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Kot AM, Laszek P, Kieliszek M, Pobiega K, Błażejak S. Biotechnological potential of red yeast isolated from birch forests in Poland. Biotechnol Lett 2024; 46:641-669. [PMID: 38687405 DOI: 10.1007/s10529-024-03482-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/25/2024] [Accepted: 03/10/2024] [Indexed: 05/02/2024]
Abstract
OBJECTIVES This study aimed to isolate red yeast from sap, bark and slime exudates collected from Polish birch forests and then assessment of their biotechnological potential. RESULTS 24 strains of red yeast were isolated from the bark, sap and spring slime fluxes of birch (Betula pendula). Strains belonging to Rhodotorula mucilaginosa (6), Rhodosporidiobolus colostri (4), Cystrofilobasidium capitaum (3), Phaffia rhodozyma (3) and Cystobasidium psychroaquaticum (3) were dominant. The highest efficiency of carotenoid biosynthesis (5.04 mg L-1) was obtained by R. mucilaginosa CMIFS 004, while lipids were most efficiently produced by two strains of P. rhodozyma (5.40 and 5.33 g L-1). The highest amount of exopolysaccharides (3.75 g L-1) was produced by the R. glutinis CMIFS 103. Eleven strains showed lipolytic activity, nine amylolytic activity, and only two proteolytic activity. The presence of biosurfactants was not found. The growth of most species of pathogenic moulds was best inhibited by Rhodotorula yeasts. CONCLUSION Silver birch is a good natural source for the isolation of new strains of red yeast with wide biotechnological potential.
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Affiliation(s)
- Anna M Kot
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland.
| | - Paulina Laszek
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Marek Kieliszek
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Katarzyna Pobiega
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
| | - Stanisław Błażejak
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences, Nowoursynowska 159C, 02-776, Warsaw, Poland
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Rering CC, Rudolph AB, Li QB, Read QD, Muñoz PR, Ternest JJ, Hunter CT. A quantitative survey of the blueberry (Vaccinium spp.) culturable nectar microbiome: variation between cultivars, locations, and farm management approaches. FEMS Microbiol Ecol 2024; 100:fiae020. [PMID: 38366934 PMCID: PMC10903978 DOI: 10.1093/femsec/fiae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/25/2024] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Microbes in floral nectar can impact both their host plants and floral visitors, yet little is known about the nectar microbiome of most pollinator-dependent crops. In this study, we examined the abundance and composition of the fungi and bacteria inhabiting Vaccinium spp. nectar, as well as nectar volume and sugar concentrations. We compared wild V. myrsinites with two field-grown V. corymbosum cultivars collected from two organic and two conventional farms. Differences in nectar traits and microbiomes were identified between V. corymbosum cultivars but not Vaccinium species. The microbiome of cultivated plants also varied greatly between farms, whereas management regime had only subtle effects, with higher fungal populations detected under organic management. Nectars were hexose-dominant, and high cell densities were correlated with reduced nectar sugar concentrations. Bacteria were more common than fungi in blueberry nectar, although both were frequently detected and co-occurred more often than would be predicted by chance. "Cosmopolitan" blueberry nectar microbes that were isolated in all plants, including Rosenbergiella sp. and Symmetrospora symmetrica, were identified. This study provides the first systematic report of the blueberry nectar microbiome, which may have important implications for pollinator and crop health.
