Unraveling the diversity and spatial distribution of Soil-borne Fungal Mycobiomes with response to environmental parameters, cropping schemes and cropping seasons

Abstract

The arid zones are vital agricultural areas, yet they encounter substantial obstacles due to destructive plant diseases caused by soil-borne fungal pathogens. Gaining knowledge about the structure and behavior of the fungus community in the soil and its connection to these ailments is crucial for developing efficient ways to manage the diseases. This study aimed to examine the fungal communities found in soil in areas with high temperatures and multiple cropping schemes. The main objectives of this study were to provide insight into the relationship between these fungal communities, environmental circumstances, and the occurrence of severe plant diseases. Soil samples were collected from agricultural fields exhibiting disease outbreaks, and the fungus diversity was analyzed using modern techniques. The results of this study revealed a diverse array of soil-dwelling fungi, encompassing both beneficial and detrimental species. The presence of pathogenic fungi, specifically basidiomycetes and ascomycetes, in soils where disease outbreaks occur frequently suggests that they play a substantial role in the development of these diseases. Temperature, moisture, and soil conditions also affected fungal community structure and disease dynamics. These findings highlight the importance of soil-borne fungus mycobiome in forecasting and managing plant diseases. To reduce severe plant diseases and preserve agricultural sustainability in these areas, integrated disease management must include the complex interactions between soil fungus, plant hosts, and environmental conditions. To understand fungal pathophysiology and develop targeted disease preventive and control measures, a comprehensive study is required.

Keywords

• Soil
• Fungal mycobiomes
• Cropping Schemes
• Environment
• Spatial distribution
• Characterization
• Beneficial fungi

Toprak Kaynaklı Fungal Mikobiomların Çeşitliliği ve Alansal Dağılımının Çevresel Parametreler, Üretim Sistemleri ve Üretim Sezonlarına Göre İncelenmesi

Abstract

Kurak bölgeler tarım için önemli alanlardır ve bu alanlarda toprak kaynaklı fungal patojenlerin neden olduğu yıkıcı bitki hastalıkları nedeniyle önemli engellerle karşılaşmaktadırlar. Topraktaki fungusların yapısı ve davranışı ile bunların bu hastalıklarla bağlantısı hakkında bilgi edinmek, hastalıklarla mücadelede etkili yöntemler geliştirmek için çok önemlidir. Bu çalışmanın amacı, yüksek sıcaklıklığa sahip bölgelerde toprakta bulunan fungal çeşitliliğin analizi ve bunların çevre koşulları ve önemli bitki hastalıklarının yaygınlığı arasındaki ilişkiyi aydınlatmaktır. Hastalık salgınlarının görüldüğü tarım alanlarından toprak örnekleri toplandı ve modern teknikler kullanılarak fungus varyeteleri analiz edildi. Bu çalışma, hem faydalı hem de zararlı türleri kapsayan, toprakta yaşayan çok çeşitli fungusları belirledi. Patojenik fungusların, özellikle de basidiomycetes ve ascomycetes türlerinin, hastalık salgınlarının sıkça görüldüğü topraklarda yaygın olduğu keşfedildi ve dolayısıyla bu durum, bunların örnekleme alanlarında hastalık gelişimine önemli katkı sağladıklarını gösteriyor. Sıcaklık, nem ve toprak koşulları da fungal topluluğun yapısını ve hastalık dinamiklerini etkiledi. Bu bulgular, bitki hastalıklarının tahmin edilmesinde ve yönetilmesinde toprak kaynaklı fungus mikobiyomunun önemini vurgulamaktadır. Şiddetli bitki hastalıklarını azaltmak ve bu yerlerdeki tarımsal sürdürülebilirliği korumak için entegre hastalık yönetimi, toprak kökenli funguslar, konukçu bitkiler ve çevre koşulları arasındaki karmaşık etkileşimleri içermelidir. Fungal patofizyolojisini anlamak ve hedefe yönelik hastalık önleme v e kontrol önlemleri geliştirmek için daha fazla çalışmaya ihtiyaç duyulmaktadır.

