Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling Sites and Collections
2.2. Processing of Plant Material, Rhizosphere, and Soil Samples
2.3. Illumina DNA Sequencing
2.4. Cluster and Data Analysis
3. Results
3.1. Illumina DNA Sequencing
3.2. Cluster and Data Analysis
3.2.1. Molecular Operational Taxonomic Units Assignment
3.2.2. Relative Abundance among Different Substrates
3.2.3. Grouping of Fungal Communities in Plant Tissues and Cultivars
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 |
PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 |
NS5511 × 2 | NS5511 × 2 | NS5511 × 2 | NS5511 × 2 | NS5511 × 2 | NS5511 × 2 |
Dry bean × 6 | Cowpea × 6 | Soybean × 6 | Sorghum (8816) × 6 | Fallow × 6 | Bambara groundnut × 6 |
NS5511 × 2 | NS5511 × 2 | NS5511 × 2 | NS5511 × 2 | NS5511 × 2 | NS5511 × 2 |
PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 |
PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 |
Fallow × 6 | Sorghum (8816) × 6 | Dry bean × 6 | Bambara groundnut × 6 | Soybean × 6 | Cowpea × 6 |
PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 | PAN8816 × 2 |
NS5511 × 2 | NS5511 × 2 | NS5511 × 2 | NS5511 × 2 | NS5511 × 2 | NS5511 × 2 |
PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 | PAN8076W × 2 |
Soybean × 6 | Bambara groundnut × 6 | Fallow × 6 | Dry bean × 6 | Cowpea × 6 | Sorghum (8816) × 6 |
Cultivar | Sample | Number of Reads before QC (bp) | Number of Reads after QC (bp) | Total MOTUs |
---|---|---|---|---|
PAN8076W | Seeds | 56,429 | 38,879 | 252 |
Leaves | 77,662 | 59,724 | 341 | |
Stems | 78,912 | 17,128 | 133 | |
Roots | 80,959 | 67,341 | 514 | |
Rhizosphere soils | 93,649 | 83,071 | 463 | |
Bulk soils | 77,500 | 58,539 | 568 | |
PAN8816 | Seeds | 86,996 | 75,159 | 354 |
Leaves | 72,655 | 52,055 | 368 | |
Stems | 65,161 | 44,167 | 281 | |
Roots | 79,755 | 60,665 | 509 | |
Rhizosphere soils | 95,588 | 78,004 | 590 | |
Bulk soils | 91,469 | 75,901 | 591 | |
NS5511 | Seeds | 103,073 | 85,644 | 386 |
Leaves | 85,671 | 78,788 | 368 | |
Stems | 79,208 | 40,787 | 282 | |
Roots | 82,309 | 73,416 | 455 | |
Rhizosphere soils | 93,861 | 82,108 | 653 | |
Bulk soils | 88,034 | 73,200 | 551 |
Molecular Operational Taxonomic Units | Above Ground | Below Ground | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Seeds | Leaves | Stems | Roots | Rhizosphere Soils | Bulk Soils | |||||||||||||
PAN8076W | PAN8816 | NS5511 | PAN8076W | PAN8816 | NS5511 | PAN8076W | PAN8816 | NS5511 | PAN8076W | PAN8816 | NS5511 | PAN8076W | PAN8816 | NS5511 | PAN8076W | PAN8816 | NS5511 | |
Ascomycota | ||||||||||||||||||
Dothideomycetes | ||||||||||||||||||
Davidielleace sp. 1 (Cladosporium) | 7.7 | 26.0 * | 6.4 | 2.7 | 4.7 | 1.2 | 6.3 | 6.1 | 9.9 | 16.3 * | 2.7 | 8.0 | 21.7* | 6.7 | 3.2 | 3.2 | ||
Aureobasidium sp. 1 | 2.5 | 2.2 | 2.6 | 1.1 | 1.6 | 1.7 | 1.5 | |||||||||||
