Browse > Article
http://dx.doi.org/10.1080/12298093.2019.1700658

Diversity of Fungi in Soils with Different Degrees of Degradation in Germany and Panama  

Rosas-Medina, Miguel (Department of Mycology, Cluster for Integrative Fungal Research (IPF), Institute of Ecology, Evolution and Diversity, Goethe-University)
Macia-Vicente, Jose G. (Department of Mycology, Cluster for Integrative Fungal Research (IPF), Institute of Ecology, Evolution and Diversity, Goethe-University)
Piepenbring, Meike (Department of Mycology, Cluster for Integrative Fungal Research (IPF), Institute of Ecology, Evolution and Diversity, Goethe-University)
Publication Information
Mycobiology / v.48, no.1, 2020 , pp. 20-28 More about this Journal
Abstract
Soil degradation can have an impact on the soil microbiota, but its specific effects on soil fungal communities are poorly understood. In this work, we studied the impact of soil degradation on the richness and diversity of communities of soil fungi, including three different degrees of degradation in Germany and Panama. Soil fungi were isolated monthly using the soil-sprinkling method for 8 months in Germany and 3 months in Panama, and characterized by morphological and molecular data. Soil physico-chemical properties were measured and correlated with the observed values of fungal diversity. We isolated a total of 71 fungal species, 47 from Germany, and 32 from Panama. Soil properties were not associated with fungal richness, diversity, or composition in soils, with the exception of soil compaction in Germany. The geographic location was a strong determinant of the soil fungal species composition although in both countries there was dominance by members of the orders Eurotiales and Hypocreales. In conclusion, the results of this work do not show any evident influence of soil degradation on communities of soil fungi in Germany or Panama.
Keywords
Diversity; soil degradation; species richness; soil fungal communities; environmental factors;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Goldmann K, Schroter K, Pena R, et al. Divergent habitat filtering of root and soil fungal communities in temperate beech forests. Sci Rep. 2016;6(1):31439.   DOI
2 Kirk P, Cannon P, Minter D, et al. Dictionary of the fungi. 10th ed. Europe (UK): CABI; 2008.
3 Heather J, Chain B. The sequence of sequencers: the history of sequencing DNA. Genomics. 2016;107(1):1-8.   DOI
4 Laehnemann D, Borkhardt A, McHardy A. Denoising DNA deep sequencing data-highthroughput sequencing errors and their correction. Brief Bioinform. 2015;1:1-26.
5 Val-Moraes SP, Pedrinho EA, Lemos EG, et al. Molecular identification of fungal communities in a soil cultivated with vegetables and soil suppressiveness to Rhizoctonia solani. Appl Environ Soil Sci. 2013;1:1-7.
6 Sterkenburg E, Bahr A, Durling M, et al. Changes in fungal communities along a boreal forest soil fertility gradient. New Phytol. 2015;207(4):1145-1158.   DOI
7 Requena N, Perez-Solis E, Azcon-Aguilar C, et al. Management of indigenous plant-microbe symbioses aids restoration of desertified ecosystems. Appl Environ Micorbiol. 2001;67(2):495-498.   DOI
8 Jeffries P, Gianinazzi S, Perotto S, et al. The contribution of arbuscular mycorrhizal fungi in sustainable maintenance of plant health and soil fertility. Biol Fertil Soils. 2003;37:1-16.   DOI
9 Tedersoo L, Bahram M, Polme S, et al. Global diversity and geography of soil fungi. Science. 2014;346(6213):1256688.   DOI
10 Tardy V, Chabbi A, Charrier X, et al. Land use history shifts in situ fungal and bacterial successions following wheat straw input into the soil. PLoS One. 2015;10(6):e0130672-17.   DOI
11 Eswaran H, Lal R, Reich PF. Land degradation. An overview conference on land degradation and desertification. Proceedings 2nd International Conference on Land Degradation and Desertification; Khon Kaen, Thailand; New Dehli, India: Oxford Press; 2001.
12 Rowell D. Soil science: methods and applications. 1st ed. Reading (UK): Department of Soil Science, University of Reading; 2014.
13 Aktar W, Sengupta D, Chowdhury A. Impact of pesticides use in agriculture: their benefits and hazards. Interdisc Toxicol. 2009;2(1):1-12.   DOI
14 Siles J, Margesin R. Abundance and diversity of bacterial, archaeal, and fungal communities along an altitudinal gradient in alpine forest soils: what are the driving factors? Microb Ecol. 2016;72(1):207-220.   DOI
15 Ferrol N, Calvente R, Cano C, et al. Analysing arbuscular mycorrhizal fungal diversity in shrubassociated resource islands from a desertification threatened semiarid Mediterranean ecosystem. Appl Soil Ecol. 2004;25(2):123-133.   DOI
16 Grundmann G. Spatial scales of soil bacterial diversity the size of a clone. FEMS Microb Ecol. 2004;48(2):119-127.   DOI
17 Mithal V, Garg A, Boriah S, et al. Monitoring global forest cover using data mining. ACM Trans Intell Syst Technol. 2011;36:1-23.   DOI
18 Chakravarthy A, Sridhara S. Economic and ecological significance of arthropods in diversified ecosystems: sustaining regulatory mechanisms. Berlin, Germany: Springer; 2016.