Keywords

• Toprak
• Fungal mikrobiyomlar
• Çevre
• Alansal dağılım
• Teşhis
• Faydalı fungus

References

1. M. Frąc, S.E. Hannula, M. Bełka, M. Jędryczka (2018). Fungal biodiversity and their role in soil health, Frontiers in Microbiology 9, 707.
2. R. Thakur, S. Verma, S. Gupta, G. Negi, P. Bhardwaj (2021). Role of Soil Health in Plant Disease Management: A Review, Agricultural Reviews.
3. J.M. SUN, W. Irzykowski, M. Jedryczka, F.X. HAN (2005). Analysis of the genetic structure of Sclerotinia sclerotiorum (Lib.) de Bary populations from different regions and host plants by random amplified polymorphic DNA markers, Journal of Integrative Plant Biology 47(4), 385-395.
4. L. Žifčáková, T. Větrovský, A. Howe, P. Baldrian (2016). Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter, Environmental microbiology 18(1), 288-301.
5. P. Baldrian, Interactions of heavy metals with white-rot fungi, Enzyme and Microbial technology 32(1) (2003) 78-91.
6. L. Ezzouhri, E. Castro, M. Moya, F. Espinola, K. Lairini (2009). Heavy metal tolerance of filamentous fungi isolated from polluted sites in Tangier, Morocco, African journal of microbiology research 3(2), 35-48.
7. J. López-Bucio, R. Pelagio-Flores, A. Herrera-Estrella (2015). Trichoderma as biostimulant: exploiting the multilevel properties of a plant beneficial fungus, Scientia horticulturae 196, 109-123.
8. Y. Rouphael, P. Franken, C. Schneider, D. Schwarz, M. Giovannetti, M. Agnolucci, S. De Pascale, P. Bonini, G. Colla (2015). Arbuscular mycorrhizal fungi act as biostimulants in horticultural crops, Scientia Horticulturae 196, 91-108.