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Affiliation(s)
- Caitlin C Rering
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, 1700 SW 23rd Dr, Gainesville, FL 32608, United States
| | - Arthur B Rudolph
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, 1700 SW 23rd Dr, Gainesville, FL 32608, United States
| | - Qin-Bao Li
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, 1700 SW 23rd Dr, Gainesville, FL 32608, United States
| | - Quentin D Read
- Agricultural Research Service, Southeast Area, United States Department of Agriculture, 840 Oval Drive, Raleigh, NC 27606, United States
| | - Patricio R Muñoz
- Horticultural Sciences Department, University of Florida, 2550 Hull Rd, Gainesville, FL 32611, United States
| | - John J Ternest
- Department of Entomology and Nematology, University of Florida, 1881 Natural Area Dr, Gainesville, FL 32611, United States
| | - Charles T Hunter
- Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, 1700 SW 23rd Dr, Gainesville, FL 32608, United States
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3
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Rering CC, Lanier AM, Peres NA. Blueberry floral probiotics: nectar microbes inhibit the growth of Colletotrichum pathogens. J Appl Microbiol 2023; 134:lxad300. [PMID: 38061796 DOI: 10.1093/jambio/lxad300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/24/2023] [Accepted: 12/05/2023] [Indexed: 12/29/2023]
Abstract
AIMS To identify whether microorganisms isolated from blueberry flowers can inhibit the growth of Colletotrichum, an opportunistic plant pathogen that infects flowers and threatens yields, and to assess the impacts of floral microbes and Colletotrichum pathogens on artificial nectar sugars and honey bee consumption. METHODS AND RESULTS The growth inhibition of Colletotrichum (Colletotrichum acutatum, Colletotrichum fioriniae, and Colletotrichum gloeosporioides) was screened using both artificial nectar co-culture and dual culture plate assays. All candidate nectar microbes were screened for antagonism against a single C. acutatum isolate. Then, the top four candidate nectar microbes showing the strongest inhibition of C. acutatum (Neokomagataea thailandica, Neokomagataea tanensis, Metschnikowia rancensis, and Symmetrospora symmetrica) were evaluated for antagonism against three additional C. acutatum isolates, and single isolates of both C. fioriniae and C. gloeosporioides. In artificial nectar assays, single and three-species cultures inhibited the growth of two of four C. acutatum isolates by ca. 60%, but growth of other Colletotrichum species was not affected. In dual culture plate assays, inhibition was observed for all Colletotrichum species for at least three of four selected microbial antagonists (13%‒53%). Neither honey bee consumption of nectar nor nectar sugar concentrations were affected by any microbe or pathogen tested. CONCLUSIONS Selected floral microbes inhibited growth of all Colletotrichum species in vitro, although the degree of inhibition was specific to the assay and pathogen examined. In all microbial treatments, nectar sugars were preserved, and honey bee preference was not affected.
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Affiliation(s)
- Caitlin C Rering
- Chemistry Research Unit, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL 32608, United States
| | - Alexia M Lanier
- Chemistry Research Unit, Agricultural and Veterinary Entomology, Agricultural Research Service, United States Department of Agriculture, Gainesville, FL 32608, United States
| | - Natalia A Peres
- Department of Horticulture, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, United States
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Ettinger CL, Wu-Woods J, Kurbessoian T, Brown DJ, de Souza Pacheco I, Vindiola BG, Walling LL, Atkinson PW, Byrne FJ, Redak R, Stajich JE. Geographical survey of the mycobiome and microbiome of Southern California glassy-winged sharpshooters. mSphere 2023; 8:e0026723. [PMID: 37800904 PMCID: PMC10597469 DOI: 10.1128/msphere.00267-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/24/2023] [Indexed: 10/07/2023] Open
Abstract
The glassy-winged sharpshooter, Homalodisca vitripennis Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen, Xylella fastidiosa. While studies have focused on X. fastidiosa or known symbionts of H. vitripennis, little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here, we characterize the mycobiome and the microbiome of H. vitripennis across Southern California and explore correlations with captivity and host insecticide resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer 1 region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while the H. vitripennis mycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wild H. vitripennis. Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide resistance status in wild H. vitripennis. This study serves as a foundational look at the H. vitripennis mycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide resistance status and investigate whether microbial communities should be considered in H. vitripennis management practices. IMPORTANCE The glassy-winged sharpshooter is an invasive leafhopper that feeds on the xylem of plants and transmits the devastating pathogen, Xylella fastidiosa, resulting in significant economic damage to California's agricultural system. While studies have focused on this pathogen or obligate symbionts of the glassy-winged sharpshooter, there is limited knowledge of the bacterial and fungal communities that make up its microbiome and mycobiome. To address this knowledge gap, we explored the composition of the mycobiome and the microbiome of the glassy-winged sharpshooter across Southern California and identified differences associated with geography, captivity, and host insecticide resistance status. Understanding sources of variation in the microbial communities associated with the glassy-winged sharpshooter is an important consideration for developing management strategies to control this invasive insect. This study is a first step toward understanding the role microbes may play in the glassy-winged sharpshooter's resistance to insecticides.
