFusarium larvarumcomplex and other Hypocrealean fungi. Mycologia 2017; 101:449-72. [DOI: 10.3852/08-163] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Fernando Peláez
- Centro de Investigación Básica, Merck, Sharp & Dohme de España S. A., Josefa Valcárcel 38, Madrid, E-28027, Spain
| | | | | | | | | | - Terry Roemer
- Merck Research Laboratories, 126 E. Lincoln Avenue, Rahway, New Jersey 07065
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Visagie CM, Yilmaz N, Renaud JB, Sumarah MW, Hubka V, Frisvad JC, Chen AJ, Meijer M, Seifert KA. A survey of xerophilic Aspergillus from indoor environment, including descriptions of two new section Aspergillus species producing eurotium-like sexual states. MycoKeys 2017. [DOI: 10.3897/mycokeys.19.11161] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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35
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Unterseher M, Siddique AB, Brachmann A, Peršoh D. Diversity and Composition of the Leaf Mycobiome of Beech (Fagus sylvatica) Are Affected by Local Habitat Conditions and Leaf Biochemistry. PLoS One 2016; 11:e0152878. [PMID: 27078859 PMCID: PMC4831807 DOI: 10.1371/journal.pone.0152878] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 03/21/2016] [Indexed: 11/18/2022] Open
Abstract
Comparative investigations of plant-associated fungal communities (mycobiomes) in distinct habitats and under distinct climate regimes have been rarely conducted in the past. Nowadays, high-throughput sequencing allows routine examination of mycobiome responses to environmental changes and results at an unprecedented level of detail. In the present study, we analysed Illumina-generated fungal ITS1 sequences from European beech (Fagus sylvatica) originating from natural habitats at two different altitudes in the German Alps and from a managed tree nursery in northern Germany. In general, leaf-inhabiting mycobiome diversity and composition correlated significantly with the origin of the trees. Under natural condition the mycobiome was more diverse at lower than at higher elevation, whereas fungal diversity was lowest in the artificial habitat of the tree nursery. We further identified significant correlation of leaf chlorophylls and flavonoids with both habitat parameters and mycobiome biodiversity. The present results clearly point towards a pronounced importance of local stand conditions for the structure of beech leaf mycobiomes and for a close interrelation of phyllosphere fungi and leaf physiology.
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Affiliation(s)
- Martin Unterseher
- Ernst-Moritz-Arndt Universität Greifswald, Institut für Botanik und Landschaftsökologie, Greifswald, Germany
- * E-mail:
| | - Abu Bakar Siddique
- Ernst-Moritz-Arndt Universität Greifswald, Institut für Botanik und Landschaftsökologie, Greifswald, Germany
| | | | - Derek Peršoh
- Ruhr-Universität Bochum, AG Geobotanik, Bochum, Germany
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Ortega-Morales BO, Narváez-Zapata J, Reyes-Estebanez M, Quintana P, De la Rosa-García SDC, Bullen H, Gómez-Cornelio S, Chan-Bacab MJ. Bioweathering Potential of Cultivable Fungi Associated with Semi-Arid Surface Microhabitats of Mayan Buildings. Front Microbiol 2016; 7:201. [PMID: 26941725 PMCID: PMC4763013 DOI: 10.3389/fmicb.2016.00201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/05/2016] [Indexed: 11/13/2022] Open
Abstract
Soil and rock surfaces support microbial communities involved in mineral weathering processes. Using selective isolation, fungi were obtained from limestone surfaces of Mayan monuments in the semi-arid climate at Yucatan, Mexico. A total of 101 isolates representing 53 different taxa were studied. Common fungi such as Fusarium, Pestalotiopsis, Trichoderma, and Penicillium were associated with surfaces and were, probably derived from airborne spores. In contrast, unusual fungi such as Rosellinia, Annulohypoxylon, and Xylaria were predominantly identified from mycelium particles of biofilm biomass. Simulating oligotrophic conditions, agar amended with CaCO3 was inoculated with fungi to test for carbonate activity. A substantial proportion of fungi, in particular those isolated from mycelium (59%), were capable of solubilizing calcium by means of organic acid release, notably oxalic acid as evidenced by ion chromatography. Contrary to our hypothesis, nutrient level was not a variable influencing the CaCO3 solubilization ability among isolates. Particularly active fungi (Annulohypoxylon stygium, Penicillium oxalicum, and Rosellinia sp.) were selected as models for bioweathering experiments with limestone-containing mesocosms to identify if other mineral phases, in addition to oxalates, were linked to bioweathering processes. Fungal biofilms were seen heavily covering the stone surface, while a biomineralized front was also observed at the stone-biofilm interface, where network of hyphae and mycogenic crystals was observed. X-ray diffraction analysis (XRD) identified calcite as the main phase, along with whewellite and wedellite. In addition, lower levels of citrate were detected by Attenuated Total Reflectance-Fourier-Transform Infrared Spectroscopy (ATR-FTIR). Overall, our results suggest that a diverse fungal community is associated with limestone surfaces insemi-arid climates. A subset of this community is geochemically active, excreting organic acids under quasi-oligotrophic conditions, suggesting that the high metabolic cost of exuding organic acids beneficial under nutrient limitation. Oxalic acid release may deteriorate or stabilize limestone surfaces, depending on microclimatic dynamics.