Didymellaceae sp. 1 (Phoma) | 6.1 | 11.0 | 11.3 | 7.5 | 9.5 | 5.2 | 2.6 | 5.2 | 6.7 | 6.6 | 5.2 | 5.4 | 5.1 | 7.0 | 7.7 | 5.1 | 8.1 | |
Cochliobolus | 5.1 | 1.2 | ||||||||||||||||
Saccharomycetes | ||||||||||||||||||
Meyerozyma sp. 1 | 2.5 | 2.4 | 4.0 | 2.7 | ||||||||||||||
Candida sp. 1 | 3.0 | 1.5 | 1.0 | 7.0 | 1.9 | 1.6 | 18.9 * | 2.5 | 6.5 | 7.2 | 1.4 | |||||||
Wickerhamomyces sp. 1 | 1.1 | 1.3 | 5.5 | 1.5 | 16.8 | 4.7 | 4.9 | |||||||||||
Pichia sp. 1 | 4.8 | 8.4 | 2.6 | 2.3 | 1.4 | |||||||||||||
Hanseniaspora sp. 1 | 5.4 | |||||||||||||||||
Zygoascus sp. 1 | 2.5 | |||||||||||||||||
Sordariomycetes | ||||||||||||||||||
Fusarium sp. 1 (Nectriaceae other) | 10.1 | 13.8 | 6.1 | 31.5 * | 28.6 * | 15.0 * | 55.8* | 38.3 * | 14.7 | 13.5 | 10.5 | 3.5 | 3.6 | 3.2 | 6.9 | 9.7 | 7.7 | |
Fusarium sp. 2 | 1.1 | 4.9 | 9.6 | 1.6 | 1.9 | 2.4 | 1.7 | 4.5 | 14.7 * | 10.7 | 2.5 | 7.5 | 9.5 | 14.7 * | 11.7 | |||
Myrmecridium | 1.3 | |||||||||||||||||
Nigrospora | 1.1 | |||||||||||||||||
Basidiomycota | ||||||||||||||||||
Agaricomycetes | ||||||||||||||||||
Marasmius | 3.2 | 1.5 | ||||||||||||||||
Ceratobasidium | 10.4 | 3.0 | 15.3 | 1.8 | 4.6 | 6.7 | 1.7 | 3.5 | 4.6 | |||||||||
Microbotryomycetes | ||||||||||||||||||
Rhodotorula | 4.9 | 1.7 | 1.1 | 1.9 | 2.5 | 3.6 | ||||||||||||
Sporobolomyces | 1.1 | |||||||||||||||||
Tremellomycetes | ||||||||||||||||||
Cryptococcus | 8.7 | 8.8 | 4.3 | 3.5 | 9.9 | 20.1 | 6.0 | 21.3 | 17.0 | 5.9 | 11.0 | 18.0 * | 20.0 * | 12.9 | 11.9 * | 0.4 | 21.2 * | |
Zygomycota | ||||||||||||||||||
Incertae_sedis | ||||||||||||||||||
Mortierella | 2.9 | |||||||||||||||||
Actinomucor | 8.4 | |||||||||||||||||
Mucor | 16.3 * | 30.0 * | 7.8 | 2.0 | 4.6 | 5.1 | 33.7 * | 10.3 | 12.0 | 7.2 | 13.5 | 8.9 | 13.3 | 18.0 | 3.5 | 2.3 | 8.7 | |
Rhizopus | 1.2 | |||||||||||||||||
Unidentified | ||||||||||||||||||
Unidentified | 1.9 | 2.0 | 5.1 | 7.4 | 5.0 | 10.1 | 1.2 | 2.1 | 3.5 | 5.9 | 6.1 | 3.0 | 3.4 | 4.9 | 6.0 | 9.2 | 8.1 |
Molecular Operational | Above Ground | Below Ground | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Taxonomic Units | Seeds | Leaves | Stems | Roots | Rhizosphere Soils | Bulk Soils | ||||||||||||
PAN8097W | PAN8816 | NS5511 | PAN8097W | PAN8816 | NS5511 | PAN8097W | PAN8816 | NS5511 | PAN8097W | PAN8816 | NS5511 | PAN8097W | PAN8816 | NS5511 | PAN8097W | PAN8816 | NS5511 | |
Ascomycota | ||||||||||||||||||
Dothideomycetes | ||||||||||||||||||
Neofusicoccum | 0.1 | |||||||||||||||||
Mycosphaerellaceae sp. | 0.2 | 0.5 | 0.1 | 0.1 | 0.2 | 0.1 | 0.2 | 0.1 | 0.1 | 0.1 | 0.1 | 0.3 | 0.1 | |||||
Cladosporium sp. 2 | 0.1 | |||||||||||||||||
Aureobasidium sp. 2 | 0.1 | 0.4 | 0.3 | 0.8 | 0.2 | 0.9 | 0.3 | 1 | ||||||||||
Rhizopycnis | 0.1 | |||||||||||||||||
Incertae sedis sp. | 0.1 | 0.1 | 0.2 | 0.1 | 0.1 | |||||||||||||
Stagonospora | 0.1 | |||||||||||||||||
Pleosporaceae sp. | 0.1 | 0.3 | ||||||||||||||||