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Affiliation(s)
- Cassandra L. Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Jessica Wu-Woods
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Tania Kurbessoian
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Dylan J. Brown
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | | | - Beatriz G. Vindiola
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Linda L. Walling
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Peter W. Atkinson
- Department of Entomology, University of California, Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Frank J. Byrne
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Richard Redak
- Department of Entomology, University of California, Riverside, Riverside, California, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
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Maoloni A, Cardinali F, Milanović V, Reale A, Boscaino F, Di Renzo T, Ferrocino I, Rampanti G, Garofalo C, Osimani A, Aquilanti L. Impact of Different Drying Methods on the Microbiota, Volatilome, Color, and Sensory Traits of Sea Fennel ( Crithmum maritimum L.) Leaves. Molecules 2023; 28:7207. [PMID: 37894688 PMCID: PMC10609079 DOI: 10.3390/molecules28207207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Sea fennel (Crithmum maritimum L.) is a strongly aromatic herb of the Apiaceae family, whose full exploitation by the modern food industry is of growing interest. This study aimed at investigating the microbiological quality, volatile profile, and sensory traits of sea fennel spices produced using room-temperature drying, oven drying, microwave drying, and freeze drying. All the assayed methods were able to remove moisture up until water activity values below 0.6 were reached; however, except for microwave drying, none of the assayed methods were effective in reducing the loads of contaminating microorganisms. The metataxonomic analysis highlighted the presence of phytopathogens and even human pathogens, including members of the genera Bacillus, Pseudomonas, Alternaria, and Cryptococcus. When compared to fresh leaves, dried leaves showed increased L* (lightness) and c* (chroma, saturation) values and reduced hue angle. Dried leaves were also characterized by decreased levels of terpene hydrocarbons and increased levels of aldehydes, alcohols, and esters. For the sensory test, the microwave-dried samples obtained the highest appreciation by the trained panel. Overall, the collected data indicated microwave drying as the best option for producing sea fennel spices with low microbial loads, brilliant green color, and high-quality sensory traits.
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Affiliation(s)
- Antonietta Maoloni
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Federica Cardinali
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Vesna Milanović
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Anna Reale
- Istituto di Scienze dell’Alimentazione (ISA), Consiglio Nazionale delle Ricerche (CNR), 83100 Avellino, Italy; (A.R.); (F.B.); (T.D.R.)
| | - Floriana Boscaino
- Istituto di Scienze dell’Alimentazione (ISA), Consiglio Nazionale delle Ricerche (CNR), 83100 Avellino, Italy; (A.R.); (F.B.); (T.D.R.)
| | - Tiziana Di Renzo
- Istituto di Scienze dell’Alimentazione (ISA), Consiglio Nazionale delle Ricerche (CNR), 83100 Avellino, Italy; (A.R.); (F.B.); (T.D.R.)
| | - Ilario Ferrocino
- Department of Agricultural, Forest, and Food Science, University of Turin, Largo Paolo Braccini 2, Grugliasco, 10095 Turin, Italy;
| | - Giorgia Rampanti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Cristiana Garofalo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Andrea Osimani
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
| | - Lucia Aquilanti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131 Ancona, Italy; (A.M.); (F.C.); (V.M.); (G.R.); (C.G.); (A.O.)