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Affiliation(s)
- Benjamín O. Ortega-Morales
- Departamento de Microbiología Ambiental y Biotecnología, Universidad Autónoma de CampecheCampeche, Mexico
| | - José Narváez-Zapata
- Centro de Biotecnología Genómica, Instituto Politécnico NacionalReynosa, Mexico
| | - Manuela Reyes-Estebanez
- Departamento de Microbiología Ambiental y Biotecnología, Universidad Autónoma de CampecheCampeche, Mexico
| | - Patricia Quintana
- Departamento de Física Aplicada, CINVESTAV, Unidad MéridaMérida, Mexico
| | | | - Heather Bullen
- Department of Chemistry, Northern Kentucky UniversityHighland Heights, OH, USA
| | - Sergio Gómez-Cornelio
- Departamento de Microbiología Ambiental y Biotecnología, Universidad Autónoma de CampecheCampeche, Mexico
- El Colegio de la Frontera SurCampeche, Mexico
| | - Manuel J. Chan-Bacab
- Departamento de Microbiología Ambiental y Biotecnología, Universidad Autónoma de CampecheCampeche, Mexico
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Shirouzu T, Uno K, Hosaka K, Hosoya T. Early-diverging wood-decaying fungi detected using three complementary sampling methods. Mol Phylogenet Evol 2016; 98:11-20. [PMID: 26850687 DOI: 10.1016/j.ympev.2016.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/17/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
Wood-decaying fungi are essential components of degradation systems in forest ecosystems. However, their species diversity and ecological features are largely unknown. Three methods are commonly used to investigate fungal diversity: fruiting body collection, culturing, and environmental DNA analysis. Because no single method fully characterises fungal diversity, complementary approaches using two or more methods are required. However, few studies have compared the different methods and determined the best way to characterise fungal diversity. To this end, we investigated wood-decomposing Dacrymycetes (Agaricomycotina, Basidiomycota) using a complementary approach combining fruiting body collection, culturing, and environmental DNA analysis, thereby offering an effective approach for investigating the diversity of saprotrophic mushrooms. Fruiting body collection, culturing, and environmental DNA analysis detected 11, 10, and 16 operational taxonomic units (OTUs; 25 OTUs in total) and identified three, seven, and seven novel lineages, respectively. The three methods were complementary to each other to detect greater Dacrymycetes diversity. The culturing and environmental DNA analysis identified three early-diverging lineages that were not identified in the fruiting body collection suggesting that diverse lineages lacking observable fruiting bodies remain undiscovered. Such lineages may be important to understand Dacrymycetes evolution. To detect early branches of Dacrymycetes more efficiently, we recommend a combined approach consisting of a primary environmental DNA survey to detect novel lineages and a secondary culture survey to isolate their living mycelia. This approach would be helpful for identifying otherwise-undetectable lineages, and could thus uncover missing links that are important for understanding the evolution of mushroom-forming fungi.
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Affiliation(s)
- Takashi Shirouzu
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan.
| | - Kunihiko Uno
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan.
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan.
| | - Tsuyoshi Hosoya
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan.
