Bacterial Microbiota and Soil Fertility of Crocus sativus L. Rhizosphere in the Presence and Absence of Fusarium spp.
Abstract
:1. Introduction
2. Materials and Methods
2.1. Soil Sampling
2.2. Fusariosis Pathogenesis Confirmation
2.3. DNA Extraction and 16S rRNA Metabarcoding
2.4. Prediction of Metagenomic Functions
2.5. Network Analysis
2.6. Dehydrogenase Activity of Soil Samples
2.7. Statistical Analysis
3. Results
3.1. Fusariosis Pathogenesis Confirmation
3.2. DNA Extraction and 16S rRNA Metabarcoding
3.3. Prediction of Metagenomic Functions
3.4. Network Analysis
3.5. Dehydrogenase (DHA) Activity
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Hemathilake, D.M.K.S.; Gunathilake, D.M.C.C. Agricultural Productivity and Food Supply to Meet Increased Demands. In Future Foods; Elsevier: Amsterdam, The Netherlands, 2022; pp. 539–553. [Google Scholar]
- Ambrosini, A.; de Souza, R.; Passaglia, L.M.P. Ecological Role of Bacterial Inoculants and Their Potential Impact on Soil Microbial Diversity. Plant Soil 2016, 400, 193–207. [Google Scholar] [CrossRef]
- Aktar, W.; Sengupta, D.; Chowdhury, A. Impact of Pesticides Use in Agriculture: Their Benefits and Hazards. Interdiscip. Toxicol. 2009, 2, 1–12. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Saleem, M.; Hu, J.; Jousset, A. More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health. Annu. Rev. Ecol. Evol. Syst. 2019, 50, 145–168. [Google Scholar] [CrossRef]
- Dubey, A.; Malla, M.A.; Khan, F.; Chowdhary, K.; Yadav, S.; Kumar, A.; Sharma, S.; Khare, P.K.; Khan, M.L. Soil Microbiome: A Key Player for Conservation of Soil Health under Changing Climate. Biodivers. Conserv. 2019, 28, 2405–2429. [Google Scholar] [CrossRef]
- Kennedy, A.C.; Smith, K.L. Soil Microbial Diversity and the Sustainability of Agricultural Soils. Plant Soil 1995, 170, 75–86. [Google Scholar] [CrossRef]
- Rahobisoa, J.J.; Ratrimo, V.R.; Ranaivoarisoa, A. Mitigating Coastal Erosion in Fort Dauphin, Madagascar. In Sustainable Living with Environmental Risks; Springer Nature: Cham, Switzerland, 2014; Volume 9784431548, ISBN 9784431548041. [Google Scholar]
- McDaniel, M.D.; Tiemann, L.K.; Grandy, A.S. Does Agricultural Crop Diversity Enhance Soil Microbial Biomass and Organic Matter Dynamics? A Meta-Analysis. Ecol. Appl. 2014, 24, 560–570. [Google Scholar] [CrossRef] [Green Version]
- de Deyn, G.; Gattinger, A.; Lori, M.; Symnaczik, S.; Ma, P. Organic Farming Enhances Soil Microbial Abundance and Activity—A Meta-Analysis and Meta-Regression. PLoS ONE 2017, 12, e0180442. [Google Scholar]
- Gwinn, K.D.; Hansen, Z.; Kelly, H.; Ownley, B.H. Diseases of Cannabis Sativa Caused by Diverse Fusarium Species. Front. Agron. 2022, 3, 796062. [Google Scholar] [CrossRef]
- Summerell, B.A.; Botanic, R.; Sydney, G.; Wales, N.S.; Leslie, J.F. To Fusarium Identification. Plant Dis. 2003, 117–128. [Google Scholar] [CrossRef] [Green Version]
- Lei, S.; Wang, L.; Liu, L.; Hou, Y.; Xu, Y.; Liang, M.; Gao, J.; Li, Q.; Huang, S. Infection and Colonization of Pathogenic Fungus Fusarium Proliferatum in Rice Spikelet Rot Disease. Rice Sci. 2019, 26, 60–68. [Google Scholar] [CrossRef]
- Sharma, K.D. Abel Piqueras Saffron (Crocus sativus L.) Tissue Culture: Micropropagation and Secondary Metabolite Production. Funct. Plant Sci. Biotechnol. Saffron 2010, 4, 64–73. [Google Scholar]
- Mirghasempour, S.A.; Studholme, D.J.; Chen, W.; Zhu, W.; Mao, B. Molecular and Pathogenic Characterization of Fusarium Species Associated with Corm Rot Disease in Saffron from China. J. Fungi 2022, 8, 515. [Google Scholar] [CrossRef] [PubMed]