19 Gibbs H, Salmon J. Mapping the world's degraded lands. Appl Geogr. 2015;57:12-21.   DOI
20 Buee M, Reich M, Murat C, et al. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol. 2009;184(2):449-456.   DOI
21 Hamza MA, Anderson WK. Soil compaction in cropping systems a review of the nature, causes and possible solutions. Soil Tillage Res. 2005;82(2):121-145.   DOI
22 Lauber C, Strickland M, Bradford M, et al. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biol Biochem. 2008;40(9):2407-2415.   DOI
23 Christ S, Wubet T, Buscot F. Soil fungal communities along land use gradients of three German biodiversity exploratories: a comparison of classical cloning and sequencing approach with high throughput sequencing. Proceedings of the 19th World Congress of Soil Science: Soil Solutions for a Changing World, Brisbane, Australia; 1-6 August 2010. Symposium 2.3.1 The soil-root interface 2010. p. 131-133.
24 Fischer M, Bossdorf O, Gockel S, et al. Implementing large-scale and long-term functional biodiversity research: the biodiversity exploratories. Basic Appl Ecol. 2010;11(6):473-485.   DOI
25 Piepenbring M. Inventoring the fungi of Panama. Biodivers Conserv. 2007;16(1):73-84.   DOI
26 Goldmann K, Schoning I, Buscot F, et al. Forest management type influences diversity and community composition of soil fungi across temperate forest ecosystems. Front Microbiol. 2015;24:6.
27 Wubet T, Christ S, Schoning I, et al. Differences in soil fungal communities between European beech (Fagus sylvatica L.) dominated forests are related to soil and understory vegetation. PLoS One. 2012;10:1-14.
28 Castro de Doens L, Reyes E, Simonovic L, et al. Atlas de las tierras secas y degradadas de Panama. Autoridad Nacional del Ambiente. Unidad de Cambio Climatico y Desertificacion. Comite Nacional de Lucha contra la Sequia y la Desertificacion. Panama, Central America: Proyectos Editoriales; 2017.
29 Rosas-Medina M, Piepenbring M. New records of microfungi from degraded soil close to dry seasonal forest in Western Panama. Nova Hedw. 2018;105:3-4.
30 Puttrich L. Forest and Forestry in Hesse. Multipurpose sustainable forest management - commitment for generations. 1st ed. Frankfurt: Hessian ministry for environmental, energy, agriculture and consumer protection. 2012.
31 Cerrud R, Villanueva C, Ibrahim M, et al. Caracterizacion de los sistemas silvopastoriles tradicionales del distrito de Bugaba, Provincia de Chiriqui, Panama. Agrofor Am. 2004;42:43-49.
32 Cerdan O, Govers G, Bissonnais Y, et al. Rates and spatial variations of soil erosion in Europe: a study based on erosion plot data. Geomorphology. 2010;122(1-2):167-177.   DOI
33 Carrasco J, Squella F, Undurraga P. Practicas para el manejo sustentable de los recursos naturales en la recuperacion de suelos degradados. Serie Actas N 16; Santiago, Chile: Instituto de Investigaciones Agropecuarias; 2002.
34 Agnihothrudu V. A comparison of some techniques for the isolation of fungi from tea soils. Mycopathol Mycol Appl. 1961;9:235-242.
35 Porta J. Tecnicas y experimentos en edafologia. 1st ed. Barcelona, Spain: Coll. Oficial d'Eng. Agron. de Catalunya; 1986. p. 282.
36 Cano A. Manual de practicas de la materia de edafologia. 1st ed. Mexico: Gobierno del Estado de Chiapas; 2011.
37 Warcup JH. The soil-plate method for isolation of fungi from soil. Nature. 1950;166(4211):117-118.   DOI
38 Zuniga F. Tecnicas de muestreo para manejadores de recursos naturales. 1st ed. Yucatan, Mexico: INE-Instituto de Geografia, UNAM; 2004.
39 Booth C. The genus Fusarium. CMI Kew Surrey. 1971;1:19-31.
40 Chaverri P, Samuels G. Hypocrea/Trichoderma (Ascomycota, Hypocreales, Hypocreaceae): species with green ascospores. Stud Mycol. 2003;48:1-116.
41 Domsch K, Gams W, Anderson T. Compendium of soil fungi. 2nd ed. Berchtesgadener, Germany: IHW-Verlag, Eching; 2007.
42 Hesseltine C, Ellis J. The genus Absidia: Gongronella and cylindrical-spored species of Absidia. Mycologia. 1964;56(4):568-601.   DOI
43 Martinez E. Estudios de especies micotoxigenas del genero Penicillium. 1st ed. Barcelona: Universitat Autonoma de Barcelona; 2003.