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38
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Exploitation of Fungal Biodiversity for Discovery of Novel Antibiotics. Curr Top Microbiol Immunol 2016; 398:303-338. [PMID: 27422786 DOI: 10.1007/82_2016_496] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fungi were among the first sources for antibiotics. The discovery and development of the penicillin-type and cephalosporin-type β-lactams and their synthetic versions were transformative in emergence of the modern pharmaceutical industry. They remain some of the most important antibiotics, even 70 years after their discovery. Meanwhile, thousands of fungal metabolites have been discovered, yet these metabolites have only contributed a few additional compounds that have entered clinical development. Substantial expansion in fungal biodiversity assessment along with the availability of modern "-OMICS" technology and revolutionary developments in fungal biotechnology have been made in the last 15 years subsequent to the exit of most of the big Pharma companies from the field of novel antibiotics discovery. Therefore, the timing seems opportune to revisit these fascinating chemically rich organisms as a reservoir of small-molecule templates for lead discovery. This review will describe ongoing interdisciplinary scenarios in which specialists in fungal biology collaborate with chemists, pharmacologists and biochemical and process engineers in order to reveal and make new antibiotics. The utility of a pre-selection process based on phylogenetic data and distribution of secondary metabolite encoding gene cluster will be highlighted. Examples of novel bioactive metabolites from fungi derived from special ecological groups and new phylogenetic lineages will also be discussed.
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39
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Fernandes EG, Pereira OL, da Silva CC, Bento CBP, de Queiroz MV. Diversity of endophytic fungi in Glycine max. Microbiol Res 2015; 181:84-92. [PMID: 26111593 DOI: 10.1016/j.micres.2015.05.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 05/27/2015] [Accepted: 05/30/2015] [Indexed: 01/13/2023]
Abstract
Endophytic fungi are microorganisms that live within plant tissues without causing disease during part of their life cycle. With the isolation and identification of these fungi, new species are being discovered, and ecological relationships with their hosts have also been studied. In Glycine max, limited studies have investigated the isolation and distribution of endophytic fungi throughout leaves and roots. The distribution of these fungi in various plant organs differs in diversity and abundance, even when analyzed using molecular techniques that can evaluate fungal communities in different parts of the plants, such as denaturing gradient gel electrophoresis (DGGE). Our results show there is greater species richness of culturable endophytic filamentous fungi in the leaves G. max as compared to roots. Additionally, the leaves had high values for diversity indices, i.e. Simpsons, Shannon and Equitability. Conversely, dominance index was higher in roots as compared to leaves. The fungi Ampelomyces sp., Cladosporium cladosporioides, Colletotrichum gloeosporioides, Diaporthe helianthi, Guignardia mangiferae and Phoma sp. were more frequently isolated from the leaves, whereas the fungi Fusarium oxysporum, Fusarium solani and Fusarium sp. were prevalent in the roots. However, by evaluating the two communities by DGGE, we concluded that the species richness was higher in the roots than in the leaves. UPGMA analysis showed consistent clustering of isolates; however, the fungus Leptospora rubella, which belongs to the order Dothideales, was grouped among species of the order Pleosporales. The presence of endophytic Fusarium species in G. max roots is unsurprising, since Fusarium spp. isolates have been previously described as endophyte in other reports. However, it remains to be determined whether the G. max Fusarium endophytes are latent pathogens or non-pathogenic forms that benefit the plant. This study provides a broader knowledge of the distribution of the fungal community in G. max leaves and roots, and identifies the genetic relationships among the isolated species.
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Affiliation(s)
- Elio Gomes Fernandes
- Departamento de Microbiologia - Bioagro, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, CEP 36570 900 Viçosa, MG, Brazil
| | - Olinto Liparini Pereira
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, CEP 36570 900 Viçosa, MG, Brazil
| | - Cynthia Cânedo da Silva
- Departamento de Microbiologia - Bioagro, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, CEP 36570 900 Viçosa, MG, Brazil
| | - Claudia Braga Pereira Bento
- Departamento de Microbiologia - Bioagro, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, CEP 36570 900 Viçosa, MG, Brazil
| | - Marisa Vieira de Queiroz
- Departamento de Microbiologia - Bioagro, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, CEP 36570 900 Viçosa, MG, Brazil.
