[
Al-Yahya’ei M.N., Oehl F., Vallino M., Lumini E., Redecker D., Wiemken A., Bonfante P., 2011. Unique arbuscular mycorrhizal fungal communities uncovered in date palm plantations and surrounding desert habitats of Southern Arabia. Mycorrhiza, 21(3): 195-209, https://doi.org/10.1007/s00572-010-0323-5.
]Search in Google Scholar
[
Anjos L., Gaistardo C., Deckers J., Dondeyne S., Eberhardt E. et al., 2014. World reference base for soil resources 2014. International soil classification system for naming soils and creating legends for soil maps. (P. Schad, C. Van Huyssteen, & E. Micheli, Eds.), World Soil Resources Reports No. 106 (JRC91947 ed.). Rome: FAO. Retrieved from http://www.fao.org/3/a-i3794e.pdf
]Search in Google Scholar
[
Bao X., Wang Y., Olsson P.A., 2019. Arbuscular mycorrhiza under water – Carbon‒phosphorus exchange between rice and arbuscular mycorrhizal fungi under different flooding regimes. Soil Biology and Biochemistry, 129: 169-177, https://doi.org/10.1016/j.soilbio.2018.11.020.
]Search in Google Scholar
[
Bardelli T., Gómez-Brandón M., Ascher-Jenull J., Fornasier F., Arfaioli P., Francioli D. et al., 2017. Effects of slope exposure on soil physico-chemical and microbiological properties along an altitudinal climosequence in the Italian Alps. Science of the Total Environment, 575: 1041-1055, https://doi.org/10.1016/j.scitotenv.2016.09.176.
]Search in Google Scholar
[
Bengtsson-Palme J., Ryberg M., Hartmann M., Branco S., Wang Z. et al., 2013. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution, 4(10): 914-919, https://doi.org/10.1111/2041-210X.12073.
]Search in Google Scholar
[
Borowik A., Wyszkowska J., 2016. Soil moisture as a factor affecting the microbiological and biochemical activity of soil. Plant, Soil and Environment, 62(6): 250-255, https://doi.org/10.17221/158/2016-PSE.
]Search in Google Scholar
[
Callahan B.J., McMurdie P.J., Rosen M.J., Han A.W., Johnson A.J.A., Holmes S.P., 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7): 581-583, https://doi.org/10.1038/nmeth.3869.
]Search in Google Scholar
[
Cozzolino V., Di Meo V., Monda H., Spaccini R., Piccolo A., 2016. The molecular characteristics of compost affect plant growth, arbuscular mycorrhizal fungi, and soil microbial community composition. Biology and Fertility of Soils, 52(1): 15-29, https://doi.org/10.1007/s00374-015-1046-8.
]Search in Google Scholar
[
Dong X., Yang L., Harbo L.S., Yan X., Chen J. et al., 2023. Effects of land use on soil microbial community structure and diversity in the Yellow River floodplain. Journal of Plant Ecology, 16(1), https://doi.org/10.1093/jpe/rtac075.
]Search in Google Scholar
[
Drenovsky R.E., Vo D., Graham K.J., Scow K.M., 2004. Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microbial Ecology, 48(3): 424-430, https://doi.org/10.1007/s00248-003-1063-2.
]Search in Google Scholar
[
Drenovsky R.E., Steenwerth K.L., Jackson L.E., Scow K.M., 2010. Land use and climatic factors structure regional patterns in soil microbial communities. Global Ecology and Biogeography, 19(1): 27-39, https://doi.org/10.1111/j.1466-8238.2009.00486.x.
]Search in Google Scholar
[
Duniere L., Xu S., Long J., Elekwachi C., Wang Y. et al., 2017. Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage. BMC Micro-biology, 17(1): 50, https://doi.org/10.1186/s12866-017-0947-0.
]Search in Google Scholar
[
Frąc M., Hannula S.E., Bełka M., Jędryczka M., 2018. Fungal biodiversity and their role in soil health. Frontiers in Micro-biology, 9(707), https://doi.org/10.3389/fmicb.2018.00707.