Alternaria | 0.1 | 0.1 | 0.2 | 0.1 | 0.3 | 0.2 | 0.2 | 0.1 | 0.1 | 0.2 | 0.2 | 0.1 | 0.1 | |||||
Bipolaris | 0.5 | 0.1 | 0.1 | 0.1 | 0.1 | 0.1 | 0.1 | 0.3 | ||||||||||
Cochliobolus | 0.9 | 0.5 | 0.6 | 0.1 | 0.3 | 0.1 | 0.1 | 0.8 | 0.2 | |||||||||
Curvularia | 0.1 | 0.1 | ||||||||||||||||
Didymellaceae sp. 2 (Epicoccum) | 0.1 | 0.1 | 0.4 | 0.1 | 0.1 | 0.1 | 0.2 | 0.1 | 0.1 | 0.2 | 0.2 | 0.2 | 0.2 | 0.1 | 0.1 | |||
Unidentified | 0.1 | |||||||||||||||||
Eurotiomycetes | ||||||||||||||||||
Exophiala | 0.2 | 0.2 | 0.2 | 0.1 | 0.2 | 0.1 | 0.4 | 0.4 | ||||||||||
Rhinocladiella | 0.4 | |||||||||||||||||
Orbiliomycetes | ||||||||||||||||||
Arthrobotrys | 0.2 | 0.2 | ||||||||||||||||
Dactylella | 0.1 | |||||||||||||||||
Pezizomycetes | ||||||||||||||||||
Peziza | 0.1 | 1 | 0.3 | |||||||||||||||
Unidentified sp. | 0.1 | |||||||||||||||||
Saccharomycetes | ||||||||||||||||||
Meyerozyma sp. 2 | 0.1 | 0.1 | 0.1 | 0.1 | 0.1 | 0.3 | 0.3 | 0.1 | 0.2 | 0.3 | 0.6 | |||||||
Candida sp. 2 | 0.4 | 0.1 | 1 | 1 | 0.4 | 0.8 | ||||||||||||
Cyberlindnera | 0.1 | 0.1 | 0.1 | 0.2 | 0.3 | |||||||||||||
Wickerhamomyces sp. 2 | 0.9 | 0.2 | 0.7 | 0.2 | 0.3 | 0.3 | 0.2 | 0.1 | 0.2 | |||||||||
Clavispora | 0.1 | 0.2 | ||||||||||||||||
Pichia sp. 2 | 0.1 | 0.1 | 1 | 0.1 | 0.8 | 0.1 | 0.2 | 0.7 | 0.1 | |||||||||
Hanseniaspora sp. 2 | 0.3 | 0.1 | 0.1 | 5 | 0.7 | |||||||||||||
Zygoascus sp. 2 | 0.1 | 0.1 | ||||||||||||||||
Sordariomycetes | ||||||||||||||||||
Diaporthales sp. | 0.2 | 0.1 | 0.1 | 0.1 | ||||||||||||||
Bionectria | 0.6 | 0.1 | 0.1 | |||||||||||||||
Fusarium sp. 3 | 0.9 | 0.8 | ||||||||||||||||
Fusarium sp. 4 (assigned as Gibberella) | 0.1 | 0.2 | 0.5 | 0.3 | 0.1 | 0.2 | 0.2 | 0.4 | 0.2 | 0.1 | 0.1 | 0.3 | 0.1 | |||||
Myrmecridium | 0.1 | 0.1 | 0.1 | 0.5 | 0.1 | |||||||||||||
Sphaeronaemella | 0.1 | 0.1 | 0.1 | |||||||||||||||
Microascaceae sp. | 0.1 | |||||||||||||||||
Colletotrichum | 0.2 | |||||||||||||||||
Sordariales sp. | 0.8 | 0.6 | ||||||||||||||||
Lasiosphaeriaceae sp. | 0.1 | 0.4 | ||||||||||||||||
Unidentified | 0.1 | 0.1 | 0.3 | 0.9 | ||||||||||||||
Nigrospora | 0.1 | 0.2 | 0.2 | 0.6 | 0.2 | 1 | 0.2 | 0.1 | ||||||||||
Microdochium | 0.1 | 0.1 | 0.3 | 0.1 | ||||||||||||||
Daldinia | 0.1 | 0.1 | 0.1 | 0.2 | 0.1 | |||||||||||||
Basidiomycota | ||||||||||||||||||
Agaricomycetes | ||||||||||||||||||
Agaricus | 0.7 | 0.1 | ||||||||||||||||
Agrocybe | 0.1 | |||||||||||||||||
Conocybe | 0.1 | |||||||||||||||||
Panaeolus | 0.1 | |||||||||||||||||
Marasmius | 0.1 | 0.6 | 0.3 | 0.2 | 0.2 | 1 | 0.1 | |||||||||||
Coprinellus | 0.1 | 0.1 | ||||||||||||||||
Coprinopsis | 0.1 | |||||||||||||||||
Athelia | 0.1 | 0.1 | 0.1 | |||||||||||||||
Ceratobasidium | 0.2 | 0.5 | 0.9 | 0.5 | 0.2 | 0.7 | 0.8 | 0.1 | 0.6 | |||||||||
Thanatephorus | 0.2 | 0.2 | ||||||||||||||||
Corticiaceae sp. | 0.1 | 0.1 | ||||||||||||||||
Waitea | 0.1 | |||||||||||||||||