9. M. Frąc, S. Jezierska-Tys, T. Yaguchi (2015). Occurrence, detection, and molecular and metabolic characterization of heat-resistant fungi in soils and plants and their risk to human health, Advances in Agronomy 132, 161-204.
10. M. Frąc, J. Weber, A. Gryta, M. Dębicka, A. Kocowicz, E. Jamroz, K. Oszust, L. Żołnierz (2017). Microbial functional diversity in Podzol ectohumus horizons affected by alkaline fly ash in the vicinity of electric power plant, Geomicrobiology Journal 34(7), 579-586.
11. A. Gałązka, J. Grządziel (2018). Fungal genetics and functional diversity of microbial communities in the soil under long-term monoculture of maize using different cultivation techniques, Frontiers in microbiology 9, 76.
12. T.M. Bowles, V. Acosta-Martínez, F. Calderón, L.E. Jackson (2014). Soil enzyme activities, microbial communities, and carbon and nitrogen availability in organic agroecosystems across an intensively-managed agricultural landscape, Soil Biology and Biochemistry 68, 252-262.
13. R.G. Burns, J.L. DeForest, J. Marxsen, R.L. Sinsabaugh, M.E. Stromberger, M.D. Wallenstein, M.N. Weintraub, A. Zoppini (2013). Soil enzymes in a changing environment: current knowledge and future directions, Soil Biology and Biochemistry 58, 216-234.
14. C. Ai, G. Liang, J. Sun, X. Wang, W. Zhou (2012). Responses of extracellular enzyme activities and microbial community in both the rhizosphere and bulk soil to long-term fertilization practices in a fluvo-aquic soil, Geoderma 173, 330-338.
15. L. Brussaard, P.C. De Ruiter, G.G. Brown (2007). Soil biodiversity for agricultural sustainability, Agriculture, ecosystems & environment 121(3), 233-244.
16. R. Ghimire, J.B. Norton, P.D. Stahl, U. Norton (2014). Soil microbial substrate properties and microbial community responses under irrigated organic and reduced-tillage crop and forage production systems, PloS one 9(8), e103901.
17. Z. Wang, T. Li, X. Wen, Y. Liu, J. Han, Y. Liao, J.M. DeBruyn (2017). Fungal communities in rhizosphere soil under conservation tillage shift in response to plant growth, Frontiers in microbiology 8, 1301.
18. L. Duniere, S. Xu, J. Long, C. Elekwachi, Y. Wang, K. Turkington, R. Forster, T.A. McAllister (2017). Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage, BMC microbiology 17(1), 1-16.
19. M.C. Fisher, D.A. Henk, C.J. Briggs, J.S. Brownstein, L.C. Madoff, S.L. McCraw, S.J. Gurr (2012) . Emerging fungal threats to animal, plant and ecosystem health, Nature 484(7393), 186-194.
20. R.A. Farrer, L.A. Weinert, J. Bielby, T.W. Garner, F. Balloux, F. Clare, J. Bosch, A.A. Cunningham, C. Weldon, L.H. du Preez (2011). Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage, Proceedings of the National Academy of Sciences 108(46),18732-18736.
21. M.-Q. Liang, C.-F. Zhang, C.-L. Peng, Z.-L. Lai, D.-F. Chen, Z.-H. Chen (2011). Plant growth, community structure, and nutrient removal in monoculture and mixed constructed wetlands, Ecological Engineering 37(2), 309-316.
22. M. Rodriguez, J. Brisson (2016). Does the combination of two plant species improve removal efficiency in treatment wetlands?, Ecological Engineering 91, 302-309.
23. F.M. Toma, N.Q.F. Abdulla (2012). Isolation, Identification and Seasonal Distribution of Soilborne Fungi in Different Areas of Erbil Governorate, Journal of Advanced Laboratory Research in Biology 3(4), 246-255.
24. M. Nitu, M. Rahaman, F. Aminuzzaman, N. Sultana (2020). Occurrence and Diversity of Soil Microflora in Potato Fields of Bangladesh, Journal of Advances in Microbiology, 1-15.
25. C. Nwofor, C. Oyeka, N. Onyenwe, M. Echeta, Y. Tatfeng (2021). Prevalence of Non-Dermatophytic Molds Associated with Cutaneous Mycoses in Cattle in Abia and Imo States, Nigeria, Archives of Current Research International, 43-56.
26. F.A. Toscano-Verduzco, P.A. Cedeño-Valdivia, W. Chan-Cupul, H.A. Hernández-Ortega, E. Ruiz-Sánchez, E. Galindo-Velasco, E. Cruz-Crespo (2020). Phosphates solubilization, indol-3-acetic acid and siderophores production by Beauveria brongniartii and its effect on growth and fruit quality of Capsicum chinense, The Journal of Horticultural Science and Biotechnology 95(2), 235-246.
27. N. Faqi Abdulla (2010). Isolation, Identification and Seasonal Distribution of Soil Borne Fungi in Different Areas of Erbil Governorate, M. Sc. Thesis. College of science. Salahaddin University-Erbil.
28. S. Rønhede, B. Jensen, S. Rosendahl, B.B. Kragelund, R.K. Juhler, J. Aamand (2005). Hydroxylation of the herbicide isoproturon by fungi isolated from agricultural soil, Applied and Environmental Microbiology 71(12), 7927-7932.
29. P. Tambekar, S. Wate (2007). Study of phosphate solubilization efficiencies of fungi and bacteria isolated from saline belt of Puma river basin, Research Journal of Agriculture and Biological Sciences 3(6), 701-703.
30. P. Sanjotha, P. Mahantesh, C. Patil (2011). Isolation and screening of efficiency of phosphate solubilizing microbes, Int J Microbiol Res 3(1), 56-8.
31. N. McClenny (2007). An Unusual Aspergillus Species at a Major Cancer Center: Implications for the Clinical Laboratory San Francisco State University, San Francisco, CA Course DL-977 1.0 CE/Contact Hour Level: Beginning to Intermediate, MPA, MT (ASCP).
32. C. Pornsuriya, F. Lin, S. Kanokmedhakul, K. Soytong (2008). New record of Chaetomium species isolated from soil under pineapple plantation in Thailand, Journal of Agricultural Technology 4(2), 91-103.