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A century later: rediscovery, culturing and phylogenetic analysis of Diploöspora rosea, a rare onygenalean hyphomycete. Antonie van Leeuwenhoek 2015; 108:1023-35. [DOI: 10.1007/s10482-015-0555-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/11/2015] [Indexed: 11/26/2022]
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Najah M, Calbrix R, Mahendra-Wijaya IP, Beneyton T, Griffiths AD, Drevelle A. Droplet-based microfluidics platform for ultra-high-throughput bioprospecting of cellulolytic microorganisms. ACTA ACUST UNITED AC 2015; 21:1722-32. [PMID: 25525991 DOI: 10.1016/j.chembiol.2014.10.020] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 09/30/2014] [Accepted: 10/20/2014] [Indexed: 01/05/2023]
Abstract
Discovery of microorganisms producing enzymes that can efficiently hydrolyze cellulosic biomass is of great importance for biofuel production. To date, however, only a miniscule fraction of natural biodiversity has been tested because of the relatively low throughput of screening systems and their limitation to screening only culturable microorganisms. Here, we describe an ultra-high-throughput droplet-based microfluidic system that allowed the screening of over 100,000 cells in less than 20 min. Uncultured bacteria from a wheat stubble field were screened directly by compartmentalization of single bacteria in 20 pl droplets containing a fluorogenic cellobiohydrolase substrate. Sorting of droplets based on cellobiohydrolase activity resulted in a bacterial population with 17- and 7-fold higher cellobiohydrolase and endogluconase activity, respectively, and very different taxonomic diversity than when selected for growth on medium containing starch and carboxymethylcellulose as carbon source.
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Affiliation(s)
- Majdi Najah
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée Gaspard Monge, 67083 Strasbourg Cedex, France; Division Biotechnologies, Ets. J. Soufflet, quai Sarrail, 10400 Nogent-sur-Seine, France
| | - Raphaël Calbrix
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée Gaspard Monge, 67083 Strasbourg Cedex, France
| | - I Putu Mahendra-Wijaya
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée Gaspard Monge, 67083 Strasbourg Cedex, France; Division Biotechnologies, Ets. J. Soufflet, quai Sarrail, 10400 Nogent-sur-Seine, France
| | - Thomas Beneyton
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| | - Andrew D Griffiths
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée Gaspard Monge, 67083 Strasbourg Cedex, France; École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, 10 rue Vauquelin, 75231 Paris Cedex 05, France.
| | - Antoine Drevelle
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, CNRS UMR 7006, 8 allée Gaspard Monge, 67083 Strasbourg Cedex, France; Division Biotechnologies, Ets. J. Soufflet, quai Sarrail, 10400 Nogent-sur-Seine, France.
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Stefani FOP, Bell TH, Marchand C, de la Providencia IE, El Yassimi A, St-Arnaud M, Hijri M. Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils. PLoS One 2015; 10:e0128272. [PMID: 26053848 PMCID: PMC4460130 DOI: 10.1371/journal.pone.0128272] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/23/2015] [Indexed: 12/21/2022] Open
Abstract
Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.
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Affiliation(s)
- Franck O. P. Stefani
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Terrence H. Bell
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Charlotte Marchand
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Ivan E. de la Providencia
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Abdel El Yassimi
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Marc St-Arnaud
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
| | - Mohamed Hijri
- Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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Ortíz-López FJ, Monteiro MC, González-Menéndez V, Tormo JR, Genilloud O, Bills GF, Vicente F, Zhang C, Roemer T, Singh SB, Reyes F. Cyclic colisporifungin and linear cavinafungins, antifungal lipopeptides isolated from Colispora cavincola. JOURNAL OF NATURAL PRODUCTS 2015; 78:468-475. [PMID: 25636062 DOI: 10.1021/np500854j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Colisporifungin (1), a cyclic depsilipopeptide structurally related to the aselacins, and cavinafungins A and B, two linear peptides, were isolated from liquid culture broths of the hitherto unstudied fungus Colispora cavincola using a Candida albicans whole-cell assay as well as a bioassay to detect compounds potentiating the antifungal activity of caspofungin. The structural elucidation, including the absolute configuration of the new molecules, was accomplished using a combination of spectroscopic and chemical techniques, including 1D and 2D NMR, HRMS, and Marfey's analysis. The cyclic peptide colisporifungin displayed a strong potentiation of the growth inhibitory effect of caspofungin against Aspergillus fumigatus and, to a lesser extent, against Candida albicans. The linear peptides displayed broad-spectrum antifungal activities inhibiting growth of Candida species (MIC values 0.5-4 μg/mL) as well as A. fumigatus with a prominent inhibition of 8 μg/mL.
