Mycobiome Composition and Diversity under the Long-Term Application of Spent Mushroom Substrate and Chicken Manure

Abstract

Waste exogenous organic matter, including spent mushroom substrate (SMS) and chicken manure (CM), can be used as the basis of a soil-improving cropping system in sustainable agriculture. However, there is—as yet—a lack of information about important quality indicators such as the fungal community relative abundance, structure and biodiversity in soils treated with these additives. In this study, the responses of the soil fungal community composition and mycobiome diversity to SMS and CM application compared to the control soil were evaluated using a combination of the following molecular approaches: quantitative polymerase chain reactions, denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism, and next-generation sequencing. The most abundant phylum for both treatments was Ascomycota, followed by Basidiomycota. The application of SMS and CM increased the abundance of fungi, including Tremellomycetes and Pezizomycetes for the SMS additive, while the Mortierellomycetes, Pezizomycetes, and Leotiomycetes levels increased after CM addition. SMS and CM beneficially reduced the relative abundance of several operational taxonomic units (OTUs) which are potential crop pathogens. The results provide a novel insight into the fungal community associated with organic additives, which should be beneficial in the task of managing the soil mycobiome as well as crop protection and productivity.

Response of Fungal Diversity, Community Composition, and Functions to Nutrients Management in Red Soil

“…Hence, the addition of gypsum changes the soil properties and consequently leads to a positive effect on soil microbiota. Furthermore, mushroom residue and oyster shell powder also had a positive impact on soil microbial communities, consistent with previous findings [ 21 ] that mushroom residue improved the fungal communities. The possible explanation for increasing fungal community under mushroom residue may be related to an improvement of the soil environment, e.g., soil pH [ 69 ], thus leading to soil microorganisms having a healthier ecosystem [ 21 , 70 ].…”

“…Furthermore, mushroom residue and oyster shell powder also had a positive impact on soil microbial communities, consistent with previous findings [ 21 ] that mushroom residue improved the fungal communities. The possible explanation for increasing fungal community under mushroom residue may be related to an improvement of the soil environment, e.g., soil pH [ 69 ], thus leading to soil microorganisms having a healthier ecosystem [ 21 , 70 ]. Similarly, we found that oyster shell powder also had a significant effect on improving the soil microbial diversity and community composition, and these results are consistent with previous findings [ 18 , 22 ].…”

“…However, the relative abundance of Basidiomycota and Mortierellomycota was greater under nutrient management practices compared with FFP. Basidiomycota comprises some of the most common fungi known for their ability to produce massive fruiting bodies, as well as plant-parasitic fungi that cause wood decay and decomposition of litter [ 21 , 56 ]. This fungal category could be very beneficial to plants owing to their symbiotic association with the roots of the host plant, and they may play a significant role in storing mineral nutrients, metabolites, and water [ 56 ].…”

“…Similarly, oyster shell powder has a significant effect on improving the soil pH [ 18 ]. These improvements in soil profile result in providing a better soil environment for the functioning of soil microbiota through the addition of lime [ 13 , 19 ], gypsum [ 12 , 20 ], mushroom residue [ 21 ], and oyster shell powder [ 18 , 22 ]. Magnesium (Mg) fertilizers have also been used to increase the soil pH, and earlier studies have also shown that their addition into the soil has a significant effect on soil physicochemical properties and microbial communities [ 23 , 24 ].…”

Response of Soil Fungal Diversity and Community Composition to Varying Levels of Bamboo Biochar in Red Soils

“…Ascomycota is the most common and diversified phylum of eukaryotes, as well as the decomposition of organic substrate [ 22 ], and we discovered it to be the most common fungal phylum in the red soil. Basidiomycota includes some of the most well-known fungi for their ability to generate huge fruiting bodies, as well as plant parasite fungi that cause wood degradation and litter decomposition [ 51 , 52 ]. Because of their symbiotic relationship with the host plant’s roots, this fungus category could be very advantageous to plants, as they store mineral nutrients, metabolites, and water [ 52 ].…”