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Pimentel MF, Srour AY, Warner AJ, Bond JP, Bradley CA, Rupe J, Chilvers MI, Rojas JA, Jacobs JL, Little CR, Robertson AE, Giesler LJ, Malvick D, Wise K, Tenuta A, Fakhoury AM. Ecology and diversity of culturable fungal species associated with soybean seedling diseases in the Midwestern United States. J Appl Microbiol 2022; 132:3797-3811. [PMID: 35226387 PMCID: PMC9311804 DOI: 10.1111/jam.15507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 12/03/2022]
Abstract
AIMS To isolate and characterize fungi associated with diseased soybean seedlings in Midwestern soybean production fields and to determine the influence of environmental and edaphic factors on their incidence. METHODS AND RESULTS Seedlings were collected from fields with seedling disease history in 2012 and 2013 for fungal isolation. Environmental and edaphic data associated with each field was collected. 3036 fungal isolates were obtained and assigned to 76 species. The most abundant genera recovered were Fusarium (73%) and Trichoderma (11.2%). Other genera included Mortierella, Clonostachys, Rhizoctonia, Alternaria, Mucor, Phoma, Macrophomina and Phomopsis. Most recovered species are known soybean pathogens. However, non-pathogenic organisms were also isolated. Crop history, soil density, water source, precipitation and temperature were the main factors influencing the abundance of fungal species. CONCLUSION Key fungal species associated with soybean seedling diseases occurring in several US production regions were characterized. This work also identified major environment and edaphic factors affecting the abundance and occurrence of these species. SIGNIFICANCE AND IMPACT OF THE STUDY The identification and characterization of the main pathogens associated with seedling diseases across major soybean-producing areas could help manage those pathogens, and devise more effective and sustainable practices to reduce the damage they cause.
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Affiliation(s)
- Mirian F. Pimentel
- Department of Agricultural SciencesSouthern Illinois UniversityCarbondaleIllinoisUSA
| | - Ali Y. Srour
- USDA, ARS, New England Plant, Soil, and Water LaboratoryOronoMaineUSA
| | | | - Jason P. Bond
- Department of Agricultural SciencesSouthern Illinois UniversityCarbondaleIllinoisUSA
| | - Carl A. Bradley
- Department of Plant PathologyUniversity of Kentucky Research and Educational CenterPrincetonKentuckyUSA
| | - John Rupe
- Department of Entomology and Plant PathologyUniversity of ArkansasFayettevilleArkansasUSA
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - J. Alejandro Rojas
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Janette L. Jacobs
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | | | - Alison E. Robertson
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Loren J. Giesler
- Department of Plant PathologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Dean Malvick
- Department of Plant PathologyUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Kiersten Wise
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteIndianaUSA
| | - Albert Tenuta
- Ontario Ministry of AgricultureFood and Rural Affairs (OMAFRA)RidgetownOntarioUSA
| | - Ahmad M. Fakhoury
- Department of Agricultural SciencesSouthern Illinois UniversityCarbondaleIllinoisUSA
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Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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Cloutier ML, Murrell E, Barbercheck M, Kaye J, Finney D, García-González I, Bruns MA. Fungal community shifts in soils with varied cover crop treatments and edaphic properties. Sci Rep 2020; 10:6198. [PMID: 32277120 PMCID: PMC7148350 DOI: 10.1038/s41598-020-63173-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/09/2020] [Indexed: 12/17/2022] Open
Abstract
Cover cropping is proposed to enhance soil microbial diversity and activity, with cover crop type affecting microbial groups in different ways. We compared fungal community compositions of bulk soils differing by cover crop treatment, season, and edaphic properties in the third year of an organic, conventionally tilled rotation of corn-soybean-wheat planted with winter cover crops. We used Illumina amplicon sequencing fungal assemblages to evaluate effects of nine treatments, each replicated four times, consisting of six single winter cover crop species, a three-species mixture, a six-species mixture, and fallow. Alpha-diversity of fungal communities was not affected by cover crop species identity, function, or diversity. Sampling season influenced community composition as well as genus-level abundances of arbuscular mycorrhizal (AM) fungi. Cover crop mixtures, specifically the three-species mixture, had distinct AM fungal community compositions, while cereal rye and forage radish monocultures had unique Core OTU compositions. Soil texture, pH, permanganate oxidizable carbon, and chemical properties including Cu, and P were important variables in models of fungal OTU distributions across groupings. These results showed how fungal composition and potential functions were shaped by cover crop treatment as well as soil heterogeneity.
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Affiliation(s)
- Mara L Cloutier
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, 16801, PA, USA.
- Biogeochemistry Dual Title PhD Program-Pennsylvania State University, University Park, 16801, PA, USA.
| | | | - Mary Barbercheck
- Department of Entomology, Pennsylvania State University, University Park, 16801, PA, USA
| | - Jason Kaye
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, 16801, PA, USA
- Biogeochemistry Dual Title PhD Program-Pennsylvania State University, University Park, 16801, PA, USA
| | - Denise Finney
- Department of Biology, Ursinus College, Collegeville, 19426, PA, USA
| | - Irene García-González
- Departamento de Producción Agraria, Universidad Politécnica de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain
| | - Mary Ann Bruns
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, 16801, PA, USA
- Biogeochemistry Dual Title PhD Program-Pennsylvania State University, University Park, 16801, PA, USA
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