]Search in Google Scholar
[
Francioli D., Cid G., Hajirezaei M.R., Kolb S., 2022. Response of the wheat mycobiota to flooding revealed substantial shifts towards plant pathogens. Frontiers in Plant Science, 13, 1028153, https://doi.org/10.3389/fpls.2022.1028153.
]Search in Google Scholar
[
Furtak K., Gałązka A., 2019. Edaphic factors and their influence on microbiological biodiversity of the soil environment. Postępy Mikrobiologii - Advancements of Microbiology, 58(4): 375-384, https://doi.org/https://doi.org/10.21307/PM-2019.58.4.375.
]Search in Google Scholar
[
Furtak K., Gałązka A., Niedźwiecki J., 2020. Changes in soil enzymatic activity caused by hydric stress. Polish Journal of Environmental Studies, 29(4): 1–8, https://doi.org/10.15244/pjoes/112896.
]Search in Google Scholar
[
Furtak K., Grządziel J., Gałązka A., Niedźwiecki J., 2019. Analysis of soil properties, bacterial community composition, and metabolic diversity in fluvisols of a floodplain area. Sustainability, 11(14), https://doi.org/10.3390/su11143929.
]Search in Google Scholar
[
Furtak K., Grządziel J., Gałązka A., Niedźwiecki J., 2020. Prevalence of unclassified bacteria in the soil bacterial community from floodplain meadows (fluvisols) under simulated flood conditions revealed by a metataxonomic approachss. Catena, 188, https://doi.org/10.1016/j.catena.2019.104448.
]Search in Google Scholar
[
Furtak K., Wolińska A., 2023. The impact of extreme weather events as a consequence of climate change on the soil moisture and on the quality of the soil environment and agriculture – A review. Catena, 231, 107378, https://doi.org/10.1016/j.catena.2023.107378.
]Search in Google Scholar
[
Glynou K., Ali T., Buch A.K., Haghi Kia S., Ploch S. et al., 2016. The local environment determines the assembly of root endophytic fungi at a continental scale. Environmental Microbiology, 18(8): 2418-2434, https://doi.org/10.1111/1462-2920.13112.
]Search in Google Scholar
[
Guo J., Ling N., Chen Z., Xue C., Li L. et al., 2020. Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes. New Phytologist, 226(1): 232-243, https://doi.org/10.1111/nph.16345.
]Search in Google Scholar
[
Heijden M.G.A., Martin F.M., Selosse M., Sanders I.R., 2015. Mycorrhizal ecology and evolution: the past, the present, and the future. New Phytologist, 205(4): 1406-1423, https://doi.org/10.1111/nph.13288.
]Search in Google Scholar
[
Helfrich M., Ludwig B., Thoms C., Gleixner G., Flessa H., 2015. The role of soil fungi and bacteria in plant litter decomposition and macroaggregate formation determined using phospholipid fatty acids. Applied Soil Ecology, 96: 261-264, https://doi.org/10.1016/j.apsoil.2015.08.023.
]Search in Google Scholar
[
Hiscox J., Savoury M., Müller C.T., Lindahl B.D., Rogers H.J., Boddy L., 2015. Priority effects during fungal community establishment in beech wood. ISME Journal, 9(10): 2246-2260, https://doi.org/10.1038/ismej.2015.38.
]Search in Google Scholar
[
Jamiołkowska A., Ksiȩżniak A., Gałązka A., Hetman B., Kopacki M., Skwaryło-Bednarz B., 2018. Impact of abiotic factors on development of the community of arbuscular mycorrhizal fungi in the soil: A Review. International Agro-physics, 32(1): 133-140, Walter de Gruyter GmbH. https://doi.org/10.1515/intag-2016-0090.