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Affiliation(s)
- Francisco Javier Ortíz-López
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Maria Cândida Monteiro
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Víctor González-Menéndez
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - José R Tormo
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Olga Genilloud
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Gerald F Bills
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Francisca Vicente
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
| | - Chaowei Zhang
- ‡Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Terry Roemer
- ‡Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Sheo B Singh
- ‡Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Fernando Reyes
- †Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico de Ciencias de la Salud, E-18016, Armilla, Granada, Spain
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Visagie CM, Hirooka Y, Tanney JB, Whitfield E, Mwange K, Meijer M, Amend AS, Seifert KA, Samson RA. Aspergillus, Penicillium and Talaromyces isolated from house dust samples collected around the world. Stud Mycol 2014; 78:63-139. [PMID: 25492981 PMCID: PMC4255536 DOI: 10.1016/j.simyco.2014.07.002] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
As part of a worldwide survey of the indoor mycobiota, dust was collected from nine countries. Analyses of dust samples included the culture-dependent dilution-to-extinction method and the culture-independent 454-pyrosequencing. Of the 7 904 isolates, 2 717 isolates were identified as belonging to Aspergillus, Penicillium and Talaromyces. The aim of this study was to identify isolates to species level and describe the new species found. Secondly, we wanted to create a reliable reference sequence database to be used for next-generation sequencing projects. Isolates represented 59 Aspergillus species, including eight undescribed species, 49 Penicillium species of which seven were undescribed and 18 Talaromyces species including three described here as new. In total, 568 ITS barcodes were generated, and 391 β-tubulin and 507 calmodulin sequences, which serve as alternative identification markers.
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Affiliation(s)
- C M Visagie
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
| | - Y Hirooka
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - J B Tanney
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - E Whitfield
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - K Mwange
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - M Meijer
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
| | - A S Amend
- Department of Botany, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, HI 96822, USA
| | - K A Seifert
- Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada
| | - R A Samson
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands
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Habitat preferences, distribution, and temporal persistence of a novel fungal taxon in Alaskan boreal forest soils. FUNGAL ECOL 2014. [DOI: 10.1016/j.funeco.2014.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhang T, Victor TR, Rajkumar SS, Li X, Okoniewski JC, Hicks AC, Davis AD, Broussard K, LaDeau SL, Chaturvedi S, Chaturvedi V. Mycobiome of the bat white nose syndrome affected caves and mines reveals diversity of fungi and local adaptation by the fungal pathogen Pseudogymnoascus (Geomyces) destructans. PLoS One 2014; 9:e108714. [PMID: 25264864 PMCID: PMC4181696 DOI: 10.1371/journal.pone.0108714] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 09/02/2014] [Indexed: 12/27/2022] Open
Abstract
Current investigations of bat White Nose Syndrome (WNS) and the causative fungus Pseudogymnoascus (Geomyces) destructans (Pd) are intensely focused on the reasons for the appearance of the disease in the Northeast and its rapid spread in the US and Canada. Urgent steps are still needed for the mitigation or control of Pd to save bats. We hypothesized that a focus on fungal community would advance the understanding of ecology and ecosystem processes that are crucial in the disease transmission cycle. This study was conducted in 2010–2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. We used culture-dependent (CD) and culture-independent (CI) methods to catalogue all fungi (‘mycobiome’). CD methods included fungal isolations followed by phenotypic and molecular identifications. CI methods included amplification of DNA extracted from environmental samples with universal fungal primers followed by cloning and sequencing. CD methods yielded 675 fungal isolates and CI method yielded 594 fungal environmental nucleic acid sequences (FENAS). The core mycobiome of WNS comprised of 136 operational taxonomic units (OTUs) recovered in culture and 248 OTUs recovered in clone libraries. The fungal community was diverse across the sites, although a subgroup of dominant cosmopolitan fungi was present. The frequent recovery of Pd (18% of samples positive by culture) even in the presence of dominant, cosmopolitan fungal genera suggests some level of local adaptation in WNS-afflicted habitats, while the extensive distribution of Pd (48% of samples positive by real-time PCR) suggests an active reservoir of the pathogen at these sites. These findings underscore the need for integrated disease control measures that target both bats and Pd in the hibernacula for the control of WNS.
