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

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.

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Long-Term Monoculture Negatively Regulates Fungal Community Composition and Abundance of Tea Orchards

Agronomy ◽

10.3390/agronomy9080466 ◽

2019 ◽

Vol 9 (8) ◽

pp. 466 ◽

Cited By ~ 4

Author(s):

Yasir Arafat ◽

Muhammad Tayyab ◽

Muhammad Umar Khan ◽

Ting Chen ◽

Hira Amjad ◽

...

Keyword(s):

Soil Ph ◽

Fungal Community ◽

Cropping System ◽

Alpha Diversity ◽

Fungal Species ◽

Fungal Communities ◽

Continuous Cropping ◽

Fungal Community Composition ◽

Continuous Cropping System ◽

Tea Plants

Continuous cropping frequently leads to soil acidification and major soil-borne diseases in tea plants, resulting in low tea yield. We have limited knowledge about the effects of continuous tea monoculture on soil properties and the fungal community. Here, we selected three replanted tea fields with 2, 15, and 30 years of monoculture history to assess the influence of continuous cropping on fungal communities and soil physiochemical attributes. The results showed that continuous tea monoculture significantly reduced soil pH and tea yield. Alpha diversity analysis showed that species richness declined significantly as the tea planting years increased and the results based on diversity indicated inconsistency. Principal coordinate analysis (PCoA) revealed that monoculture duration had the highest loading in structuring fungal communities. The relative abundance of Ascomycota, Glomeromycota, and Chytridiomycota decreased and Zygomycota and Basidiomycota increased with increasing cropping time. Continuous tea cropping not only decreased some beneficial fungal species such as Mortierella alpina and Mortierella elongatula, but also promoted potentially pathogenic fungal species such as Fusarium oxysporum, Fusarium solani, and Microidium phyllanthi over time. Overall, continuous tea cropping decreased soil pH and potentially beneficial microbes and increased soil pathogenic microbes, which could be the reason for reducing tea yield. Thus, developing sustainable tea farming to improve soil pH, microbial activity, and enhanced beneficial soil microbes under a continuous cropping system is vital for tea production.

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Fungal community composition and diversity vary with soil depth and landscape position in a no-till wheat-based cropping system

FEMS Microbiology Ecology ◽

10.1093/femsec/fiy098 ◽

2018 ◽

Vol 94 (7) ◽

Cited By ~ 11

Author(s):

Daniel C Schlatter ◽

Kendall Kahl ◽

Bryan Carlson ◽

David R Huggins ◽

Timothy Paulitz

Keyword(s):

Community Composition ◽

Fungal Community ◽

Soil Depth ◽

Cropping System ◽

Landscape Position ◽

Fungal Community Composition ◽

No Till

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Effects of green manure of wild rocket (Diplotaxis tenuifolia L.) on cucumber rhizosphere fungal community

Allelopathy Journal ◽

10.26651/allelo.j/2021-53-1-1330 ◽

2021 ◽

Vol 53 (1) ◽

pp. 93-100

Author(s):

X.H. Zhang ◽

H.L Xie ◽

Y.Y. Wang ◽

X.G. Zhou

Keyword(s):

Community Composition ◽

Relative Abundance ◽

Fungal Community ◽

Green Manure ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Fungal Community Composition ◽

Cucumis Sativus L ◽

Manure Treatment ◽

Wild Rocket

In pot culture, we evaluated the effects of green manure of wild rocket (Diplotaxis tenuifolia (L.) DC.) on cucumber (Cucumis sativus L.) rhizosphere fungal community composition. Cucumber rhizosphere fungal composition was analyzed by high-throughput amplicon sequencing of fungal ITS regions. Results showed that cucumber seedling rhizosphere fungal community composition was different between the fallow treatment and green manure treatment. However, green manure treatment did not affect the cucumber seedlings fungal community alpha diversity. Compared with the fallow treatment, cucumber grown in green manure of wild rocket had higher relative abundance of phylum Ascomycota but lower relative abundance of phylum Zygomycota. Moreover, green manure of wild rocket decreased operational taxonomic units (OTUs) classified as Pseudallescheria and Kernia spp. but increased OTUs classified as Humicola and Fusarium spp. in cucumber rhizosphere.