- Palmero, D.; Rubio-Moraga, A.; Galvez-Patón, L.; Nogueras, J.; Abato, C.; Gómez-Gómez, L.; Ahrazem, O. Pathogenicity and Genetic Diversity of Fusarium Oxysporum Isolates from Corms of Crocus sativus. Ind. Crops Prod. 2014, 61, 186–192. [Google Scholar] [CrossRef]
- Register, L.; Help, C. Feasibility of Using Mycoherbicides for Controlling Illicit Drug Crops; National Academies Press: Cambridge, MA, USA, 2011. [Google Scholar] [CrossRef]
- Wang, T.; Hao, Y.; Zhu, M.; Yu, S.; Ran, W.; Xue, C.; Ling, N.; Shen, Q. Characterizing Differences in Microbial Community Composition and Function between Fusarium Wilt Diseased and Healthy Soils under Watermelon Cultivation. Plant Soil 2019, 438, 421–433. [Google Scholar] [CrossRef]
- Leslie, J.F.; Summerell, B.A. The Fusarium Laboratory Manual, 1st ed.; Leslie, J.F., Summerell, B.A., Eds.; Blackwell Publishing Ltd.: Oxford, London, 2006; ISBN 9780813819198. [Google Scholar]
- Mizrahi-Man, O.; Davenport, E.R.; Gilad, Y. Taxonomic Classification of Bacterial 16S RRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs. PLoS ONE 2013, 8, e53608. [Google Scholar] [CrossRef] [Green Version]
- Bolyen, E.; Rideout, J.R.; Dillon, M.R.; Bokulich, N.A.; Abnet, C.C.; Al-Ghalith, G.A.; Alexander, H.; Alm, E.J.; Arumugam, M.; Asnicar, F.; et al. Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2. Nat. Biotechnol. 2019, 37, 852–857. [Google Scholar] [CrossRef]
- Douglas, G.M.; Maffei, V.J.; Zaneveld, J.R.; Yurgel, S.N.; Brown, J.R.; Taylor, C.M.; Huttenhower, C.; Langille, M.G.I. PICRUSt2 for Prediction of Metagenome Functions. Nat. Biotechnol. 2020, 38, 685–688. [Google Scholar] [CrossRef]
- Barberán, A.; Bates, S.T.; Casamayor, E.O.; Fierer, N. Using Network Analysis to Explore Co-Occurrence Patterns in Soil Microbial Communities. ISME J. 2012, 6, 343–351. [Google Scholar] [CrossRef] [Green Version]
- Newman, M.E.J. The Structure and Function of Complex Networks. SIAM Rev. 2003, 45, 167–256. [Google Scholar] [CrossRef] [Green Version]
- Csardi, G.; Nepusz, T. The Igraph Software Package for Complex Network Research. InterJournal Complex Syst. 2006, 1695, 1–9. [Google Scholar]
- Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N.S.; Wang, J.T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Res. 2003, 13, 2498–2504. [Google Scholar] [CrossRef]
- Assenov, Y.; Ramírez, F.; Schelhorn, S.-E.; Lengauer, T.; Albrecht, M. Computing Topological Parameters of Biological Networks. Bioinformatics 2008, 24, 282–284. [Google Scholar] [CrossRef] [PubMed]
- Casida, L.E.J.R.; Klein, D.A.; Santoro, T. Soil Enzymology, Soil Biology 22; Springer: Berlin/Heidelberg, Germany, 1964; Volume 98. [Google Scholar]
- Xie, J.; Hu, W.; Pei, H.; Dun, M.; Qi, F. Detection of Amount and Activity of Living Algae in Fresh Water by Dehydrogenase Activity (DHA). Environ. Monit. Assess. 2008, 146, 473–478. [Google Scholar] [CrossRef] [PubMed]
- Ambardar, S.; Singh, H.R.; Gowda, M.; Vakhlu, J. Comparative Metagenomics Reveal Phylum Level Temporal and Spatial Changes in Mycobiome of Belowground Parts of Crocus sativus. PLoS ONE 2016, 11, e0163300. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ambardar, S.; Sangwan, N.; Manjula, A.; Rajendhran, J.; Gunasekaran, P.; Lal, R.; Vakhlu, J. Identification of Bacteria Associated with Underground Parts of Crocus sativus by 16S RRNA Gene Targeted Metagenomic Approach. World J. Microbiol. Biotechnol. 2014, 30, 2701–2709. [Google Scholar] [CrossRef] [PubMed]
- Mahaffee, W.F.; Kloepper, J.W. Temporal Changes in the Bacterial Communities of Soil, Rhizosphere, and Endorhiza Associated with Field-Grown Cucumber (Cucumis sativus L.). Microb Ecol 1997, 34, 210–223. [Google Scholar] [CrossRef]