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Affiliation(s)
- Tao Zhang
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Tanya R. Victor
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Sunanda S. Rajkumar
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Xiaojiang Li
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Joseph C. Okoniewski
- Bureau of Wildlife, New York State Department of Environmental Conservation, Albany, New York, United States of America
| | - Alan C. Hicks
- Bureau of Wildlife, New York State Department of Environmental Conservation, Albany, New York, United States of America
| | - April D. Davis
- Rabies Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Kelly Broussard
- Rabies Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Shannon L. LaDeau
- Cary Institute of Ecosystem Studies, Millbrook, New York, United States of America
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
- * E-mail: (SC); (VC)
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
- * E-mail: (SC); (VC)
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Overy DP, Bayman P, Kerr RG, Bills GF. An assessment of natural product discovery from marine ( sensu strictu) and marine-derived fungi. Mycology 2014; 5:145-167. [PMID: 25379338 PMCID: PMC4205923 DOI: 10.1080/21501203.2014.931308] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 05/30/2014] [Indexed: 11/21/2022] Open
Abstract
The natural products community has been investigating secondary metabolites from marine fungi for several decades, but when one attempts to search for validated reports of new natural products from marine fungi, one encounters a literature saturated with reports from ‘marine-derived’ fungi. Of the 1000+ metabolites that have been characterized to date, only approximately 80 of these have been isolated from species from exclusively marine lineages. These metabolites are summarized here along with the lifestyle and habitats of their producing organisms. Furthermore, we address some of the reasons for the apparent disconnect between the stated objectives of discovering new chemistry from marine organisms and the apparent neglect of the truly exceptional obligate marine fungi. We also offer suggestions on how to reinvigorate enthusiasm for marine natural products discovery from fungi from exclusive marine lineages and highlight the need for critically assessing the role of apparently terrestrial fungi in the marine environment.
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Affiliation(s)
- David P Overy
- Department of Chemistry, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3 ; Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3 ; Nautilus Biosciences Canada, Duffy Research Center, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3
| | - Paul Bayman
- Department of Biology, University of Puerto Rico-Río Piedras , P. O. Box 23360, San Juan 00931 , Puerto Rico
| | - Russell G Kerr
- Department of Chemistry, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3 ; Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3 ; Nautilus Biosciences Canada, Duffy Research Center, University of Prince Edward Island , 550 University Ave., Charlottetown , Prince Edward Island , Canada C1A 4P3
| | - Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center , 1881 East Rd., Houston , TX 77054 , USA
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Terhonen E, Keriö S, Sun H, Asiegbu FO. Endophytic fungi of Norway spruce roots in boreal pristine mire, drained peatland and mineral soil and their inhibitory effect on Heterobasidion parviporum in vitro. FUNGAL ECOL 2014. [DOI: 10.1016/j.funeco.2014.01.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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49
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Yabuki T, Duncan I, Okuda T. Comparative study reveals unique features of the mycobiota in peat soils samples from Japan and Scotland. MYCOSCIENCE 2014. [DOI: 10.1016/j.myc.2013.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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50
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Siles JA, González-Menéndez V, Platas G, Sampedro I, García-Romera I, Bills GF. Effects of dry olive residue transformed by Coriolopsis floccosa (Polyporaceae) on the distribution and dynamic of a culturable fungal soil community. MICROBIAL ECOLOGY 2014; 67:648-658. [PMID: 24419542 DOI: 10.1007/s00248-013-0353-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/12/2013] [Indexed: 06/03/2023]
Abstract
Dry olive residue (DOR) is an abundant waste product resulting from a two-phase olive oil extraction system. Due to its high organic and mineral content, this material has been proposed as an organic soil amendment; however, it presents phytotoxic and microtoxic properties. Thus, a pretreatment is necessary before its application to soil. Among the strategies for the bioremediation of DOR is treatment with ligninolytic fungi, e.g. Coriolopsis floccosa. This work aimed to assess the diversity of culturable fungi in a soil of the southeast Iberian Peninsula and to evaluate the short-term impact of untransformed and C. floccosa-transformed DOR on soil mycobiota. A total of 1,733 strains were isolated by the particle filtration method and were grouped among 109 different species using morphological and molecular methods. The majority of isolates were ascomycetes and were concentrated among three orders: Hypocreales, Eurotiales and Capnodiales. The soil amendment with untransformed DOR was associated with a depression in fungal diversity at 30 days and changes in the proportions of the major species. However, when C. floccosa-transformed DOR was applied to the soil, changes in fungal diversity were less evident, and species composition was similar to unamended soil.
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Affiliation(s)
- José A Siles
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), C/Profesor Albareda, 1, 18008, Granada, Spain,
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