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Birnbaum C, Wood J, Lilleskov E, Lamit LJ, Shannon J, Brewer M, Grover S. Degradation Reduces Microbial Richness and Alters Microbial Functions in an Australian Peatland. MICROBIAL ECOLOGY 2023; 85:875-891. [PMID: 35867139 PMCID: PMC10156627 DOI: 10.1007/s00248-022-02071-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/01/2022] [Indexed: 05/04/2023]
Abstract
Peatland ecosystems cover only 3% of the world's land area; however, they store one-third of the global soil carbon (C). Microbial communities are the main drivers of C decomposition in peatlands, yet we have limited knowledge of their structure and function. While the microbial communities in the Northern Hemisphere peatlands are well documented, we have limited understanding of microbial community composition and function in the Southern Hemisphere peatlands, especially in Australia. We investigated the vertical stratification of prokaryote and fungal communities from Wellington Plains peatland in the Australian Alps. Within the peatland complex, bog peat was sampled from the intact peatland and dried peat from the degraded peatland along a vertical soil depth gradient (i.e., acrotelm, mesotelm, and catotelm). We analyzed the prokaryote and fungal community structure, predicted functional profiles of prokaryotes using PICRUSt, and assigned soil fungal guilds using FUNGuild. We found that the structure and function of prokaryotes were vertically stratified in the intact bog. Soil carbon, manganese, nitrogen, lead, and sodium content best explained the prokaryote composition. Prokaryote richness was significantly higher in the intact bog acrotelm compared to degraded bog acrotelm. Fungal composition remained similar across the soil depth gradient; however, there was a considerable increase in saprotroph abundance and decrease in endophyte abundance along the vertical soil depth gradient. The abundance of saprotrophs and plant pathogens was two-fold higher in the degraded bog acrotelm. Soil manganese and nitrogen content, electrical conductivity, and water table level (cm) best explained the fungal composition. Our results demonstrate that both fungal and prokaryote communities are shaped by soil abiotic factors and that peatland degradation reduces microbial richness and alters microbial functions. Thus, current and future changes to the environmental conditions in these peatlands may lead to altered microbial community structures and associated functions which may have implications for broader ecosystem function changes in peatlands.
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Affiliation(s)
- Christina Birnbaum
- Applied Chemistry and Environmental Science, School of Science, RMIT University Melbourne, Victoria, 3001, Australia.
- School of Life and Environmental Sciences, Faculty of Science & Built Environment, Deakin University, 221 Burwood Highway, Burwood, VIC, 3125, Australia.
- School of Agriculture and Environmental Science, The University of Southern Queensland, Toowoomba, QLD, 4350, Australia.
| | - Jennifer Wood
- Physiology, Anatomy and Microbiology, La Trobe University, Science Drive, Bundoora, VIC, 3086, Australia
| | - Erik Lilleskov
- USDA Forest Service, Northern Research Station, 410 MacInnes Dr, Houghton, MI, 49931, USA
| | - Louis James Lamit
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
- Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, 1 Forestry Drive, Syracuse, NY, 13210, USA
| | - James Shannon
- Research Centre for Applied Alpine Ecology, Department of Ecology, Environment and Evolution, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Matthew Brewer
- Physiology, Anatomy and Microbiology, La Trobe University, Science Drive, Bundoora, VIC, 3086, Australia
| | - Samantha Grover
- Applied Chemistry and Environmental Science, School of Science, RMIT University Melbourne, Victoria, 3001, Australia
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Runge P, Ventura F, Kemen E, Stam R. Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis. MICROBIAL ECOLOGY 2023; 85:168-183. [PMID: 35041070 PMCID: PMC9849306 DOI: 10.1007/s00248-021-01947-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.
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Affiliation(s)
- Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Köln, Germany
| | - Freddy Ventura
- Plant Pathology and Bacteriology, International Potato Centre, Avenida La Molina 1895, La Molina, Lima, Peru
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Science, Emil-Ramann-Str. 2, 85354, Freising-Weihenstephan, Germany.