]Search in Google Scholar
[
Khidir H.H., Eudy D.M., Porras-Alfaro A., Herrera J., Natvig D.O., Sinsabaugh R.L., 2010. A general suite of fungal endophytes dominate the roots of two dominant grasses in a semiarid grassland. Journal of Arid Environments, 74(1): 35-42, https://doi.org/10.1016/J.JARIDENV.2009.07.014.
]Search in Google Scholar
[
Knapp D.G., Kovács G.M., Zajta E., Groenewald J.Z., Crous P.W., 2015. Dark septate endophytic pleosporalean genera from semiarid areas. Persoonia: Molecular Phylogeny and Evolution of Fungi, 35(1): 87-100, https://doi.org/10.3767/003158515X687669.
]Search in Google Scholar
[
Kruse J., Piątek M., Lutz M., Thines M., 2018. Broad host range species in specialised pathogen groups should be treated with suspicion – a case study on Entyloma infecting Ranunculus. Persoonia: Molecular Phylogeny and Evolution of Fungi, 41: 175-201, https://doi.org/10.3767/PERSOONIA.2018.41.09.
]Search in Google Scholar
[
Kumar M., Kumar A., Singh J.K., Kumar S., Niwas R., 2018. Influence of soil temperature, moisture and planting depth on black scurf development in potato (Solanum tuberosum L.). Journal of Agrometeorology, 20(4): 342-344, https://doi.org/10.54386/JAM.V20I4.582.
]Search in Google Scholar
[
Kunicki-Golfinger W.J.H., 2008. Życie bakterii. Warszawa: Wydawnictwo Naukowe PWN.
]Search in Google Scholar
[
Lee Taylor D., Sinsabaugh R.L., 2015. The Soil Fungi. pp. 77-109. In: Soil Microbiology, Ecology and Biochemistry. Elsevier, https://doi.org/10.1016/b978-0-12-415955-6.00004-9.
]Search in Google Scholar
[
Li X., Zhang Q., Ma J., Yang Y., Wang Y., Fu C., 2020. Flooding irrigation weakens the molecular ecological network complexity of soil microbes during the process of drylandto-paddy conversion. International Journal of Environmental Research and Public Health, 17(2): 561, https://doi.org/10.3390/ijerph17020561.
]Search in Google Scholar
[
Liao H., Chapman S.J., Li Y., Yao H., 2018. Dynamics of microbial biomass and community composition after short-term water status change in Chinese paddy soils. Environmental Science and Pollution Research, 25(3): 2932-2941, https://doi.org/10.1007/s11356-017-0690-y.
]Search in Google Scholar
[
Massimo N.C., Nandi Devan M.M., Arendt K.R., Wilch M.H., Riddle J.M. et al., 2015. Fungal endophytes in aboveground tissues of desert plants: Infrequent in culture, but highly diverse and distinctive symbionts. Microbial Ecology, 70(1): 61-76, https://doi.org/10.1007/s00248-014-0563-6.
]Search in Google Scholar
[
McConnaughey M., 2014. Physical chemical properties of fungi. In: Reference Module in Biomedical Sciences. Elsevier, https://doi.org/10.1016/b978-0-12-801238-3.05231-4.
]Search in Google Scholar
[
McMurdie P.J., Holmes S., 2013. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Micro-biome Census Data. PLoS ONE, 8(4), e61217. https://doi.org/10.1371/journal.pone.0061217
]Search in Google Scholar
[
Millard P., Singh B.K., 2010. Does grassland vegetation drive soil microbial diversity? Nutrient Cycling in Agroecosystems, 88(2): 147-158, https://doi.org/10.1007/s10705-009-9314-3.
]Search in Google Scholar
[
Murali A., Bhargava A., Wright E.S., 2018. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome, 6(1), 140, https://doi.org/10.1186/s40168-018-0521-5.
]Search in Google Scholar
[
Oehl F., Laczko E., Oberholzer H.R., Jansa J., Egli S., 2017. Diversity and biogeography of arbuscular mycorrhizal fungi in agricultural soils. Biology and Fertility of Soils, 53(7): 777-797, https://doi.org/10.1007/s00374-017-1217-x.