Gloeophyllum | 0.1 | 0.1 | 0.1 | |||||||||||||||
Sebacinaceae sp. | 0.1 | 0.1 | 0.1 | 0.1 | ||||||||||||||
Cystobasidiomycetes | ||||||||||||||||||
Occultifur | 0.1 | 0,1 | ||||||||||||||||
Exobasidiomycetes | ||||||||||||||||||
Unidentified sp. | ||||||||||||||||||
Microbotryomycetes | ||||||||||||||||||
Sporidiobolales sp. | 0.1 | 0.3 | 0.1 | 0.1 | 0.2 | 0.3 | 0.1 | 0.1 | 0.3 | 0.3 | 0.9 | |||||||
Rhodotorula | 0.1 | 0.1 | 0.1 | 0.3 | 0.7 | 0.1 | 0.2 | 0.9 | 0.3 | 0.3 | 0.1 | |||||||
Sporobolomyces | 0.4 | 0.2 | 0.3 | 0.1 | 0.1 | 0.1 | 0.2 | 0.6 | 0.1 | 0.2 | 0.2 | |||||||
Unidentified sp. | 0.1 | 0.1 | 0.2 | 0.1 | 0.1 | |||||||||||||
Tremellomycetes | ||||||||||||||||||
Cystofilobasidium | 0.3 | 0.6 | ||||||||||||||||
Tremellaceae | 0.1 | |||||||||||||||||
Dioszegia | 0.1 | 0.2 | ||||||||||||||||
Tremella | 0.1 | |||||||||||||||||
Ustilaginomycetes | ||||||||||||||||||
Thecaphora | 0.1 | |||||||||||||||||
Ustilaginaceae | 0.3 | |||||||||||||||||
Pseudozyma | 0.2 | 0.2 | ||||||||||||||||
Sporisorium | 0.1 | 0.1 | 0.2 | 0.1 | ||||||||||||||
Ustilago | 0.2 | 0.3 | 0.2 | 0.1 | ||||||||||||||
Unidentified | 0.9 | 0.3 | 0.6 | 0.1 | 0.7 | 0.1 | 0.1 | |||||||||||
Chytridiomycota | ||||||||||||||||||
Rhizophydiaceae sp. | 0.5 | |||||||||||||||||
Spizellomyces | 0.1 | 0.1 | ||||||||||||||||
Glomeromycota | ||||||||||||||||||
Glomus | 0.1 | |||||||||||||||||
Glomeraceae sp. | 0.1 | |||||||||||||||||
Unidentified sp. | 0.1 | 0.1 | 0.1 | 0.1 | ||||||||||||||
Zygomycota | ||||||||||||||||||
Mortierella | 0.1 | 0.2 | 0.2 | 0.3 | ||||||||||||||
Choanephoraceae sp. | 0.2 | 0.2 | ||||||||||||||||
Mucoraceae sp. | 0.2 | 0.1 | 0.1 | 0.3 | 0.1 | 0.2 | 0.6 | 0.2 | 0.1 | 0.6 | 0.7 | |||||||
Actinomucor | 0.2 | 0.4 | ||||||||||||||||
Rhizomucor | 0.1 | |||||||||||||||||
Rhizopus | 0.3 | 0.3 | 0.1 | 0.2 | 0.6 | 0.2 | 0.8 | 0.8 | 0.1 | 0.1 | 0.2 | 0.1 | 0.1 |
Compared Categories | D.F | Sum of Sqs | R2 | p-Value |
---|---|---|---|---|
Cultivar | 2 | 0.38101 | 0.13015 | 0.321 |
Plant niche | 5 | 1.7338 | 0.59222 | 0.001 |
Above-ground vs. below-ground niches | 1 | 0.56049 | 0.19145 | 0.001 |
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Pambuka, G.T.; Kinge, T.R.; Ghosh, S.; Cason, E.D.; Nyaga, M.M.; Gryzenhout, M. Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing. J. Fungi 2021, 7, 978. https://doi.org/10.3390/jof7110978
Pambuka GT, Kinge TR, Ghosh S, Cason ED, Nyaga MM, Gryzenhout M. Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing. Journal of Fungi. 2021; 7(11):978. https://doi.org/10.3390/jof7110978
Chicago/Turabian StylePambuka, Gilmore T., Tonjock Rosemary Kinge, Soumya Ghosh, Errol D. Cason, Martin M. Nyaga, and Marieka Gryzenhout. 2021. "Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa using Targeted Environmental Sequencing" Journal of Fungi 7, no. 11: 978. https://doi.org/10.3390/jof7110978