Seasonal Shifts in Soil Microbiome Structure Are Associated with the Cultivation of the Local Runner Bean Variety around the Lake Mikri Prespa
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Experimental Site and Soil Samples
2.2. DNA Isolation, Library Preparation and Sequencing
2.3. Bioinformatic Analysis
2.4. Phylogeny-Based Functional Annotation
3. Results
3.1. Seasonal Shifts in Microbial Communities’ Diversity
3.2. Effects of Cultivation Period on the Bacterial Community Structure
3.3. Effects of Cultivation Period on Different Taxonomical Levels
3.4. Predicted Functional Diversity of the Microbiome Present in the Different Field Sites
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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Phylum (%) | Season | ||
---|---|---|---|
Spring_BC | Summer_DC | Autumn_AC | |
Proteobacteria | 28.96 | 30.04 | 28.49 |
Acidobacteria | 16.91 | 12.41 | 15.29 |
Actinobacteria | 6.26 | 14.37 | 11.25 |
Planctomycetes | 9.50 | 10.76 | 10.71 |
Bacteroidetes | 8.68 | 7.67 | 7.95 |
Verrucomicrobia | 6.64 | 3.94 | 5.24 |
Bacteria_unclassified | 5.75 | 4.89 | 4.74 |
Firmicutes | 1.75 | 3.67 | 2.80 |
Gemmatimonadetes | 2.83 | 2.30 | 2.79 |
Chloroflexi | 1.21 | 1.68 | 1.21 |
Cyanobacteria | - | 1.22 | 0.85 |
Patescibacteria | 1.94 | - | 0.69 |
Nitrospirae | 1.35 | - | 0.54 |
Total % | 91.78 | 92.95 | 92.55 |
Phylum | Class (%) | Season | ||
---|---|---|---|---|
Spring_BC | Summer_DC | Autumn_AC | ||
Acidobacteria | Acidobacteriia | 2.27 | 1.77 | 2.13 |
Blastocatellia (Subgroup_4) | 4.95 | 4.49 | 5.21 | |
Holophagae | 1.20 | 0.37 | - | |
Subgroup_6 | 9.29 | 6.02 | 7.95 | |
Actinobacteria | Acidimicrobiia | 1.64 | 2.26 | 2.01 |
Actinobacteria | 3.09 | 9.35 | 6.99 | |
Rubrobacteria | - | - | 1.07 | |
Thermoleophilia | 1.52 | 2.75 | 2.14 | |
Bacteria_unclassified | Bacteria_unclassified | 5.75 | 4.89 | 4.74 |
Bacteroidetes | Bacteroidia | 8.68 | 7.66 | 7.95 |
Chloroflexi | Anaerolineae | 0.94 | 0.92 | 0.81 |
Chloroflexia | 0.41 | 1.60 | 1.34 | |
KD4-96 | 0.61 | 0.78 | 0.23 | |
Cyanobacteria | Oxyphotobacteria | - | 1.22 | 0.85 |
Firmicutes | Bacilli | 1.75 | 3.55 | 2.68 |
Clostridia | - | 1.05 | 1.08 | |
Gemmatimonadetes | Gemmatimonadetes | 2.83 | 2.30 | 2.79 |
Nitrospirae | Nitrospira | 1.35 | - | 0.54 |
Patescibacteria | Parcubacteria | 1.94 | - | 0.29 |
Saccharimonadia | - | - | 1.22 | |
Planctomycetes | Phycisphaerae | 5.03 | 7.00 | 6.71 |
Planctomycetacia | 4.47 | 3.75 | 4.00 | |
Proteobacteria | Alphaproteobacteria | 15.13 | 18.79 | 16.95 |
Deltaproteobacteria | 3.55 | 2.71 | 2.71 | |
Gammaproteobacteria | 10.28 | 8.54 | 8.83 | |
Verrucomicrobia | Verrucomicrobiae | 6.64 | 3.94 | 5.24 |
Total % | 93.32 | 95.71 | 96.46 |
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Stavridou, E.; Karamichali, I.; Lagiotis, G.; Patsea, E.; Osathanunkul, M.; Madesis, P. Seasonal Shifts in Soil Microbiome Structure Are Associated with the Cultivation of the Local Runner Bean Variety around the Lake Mikri Prespa. Biology 2022, 11, 1595. https://doi.org/10.3390/biology11111595
Stavridou E, Karamichali I, Lagiotis G, Patsea E, Osathanunkul M, Madesis P. Seasonal Shifts in Soil Microbiome Structure Are Associated with the Cultivation of the Local Runner Bean Variety around the Lake Mikri Prespa. Biology. 2022; 11(11):1595. https://doi.org/10.3390/biology11111595
Chicago/Turabian StyleStavridou, Evangelia, Ioanna Karamichali, Georgios Lagiotis, Elena Patsea, Maslin Osathanunkul, and Panagiotis Madesis. 2022. "Seasonal Shifts in Soil Microbiome Structure Are Associated with the Cultivation of the Local Runner Bean Variety around the Lake Mikri Prespa" Biology 11, no. 11: 1595. https://doi.org/10.3390/biology11111595