]Search in Google Scholar
[
Pagano M., Correa E., Duarte N., Yelikbayev B., O’Donovan A., Gupta V., 2017. Advances in eco-efficient agriculture: The plant-soil mycobiome. Agriculture, 7(2), 14, https://doi.org/10.3390/agriculture7020014.
]Search in Google Scholar
[
Pati P.K., Sharma M., Salar R.K., Sharma A., Gupta A.P., Singh B., 2008. Studies on leaf spot disease of Withania somnifera and its impact on secondary metabolites. Indian Journal of Microbiology, 48: 432-437, Springer, https://doi.org/10.1007/s12088-008-0053-y.
]Search in Google Scholar
[
Pourmahdi A., Taheri P., 2015. Genetic diversity of Thanatephorus cucumeris infecting tomato in Iran. Journal of Phyto-pathology, 163(1): 19-32, https://doi.org/10.1111/JPH.12276.
]Search in Google Scholar
[
Richards J.K., Kariyawasam G.K., Seneviratne S., Wyatt N.A., Xu S.S. et al., 2022. A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat. New Phytologist, 233(1): 427-442, https://doi.org/10.1111/nph.17601.
]Search in Google Scholar
[
Riess K., Schon M.E., Ziegler R., Lutz M., Shivas R.G., Piątek M., Garnica S., 2019. The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae. Organisms Diversity & Evolution, 19: 13-30, https://doi.org/10.1007/s13127-018-0384-4.
]Search in Google Scholar
[
Rillig M.C., Aguilar-Trigueros C.A., Bergmann J., Verbruggen E., Veresoglou S.D., Lehmann A., 2015. Plant root and mycorrhizal fungal traits for understanding soil aggregation. New Phytologist, 205(4): 1385-1388, https://doi.org/10.1111/nph.13045.
]Search in Google Scholar
[
Ritz K., Young I.M., 2004. Interactions between soil structure and fungi. Mycologist, 18: 52-59, Cambridge University Press, https://doi.org/10.1017/S0269915X04002010.
]Search in Google Scholar
[
Ronsheim M.L., 2016. Plant genotype influences mycorrhiza benefits and susceptibility to a soil pathogen. The American Midland Naturalist, 175(1): 103-112, https://doi.org/10.1674/AMID-175-01-103-112.1.
]Search in Google Scholar
[
Sánchez-Rodríguez A.R., Nie C., Hill P.W., Chadwick D.R., Jones D.L., 2019. Extreme flood events at higher temperatures exacerbate the loss of soil functionality and trace gas emissions in grassland. Soil Biology and Biochemistry, 130: 227-236, https://doi.org/10.1016/j.soilbio.2018.12.021.
]Search in Google Scholar
[
Schmidt P.A., Bálint M., Greshake B., Bandow C., Römbke J., Schmitt I., 2013. Illumina metabarcoding of a soil fungal community. Soil Biology and Biochemistry, 65: 128-132, https://doi.org/10.1016/j.soilbio.2013.05.014.
]Search in Google Scholar
[
Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T. et al., 2003. Cytoscape: A software Environment for integrated models of biomolecular interaction networks. Genome Research, 13(11): 2498-2504, https://doi.org/10.1101/gr.1239303.
]Search in Google Scholar
[
Solís-Rodríguez U.R.J., Ramos-Zapata J.A., Hernández-Cuevas L., Salinas-Peba L., Guadarrama P., 2020. Arbuscular mycorrhizal fungi diversity and distribution in tropical low flooding forest in Mexico. Mycological Progress, 19(3): 195-204, https://doi.org/10.1007/s11557-019-01550-x.
]Search in Google Scholar
[
Team R.C., 2016. R: A language and environment for statistical computing. R Foundation for Statistical Computing.