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Unlocking the Microbiome Communities of Banana (Musa spp.) under Disease Stressed (Fusarium wilt) and Non-Stressed Conditions

Microorganisms ◽

10.3390/microorganisms8030443 ◽

2020 ◽

Vol 8 (3) ◽

pp. 443 ◽

Cited By ~ 2

Author(s):

Manoj Kaushal ◽

Rony Swennen ◽

George Mahuku

Keyword(s):

Fusarium Oxysporum ◽

Relative Abundance ◽

Fungal Community ◽

Bacterial Communities ◽

Fungal Communities ◽

Fungal Community Composition ◽

Core Microbiome ◽

Fungal Microbiota ◽

Diversity Structure ◽

Plant Components

We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, roots, and corm of the host plant. Results revealed that bacterial and fungal microbiota present in roots and corm primarily emanated from the rhizosphere. The composition of bacterial communities in the rhizosphere, roots, and corm were different, with more diversity observed in the rhizosphere and less in the corm. However, distinct sample types i.e., without (asymptomatic) and with (symptomatic) Fusarium symptoms were the major drivers of the fungal community composition. Considering the high relative abundance among samples, we identified core microbiomes with bacterial and fungal OTUs classified into 20 families and colonizing distinct plant components of banana. Our core microbiome assigned 129 bacterial and 37 fungal genera to known taxa.

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Effects of crop rotation with wild rocket on cucumber seedling rhizosphere fungal community composition

Allelopathy Journal ◽

10.26651/allelo.j/2019-47-1-1221 ◽

2019 ◽

Vol 47 (1) ◽

pp. 83-92 ◽

Cited By ~ 1

Author(s):

X. Jin ◽

D. L. Li ◽

F Z. Wu ◽

K. Pan ◽

X G. Zhou

Keyword(s):

Community Composition ◽

Crop Rotation ◽

Fungal Community ◽

Cucumber Seedling ◽

Fungal Community Composition ◽

Wild Rocket

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Faculty Opinions recommendation of Root exudates regulate soil fungal community composition and diversity.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1100212.556386 ◽

2008 ◽

Author(s):

Fergal O'Gara

Keyword(s):

Community Composition ◽

Root Exudates ◽

Fungal Community ◽

Fungal Community Composition ◽

Soil Fungal Community ◽

Soil Fungal Community Composition

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Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge

Scientific Reports ◽

10.1038/s41598-021-95099-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jorge Domínguez ◽

Manuel Aira ◽

Keith A. Crandall ◽

Marcos Pérez-Losada

Keyword(s):

Sewage Sludge ◽

Community Composition ◽

Fungal Community ◽

High Throughput Sequencing ◽

Wastewater Treatment Plants ◽

Agricultural Practices ◽

Fungal Community Composition ◽

Earthworm Casts ◽

Composition And Structure ◽

Sustainable Agricultural Practices

AbstractWastewater treatment plants produce hundreds of million tons of sewage sludge every year all over the world. Vermicomposting is well established worldwide and has been successful at processing sewage sludge, which can contribute to alleviate the severe environmental problems caused by its disposal. Here, we utilized 16S and ITS rRNA high-throughput sequencing to characterize bacterial and fungal community composition and structure during the gut- and cast-associated processes (GAP and CAP, respectively) of vermicomposting of sewage sludge. Bacterial and fungal communities of earthworm casts were mainly composed of microbial taxa not found in the sewage sludge; thus most of the bacterial (96%) and fungal (91%) taxa in the sewage sludge were eliminated during vermicomposting, mainly through the GAP. Upon completion of GAP and during CAP, modified microbial communities undergo a succession process leading to more diverse microbiotas than those found in sewage sludge. Consequently, bacterial and fungal community composition changed significantly during vermicomposting. Vermicomposting of sewage resulted in a stable and rich microbial community with potential biostimulant properties that may aid plant growth. Our results support the use of vermicompost derived from sewage sludge for sustainable agricultural practices, if heavy metals or other pollutants are under legislation limits or adequately treated.

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