44 Samson R, Hong S, Frisvad J. Old and new concepts of species differentiation in Aspergillus. Med Mycol. 2006;44(s1):133-148.   DOI
45 Chaverri P, Salgado C, Hirooka Y, et al. Delimitation of Neonectria and Cylindrocarpon (Nectriaceae, Hypocreales, Ascomycota) and related genera with Cylindrocarpon like anamorphs. Stud Mycol. 2011;68:57-78.   DOI
46 Koljalg U, Larsson KH, Abarenkov K, et al. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 2005;166(3):1063-1068.   DOI
47 Stolk A, Samson R. The Ascomycete genus Eupenicillium and related Penicillium anamorphs. Stud Mycol. 1983;23:40-43.
48 Gardes M, Bruns T. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Mol Ecol. 1993;2(2):113-118.   DOI
49 White TJ, Bruns TD, Lee SB, et al. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. 1st ed. PCR - protocols and applications - a laboratory manual publisher. Cambridge (MA): Academic Press; 1990.
50 Oksanen J, Blanchet F, Friendly M, et al. Community ecology package (Version 2.4-4) [Software] Recuperate from R: L 2017. [cited 2018 Jan. 20]. Available from: https://cran.r-project.org, https://github.com/vegandevs/vegan
51 R Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Core Team; 2014.
52 Shannon C, Weaver W. The mathematical theory of communication. 1st ed. Urbana (IL): EEUU; University of Illinois Press. 1949.
53 Moreno C, Barragan F, Pineda E, et al. Reanalyzing alpha diversity: alternatives to understand and compare information about ecological communities. Rev Mex Biodivers. 2011;82:1249-1261.
54 Saxena D, Stotzky G. Bacillus thuringiensis (Bt) toxin released from root exudates and biomass of Bt corn has no apparent effect on earthworms, nematodes, protozoa, bacteria, and fungi in soil. Soil Biol Biochem. 2001;33(9):1225-1230.   DOI
55 Baxter A, Van der Linde E. Collecting and preserving fungi. A manual for mycology. 1st ed. Pretoria South Africa: Plant Protection Research Institute;1999.
56 Van Elsas D, Frois-Duarte G, Keijzer-Wolters A, et al. Analysis of the dynamics of fungal communities in soil via fungal-specific PCR of soil DNA followed by denaturing gradient gel electrophoresis. J Microbiol Methods. 2000;43(2):133-151.   DOI
57 Samaniego-Gaxiola J, Chew-Madinaveitia Y. Diversity of soil fungi genera in three different condition agricultural fields in La Laguna Mexico. Rev Mex Biodivers. 2007;78:383-390.
58 Cruz B, Barra, Del Castillo R, Gutierrez C. La calidad del suelo y sus indicadores. Ecosistemas. 2004;13:90-97.
59 Saikia P, Ram Joshi S. Changes in microfungal community in cherrapunji, the wettest patch on earth as influenced by heavy rain and soil degradation. Adv Microbiol. 2012;02(04):456-464.   DOI
60 Wahegaonkar N, Salunkhe S, Palsingankar P, et al. Diversity of fungi from soils of Aurangabad, M.S., India. Ann Biol Res. 2011;2:198-205.
61 Gaddeyya G, Niharika S, Bharathi P, et al. Isolation and identification of soil mycoflora in different crop fields at Salur Mandal. Adv Appl Sci Res. 2012;3:2020-2026.
62 Frisvad J, Samson R. Polyphasic taxonomy of Penicillium subgenus Penicillium A guide to identification of food and air-borne terverticillate Penicillia and their mycotoxins. Stud Mycol. 2004;49:1-174.
63 Henrique L, CapelariII M. Agaricales Fungi from Atlantic rain forest fragments in Minas Gerais, Brazil. Braz J Microbiol. 2009;40:846-851.   DOI
64 Tedersoo L, May T, Smith M. Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages. Mycorrhiza. 2010;20(4):217-263.   DOI
65 Alessandro C, Jones L, Humber R, et al. Characterization and phylogeny of Isaria spp. strains (Ascomycota: Hypocreales) using ITS1-5.8SITS2 and elongation factor 1-alpha sequences. J Basic Microbiol. 2013;54:21-31.
66 Tedersoo L, Nilsson H, Abarenkov K, et al. 454 Pyrosequencing and sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol. 2010;188(1):291-301.   DOI
67 Kara O, Bolat I. Influence of soil compaction on microfungal community structure in two soil types in Bartin Province, Turkey. J Basic Microbiol. 2007;47(5):394-399.   DOI
68 Harris K, Young I, Hristopher A, et al. Effect of bulk density on the spatial organisation of the fungus Rhizoctonia solani in soil. FEMS Microbiol Ecol. 2003;44(1):45-56.   DOI
69 Ekelund F, Ronn R, Christensen S. Distribution with depth of protozoa, bacteria and fungi in soil profiles from three Danish forest sites. Soil Biol Biochem. 2001;33(4-5):475-481.   DOI
70 Fierer N, Schimel J, Holden P. Variations in microbial community composition through two soil depth profiles. Soil Biol Biochem. 2003;35(1):167-176.   DOI
71 Garcia Y, Ramirez W, Sanchez S. Soil quality indicators: a new way to evaluate this resource. Pastosy Forrajes. 2012;35:125-138.