]Search in Google Scholar
[
Tedersoo L., Sánchez-Ramírez S., Kõljalg U., Bahram M., Döring M. et al., 2018. High-level classification of the Fungi and a tool for evolutionary ecological analyses. Fungal Diversity, 90(1): 135-159, https://doi.org/10.1007/s13225-018-0401-0.
]Search in Google Scholar
[
Tonouchi A., 2009. Isolation and characterization of a novel facultative anaerobic filamentous fungus from Japanese rice field soil. International Journal of Microbiology, https://doi.org/10.1155/2009/571383.
]Search in Google Scholar
[
Unger I.M., Kennedy A.C., Muzika R.-M., 2009. Flooding effects on soil microbial communities. Applied Soil Ecology, 42(1): 1-8, https://doi.org/10.1016/j.apsoil.2009.01.007.
]Search in Google Scholar
[
Volk T.J., 2013. Fungi. pp. 624-640. In: Encyclopedia of Biodiversity: Second Edition. Elsevier Inc., https://doi.org/10.1016/B978-0-12-384719-5.00062-9.
]Search in Google Scholar
[
Wagner D., Eisenhauer N., Cesarz S., 2015. Plant species richness does not attenuate responses of soil microbial and nematode communities to a flood event. Soil Biology and Biochemistry, 89: 135-149, https://doi.org/10.1016/j.soil-bio.2015.07.001.
]Search in Google Scholar
[
Wang Y., Bao X., Li S., 2021. Effects of arbuscular mycorrhizal fungi on rice growth under different flooding and shading regimes. Frontiers in Microbiology, 12, 756752, https://doi.org/10.3389/fmicb.2021.756752.
]Search in Google Scholar
[
Wang Y., Huang Y., Qiu Q., Xin G., Yang Z., Shi S., 2011. Flooding greatly affects the diversity of arbuscular mycorrhizal fungi communities in the roots of wetland plants. PLoS ONE, 6(9), e24512, https://doi.org/10.1371/journal.pone.0024512.
]Search in Google Scholar
[
Wang Y., Li Y., Bao X., Björn L.O., Li S., Olsson P.A., 2016. Response differences of arbuscular mycorrhizal fungi communities in the roots of an aquatic and a semiaquatic species to various flooding regimes. Plant and Soil, 403(1–2): 361-373, https://doi.org/10.1007/s11104-016-2811-7.
]Search in Google Scholar
[
Wang Y., Qiu Q., Yang Z., Hu Z., Tam N.F.Y., Xin G., 2010. Arbuscular mycorrhizal fungi in two mangroves in South China. Plant and Soil, 331(1): 181-191, https://doi.org/10.1007/s11104-009-0244-2.
]Search in Google Scholar
[
Yang T., Tedersoo L., Soltis P.S., Soltis D.E., Gilbert J.A. et al., 2019. Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China. ISME Journal, 13(3): 686-697, https://doi.org/10.1038/s41396-018-0303-x.
]Search in Google Scholar
[
Yang Y., Dou Y., Huang Y., An S., 2017. Links between soil fungal diversity and plant and soil properties on the Loess Plateau. Frontiers in Microbiology, 8(NOV), 2198, https://doi.org/10.3389/fmicb.2017.02198.
]Search in Google Scholar
[
Zhai J., Yan G., Cong L., Wu Y., Dai L., Zhang Z., Zhang M., 2020. Assessing the effects of salinity and inundation on halophytes litter breakdown in Yellow River Delta wetland. Ecological Indicators, 115, https://doi.org/10.1016/j.ecolind.2020.106405.
]Search in Google Scholar
[
Zheng F.-L., Liang S.-M., Chu X.-N., Yang Y.-L., Wu Q.-S., 2020. Mycorrhizal fungi enhance flooding tolerance of peach through inducing proline accumulation and improving root architecture. Plant, Soil and Environment, 66(12): 624-631, https://doi.org/10.17221/520/2020-PSE.
]Search in Google Scholar