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Cao B, Haelewaters D, Schoutteten N, Begerow D, Boekhout T, Giachini AJ, Gorjón SP, Gunde-Cimerman N, Hyde KD, Kemler M, Li GJ, Liu DM, Liu XZ, Nuytinck J, Papp V, Savchenko A, Savchenko K, Tedersoo L, Theelen B, Thines M, Tomšovský M, Toome-Heller M, Urón JP, Verbeken A, Vizzini A, Yurkov AM, Zamora JC, Zhao RL. Delimiting species in Basidiomycota: a review. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00479-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Haelewaters D, Peterson RA, Nevalainen H, Aime MC. Inopinatum lactosum gen. & comb. nov., the first yeast-like fungus in Leotiomycetes. Int J Syst Evol Microbiol 2021; 71. [PMID: 34214028 DOI: 10.1099/ijsem.0.004862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sporobolomyces lactosus is a pink yeast-like fungus that is not congeneric with other members of Sporobolomyces (Basidiomycota, Microbotryomycetes, Sporidiobolales). During our ongoing studies of pink yeasts we determined that S. lactosus was most closely related to Pseudeurotium zonatum (Ascomycota, Leotiomycetes, Thelebolales). A molecular phylogenetic analysis using sequences of the ITS region and the small and large subunit (SSU, LSU) rRNA genes, indicated that four isolates of S. lactosus, including three ex-type isolates, were placed in Thelebolales with maximum support. A new genus is proposed to accommodate S. lactosus, Inopinatum. This is the first pink yeast reported in Leotiomycetes.
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Affiliation(s)
- Danny Haelewaters
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Robyn A Peterson
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
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Cureau N, Threlfall R, Savin M, Marasini D, Lavefve L, Carbonero F. Year, Location, and Variety Impact on Grape-, Soil-, and Leaf-Associated Fungal Microbiota of Arkansas-Grown Table Grapes. MICROBIAL ECOLOGY 2021; 82:73-86. [PMID: 33515050 DOI: 10.1007/s00248-021-01698-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
With the recent advancement of next-generation sequencing methods, there has been an increase in studies on identification of vineyard microbiota, winery-associated microbiota, and microbiota in wine fermentation. However, there have been few studies investigating the fungal microbiota of table grapes which present distinct spoilage and food safety challenges. The aims of this study were to identify and compare the impact of year, variety, and vineyard location on grape, leaf, and soil fungal communities of two varieties of table grapes, Faith and Gratitude, grown in two open-air vineyards and one high tunnel vineyard. The grape, leaf, and soil mycobiota were analyzed using high throughput amplicon sequencing of the ITS region. The sampling year and location of table grapes had an impact on grape, leaf, and soil mycobiota. Fungal diversity of grape, leaf, and soil was greater in 2017 than in 2016. Grape and leaf samples presented strong similarities in fungal communities with abundance of Sporidiobolaceae and Filobasidium in two vineyards and Cladosporium in another one. The high tunnel structure had distinct grape and leaf fungal communities compared to the two other vineyard locations. Mortierella was the predominant genus (27%) in soil samples for the three locations; however, genera of lower abundance varied between locations. These results provide extensive description of fungal communities in less-studied table grape vineyards and high tunnels, providing useful insight of potential threats and preventive strategies to help improve the production and marketability of table grapes.
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Affiliation(s)
- Natacha Cureau
- Food Science Department, University of Arkansas, Fayetteville, AR, USA
| | - Renee Threlfall
- Food Science Department, University of Arkansas, Fayetteville, AR, USA
| | - Mary Savin
- Crop, Soil, and Environmental Sciences Department, University of Arkansas, Fayetteville, AR, USA
| | - Daya Marasini
- Food Science Department, University of Arkansas, Fayetteville, AR, USA
| | - Laura Lavefve
- Food Science Department, University of Arkansas, Fayetteville, AR, USA
| | - Franck Carbonero
- Food Science Department, University of Arkansas, Fayetteville, AR, USA.