33. S. İlhan, R. Demirel, A. Asan, C. Bayçu, E. KINACI (2006). Colonial and morphological characteristics of some microfungal species isolated from agricultural soils in Eskişehir Province (Turkey), Turkish Journal of Botany 30(2), 95-104.
34. S. Ülker, A. Özel, A. Çolak, Ş.A. Karaoğlu (2011). Isolation, production, and characterization of an extracellular lipase from Trichoderma harzianum isolated from soil, Turkish Journal of Biology 35(5), 543-550.
35. N.S. Guler, N. Pehlivan, S.A. Karaoglu, S. Guzel, A. Bozdeveci (2016). Trichoderma atroviride ID20G inoculation ameliorates drought stress-induced damages by improving antioxidant defence in maize seedlings, Acta Physiologiae Plantarum 38(6), 132.
36. J. Wang, A. Replogle, R. Hussey, T. Baum, X. Wang, E.L. Davis, M.G. Mitchum (2011). Identification of potential host plant mimics of CLAVATA3/ESR (CLE)‐like peptides from the plant‐parasitic nematode Heterodera schachtii, Molecular Plant Pathology 12(2), 177-186.
37. G. Bonanomi, V. Antignani, M. Capodilupo, F. Scala (2010). Identifying the characteristics of organic soil amendments that suppress soilborne plant diseases, Soil Biology and Biochemistry 42(2), 136-144.
38. T. Watanabe (2010). Pictorial atlas of soil and seed fungi: morphologies of cultured fungi and key to species, CRC press.
39. T.G. Porch, S. Valentin, C.E. de Jensen, J.S. Beaver (2014). Identification of soil-borne pathogens in a common bean root rot nursery in Isabela, Puerto Rico, The Journal of Agriculture of the University of Puerto Rico 98(1).
40. D. Francioli, J. van Ruijven, L. Bakker, L. Mommer (2020). Drivers of total and pathogenic soil-borne fungal communities in grassland plant species, Fungal Ecology 48, 100987.
41. P. Mäder, A. Fliessbach, D. Dubois, L. Gunst, P. Fried, U. Niggli (2002). Soil fertility and biodiversity in organic farming, Science 296(5573), 1694-1697.
42. A. Álvarez-Martín, S.L. Hilton, G.D. Bending, M.S. Rodríguez-Cruz, M.J. Sánchez-Martín (2016). Changes in activity and structure of the soil microbial community after application of azoxystrobin or pirimicarb and an organic amendment to an agricultural soil, Applied Soil Ecology 106, 47-57.
43. M. Arif, M.S. Fawaz, A.T.K. Zuan, R.U. Shah, R. Ullah, A.M. Elshehawi, A.M. Al-Sadi, M.I. Ullah, M.E. Güldür, S.S. Alotaibi (2021). The impact of different biochars on Stemphylium leaf blight (SLB) suppression and productivity of onion (Allium cepa L.), Journal of King Saud University-Science 33(7), 101575.
44. G. Oyeyiola, A. Agbaje, C. Adetunji (2013). Determination of the soil microflora of a soil near microbiology laboratory at the university of Ilorin main campus, Egypt. Acad. J. Biol. Sci., G. Micr 5(1), 35-41.
45. I.C. Anderson, J.W. Cairney (2004). Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques, Environmental microbiology 6(8), 769-779.
46. H.M.Z.U. Ghazali, S. Akram, I. Fatima, M. Hussain, A. Hameed, M. Arif, M.A. Ahmed, A.A. Al-Ghamdi, M.S. Elshikh, B.O.O. Alrashidi (2022). Fungi species causing dieback and wilt diseases in shisham [Dalbergia sissoo (Roxb)] and impact of various fungicides on their management, Journal of King Saud University-Science 34(4), 101970.
47. M. Hartmann, B. Frey, J. Mayer, P. Mäder, F. Widmer (2015). Distinct soil microbial diversity under long-term organic and conventional farming, The ISME journal 9(5), 1177-1194.
48. M. McDaniel, L.K. Tiemann, A. Grandy (2014). Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? A meta‐analysis, Ecological Applications 24(3), 560-570.
49. A. Infantino, V. Balmas, N. Schianchi, S. Mocali, C. Chiellini, D. Martignoni, M.P. Aleandri, L. Tomassoli, A. Haegi, A. Grottoli (2021). Diversity of soil-borne fungal species associated to root rot and vine decline of melon in Sardinia (Italy), Journal of Plant Pathology 103(2), 421-432.
50. E.A. Ampt, J. van Ruijven, J.M. Raaijmakers, A.J. Termorshuizen, L. Mommer (2019). Linking ecology and plant pathology to unravel the importance of soil-borne fungal pathogens in species-rich grasslands, European Journal of Plant Pathology 154, 141-156.
51. I. Senanayake, A. Rathnayaka, D. Marasinghe, M. Calabon, E. Gentekaki, H. Lee, V. Hurdeal, D. Pem, L. Dissanayake, S. Wijesinghe (2020). Morphological approaches in studying fungi: Collection, examination, isolation, sporulation and preservation, Mycosphere 11(1), 2678-2754.
52. K.D. Hyde, Y. Dong, R. Phookamsak, R. Jeewon, D.J. Bhat, E.G. Jones, N.-G. Liu, P.D. Abeywickrama, A. Mapook, D. Wei (2020). Fungal diversity notes 1151–1276: taxonomic and phylogenetic contributions on genera and species of fungal taxa, Fungal diversity 100, 5-277.
53. S. Boonmee, D.N. Wanasinghe, M.S. Calabon, N. Huanraluek, S.K. Chandrasiri, G.E. Jones, W. Rossi, M. Leonardi, S.K. Singh, S. Rana (2021). Fungal diversity notes 1387–1511: Taxonomic and phylogenetic contributions on genera and species of fungal taxa, Fungal Diversity 111, 1-335.
54. T. Eslaminejad, M. Zakaria (2011). Morphological characteristics and pathogenicity of fungi associated with Roselle (Hibiscus Sabdariffa) diseases in Penang, Malaysia, Microbial pathogenesis 51(5), 325-337.
55. N. Hassan, M. Shimizu, M. Hyakumachi (2014). Occurrence of root rot and vascular wilt diseases in roselle (Hibiscus sabdariffa L.) in Upper Egypt, Mycobiology 42(1), 66-72.
56. Y. Naidu, Y. Siddiqui, M.Y. Rafii, H.M. Saud, A.S. Idris (2018). Inoculation of oil palm seedlings in Malaysia with white-rot hymenomycetes: Assessment of pathogenicity and vegetative growth, Crop Protection 110, 146-154.