- Nutrition and Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA.
- School of Food Science, Washington State University, Spokane, WA, USA.
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11
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Aime MC, Miller AN, Aoki T, Bensch K, Cai L, Crous PW, Hawksworth DL, Hyde KD, Kirk PM, Lücking R, May TW, Malosso E, Redhead SA, Rossman AY, Stadler M, Thines M, Yurkov AM, Zhang N, Schoch CL. How to publish a new fungal species, or name, version 3.0. IMA Fungus 2021; 12:11. [PMID: 33934723 PMCID: PMC8091500 DOI: 10.1186/s43008-021-00063-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomenclature) and introduced new formal requirements for valid publication of species scientific names, including the separation of provisions specific to Fungi and organisms treated as fungi in a new Chapter F. Equally transformative have been changes in the data collection, data dissemination, and analytical tools available to mycologists. This paper provides an updated and expanded discussion of current publication requirements along with best practices for the description of new fungal species and publication of new names and for improving accessibility of their associated metadata that have developed over the last 10 years. Additionally, we provide: (1) model papers for different fungal groups and circumstances; (2) a checklist to simplify meeting (i) the requirements of the ICNafp to ensure the effective, valid and legitimate publication of names of new taxa, and (ii) minimally accepted standards for description; and, (3) templates for preparing standardized species descriptions.
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Affiliation(s)
- M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Andrew N Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL, 61820, USA
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Konstanze Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - David L Hawksworth
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS, UK.,Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.,Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Paul M Kirk
- Biodiversity Informatics & Spatial Analysis, Royal Botanic Garden Kew, Richmond, London, TW9 3AE, UK
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195, Berlin, Germany
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria, 3004, Australia
| | - Elaine Malosso
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, 50740-600, Brazil
| | - Scott A Redhead
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6, Canada
| | - Amy Y Rossman
- Botany and Plant Pathology Department, Oregon State University, Corvallis, OR, 97333, USA
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Marco Thines
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Andrey M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20892, USA
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12
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Haelewaters D, Urbina H, Brown S, Newerth-Henson S, Aime MC. Isolation and Molecular Characterization of the Romaine Lettuce Phylloplane Mycobiome. J Fungi (Basel) 2021; 7:277. [PMID: 33917072 PMCID: PMC8067711 DOI: 10.3390/jof7040277] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/27/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023] Open
Abstract
Romaine lettuce (Lactuca sativa) is an important staple of American agriculture. Unlike many vegetables, romaine lettuce is typically consumed raw. Phylloplane microbes occur naturally on plant leaves; consumption of uncooked leaves includes consumption of phylloplane microbes. Despite this fact, the microbes that naturally occur on produce such as romaine lettuce are for the most part uncharacterized. In this study, we conducted culture-based studies of the fungal romaine lettuce phylloplane community from organic and conventionally grown samples. In addition to an enumeration of all such microbes, we define and provide a discussion of the genera that form the "core" romaine lettuce mycobiome, which represent 85.5% of all obtained isolates: Alternaria, Aureobasidium, Cladosporium, Filobasidium, Naganishia, Papiliotrema, Rhodotorula, Sampaiozyma, Sporobolomyces, Symmetrospora and Vishniacozyma. We highlight the need for additional mycological expertise in that 23% of species in these core genera appear to be new to science and resolve some taxonomic issues we encountered during our work with new combinations for Aureobasidiumbupleuri and Curvibasidium nothofagi. Finally, our work lays the ground for future studies that seek to understand the effect these communities may have on preventing or facilitating establishment of exogenous microbes, such as food spoilage microbes and plant or human pathogens.
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Affiliation(s)
- Danny Haelewaters
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
| | - Hector Urbina
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, USA
| | - Samuel Brown
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
| | - Shannon Newerth-Henson
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; (H.U.); (S.B.); (S.N.-H.)
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13
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Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method. Folia Microbiol (Praha) 2021; 66:457-468. [PMID: 33755859 DOI: 10.1007/s12223-021-00859-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
Fungi are considered to be the most resilient and economically important microbial community that can easily survive and optimally grow under a wide range of growth conditions. Thermophilic fungi from the geothermal sources have been less pondered upon and lie unexplored. Here, a microbiome approach was conducted to understand the concealed world of the environmental mycobiota from the two hot springs of North Sikkim district located in North-east India. The solfataric muds from the hot springs were analyzed. In both the samples, on the basis of genus level classification, genus Fusarium had the highest abundance followed by Colletotrichum, Pochonia, Pyricularia, Neurospora, etc. Analyzing the predicted genes, the functional proteins of New Yume Samdung mycobiome were found to be dominated by the genera Fusarium (22%), Trichoderma (12%), and Aspergillus (11%), whereas in the case of Old Yume Samdung, it was dominated by the genera Aspergillus (11%), Saccharomyces (6%), and Fusarium (5%). Interestingly, in the studied mycobiome, environmental yeasts were also detected. From the functional metagenomics, sulfate adenylatetransferase (SAT) proteins for sulfur assimilation were found in some of the fungal reads. Toxin protein reads such as AM-toxin biosynthesis proteins, AF-toxin biosynthesis proteins, Gliotoxin biosynthesis proteins, and aflatoxin biosynthesis proteins were detected in the mycobiomes.
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14
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Mešić A, Haelewaters D, Tkalčec Z, Liu J, Kušan I, Aime MC, Pošta A. Inocybe brijunica sp. nov., a New Ectomycorrhizal Fungus from Mediterranean Croatia Revealed by Morphology and Multilocus Phylogenetic Analysis. J Fungi (Basel) 2021; 7:199. [PMID: 33801963 PMCID: PMC8000951 DOI: 10.3390/jof7030199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 01/09/2023] Open
Abstract
A new ectomycorrhizal species was discovered during the first survey of fungal diversity at Brijuni National Park (Croatia), which consists of 14 islands and islets. The National Park is located in the Mediterranean Biogeographical Region, a prominent climate change hot-spot. Inocybe brijunica sp. nov., from sect. Hysterices (Agaricales, Inocybaceae), is described based on morphology and multilocus phylogenetic data. The holotype collection was found at the edge between grassland and Quercus ilex forest with a few planted Pinus pinea trees, on Veli Brijun Island, the largest island of the archipelago. It is easily recognized by a conspicuous orange to orange-red-brown membranaceous surface layer located at or just above the basal part of the stipe. Other distinctive features of I. brijunica are the medium brown, radially fibrillose to rimose pileus; pale to medium brown stipe with fugacious cortina; relatively small, amygdaliform to phaseoliform, and smooth basidiospores, measuring ca. 6.5-9 × 4-5.5 µm; thick-walled, utriform, lageniform or fusiform pleurocystidia (lamprocystidia) with crystals and mostly not yellowing in alkaline solutions; cheilocystidia of two types (lamprocystidia and leptocystidia); and the presence of abundant caulocystidia only in the upper 2-3 mm of the stipe. Phylogenetic reconstruction of a concatenated dataset of the internal transcribed spacer region (ITS), the nuclear 28S rRNA gene (nrLSU), and the second largest subunit of RNA polymerase II (rpb2) resolved I. brijunica and I. glabripes as sister species.
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Affiliation(s)
- Armin Mešić
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (A.M.); (Z.T.); (I.K.); (A.P.)
| | - Danny Haelewaters
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA; (J.L.); (M.C.A.)
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Zdenko Tkalčec
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (A.M.); (Z.T.); (I.K.); (A.P.)
| | - Jingyu Liu
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA; (J.L.); (M.C.A.)
| | - Ivana Kušan
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (A.M.); (Z.T.); (I.K.); (A.P.)
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA; (J.L.); (M.C.A.)
| | - Ana Pošta
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (A.M.); (Z.T.); (I.K.); (A.P.)
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