- İnceoğlu, Ö.; Al-Soud, W.A.; Salles, J.F.; Semenov, A.V.; van Elsas, J.D. Comparative Analysis of Bacterial Communities in a Potato Field as Determined by Pyrosequencing. PLoS ONE 2011, 6, e23321. [Google Scholar] [CrossRef] [Green Version]
- Rani, A.; Porwal, S.; Sharma, R.; Kapley, A.; Purohit, H.J.; Kalia, V.C. Assessment of Microbial Diversity in Effluent Treatment Plants by Culture Dependent and Culture Independent Approaches. Bioresour. Technol. 2008, 99, 7098–7107. [Google Scholar] [CrossRef]
- Wang, Y.; Chen, Y.; Zhou, Q.; Huang, S.; Ning, K.; Xu, J.; Kalin, R.M.; Rolfe, S.; Huang, W.E. A Culture-Independent Approach to Unravel Uncultured Bacteria and Functional Genes in a Complex Microbial Community. PLoS ONE 2012, 7, e47530. [Google Scholar] [CrossRef]
- Loviso, C.L.; Lozada, M.; Guibert, L.M.; Musumeci, M.A.; Sarango Cardenas, S.; Kuin, R.V.; Marcos, M.S.; Dionisi, H.M. Metagenomics Reveals the High Polycyclic Aromatic Hydrocarbon-Degradation Potential of Abundant Uncultured Bacteria from Chronically Polluted Subantarctic and Temperate Coastal Marine Environments. J. Appl. Microbiol. 2015, 119, 411–424. [Google Scholar] [CrossRef] [Green Version]
- Agri, U.; Chaudhary, P.; Sharma, A.; Kukreti, B. Physiological Response of Maize Plants and Its Rhizospheric Microbiome under the Influence of Potential Bioinoculants and Nanochitosan. Plant Soil 2022, 474, 451–468. [Google Scholar] [CrossRef]
- Deng, J.; Yin, Y.; Zhu, W.; Zhou, Y. Variations in Soil Bacterial Community Diversity and Structures Among Different Revegetation Types in the Baishilazi Nature Reserve. Front. Microbiol. 2018, 9, 2874. [Google Scholar] [CrossRef] [PubMed]
- Yang, Y.; Viscarra Rossel, R.A.; Li, S.; Bissett, A.; Lee, J.; Shi, Z.; Behrens, T.; Court, L. Soil Bacterial Abundance and Diversity Better Explained and Predicted with Spectro-Transfer Functions. Soil Biol. Biochem. 2019, 129, 29–38. [Google Scholar] [CrossRef]
- Zou, Z.; Yuan, K.; Ming, L.; Li, Z.; Yang, Y.; Yang, R.; Cheng, W.; Liu, H.; Jiang, J.; Luan, T.; et al. Changes in Alpine Soil Bacterial Communities With Altitude and Slopes at Mount Shergyla, Tibetan Plateau: Diversity, Structure, and Influencing Factors. Front. Microbiol. 2022, 13, 839499. [Google Scholar] [CrossRef] [PubMed]
- Kim, H.-S.; Lee, S.-H.; Jo, H.Y.; Finneran, K.T.; Kwon, M.J. Diversity and Composition of Soil Acidobacteria and Proteobacteria Communities as a Bacterial Indicator of Past Land-Use Change from Forest to Farmland. Sci. Total Environ. 2021, 797, 148944. [Google Scholar] [CrossRef]
- Zhou, D.; Jing, T.; Chen, Y.; Wang, F.; Qi, D.; Feng, R.; Xie, J.; Li, H. Deciphering Microbial Diversity Associated with Fusarium Wilt-Diseased and Disease-Free Banana Rhizosphere Soil. BMC Microbiol. 2019, 19, 161. [Google Scholar] [CrossRef] [Green Version]
- Shen, Z.; Ruan, Y.; Chao, X.; Zhang, J.; Li, R.; Shen, Q. Rhizosphere Microbial Community Manipulated by 2 Years of Consecutive Biofertilizer Application Associated with Banana Fusarium Wilt Disease Suppression. Biol. Fertil. Soils 2015, 51, 553–562. [Google Scholar] [CrossRef]
- Bhagat, N.; Sharma, S.; Ambardar, S.; Raj, S.; Trakroo, D.; Horacek, M.; Zouagui, R.; Sbabou, L.; Vakhlu, J. Microbiome Fingerprint as Biomarker for Geographical Origin and Heredity in Crocus sativus: A Feasibility Study. Front. Sustain. Food Syst. 2021, 5, 688393. [Google Scholar] [CrossRef]
- Djebaili, R.; Pellegrini, M.; Bernardi, M.; Smati, M.; Kitouni, M.; del Gallo, M. Biocontrol Activity of Actinomycetes Strains against Fungal and Bacterial Pathogens of Solanum lycopersicum L. and Daucus carota L.: In Vitro and In Planta Antagonistic Activity. In Proceedings of the 1st International Electronic Conference on Plant Science, Online, 1–15 December 2020; MDPI: Basel, Switzerland, 2020; p. 27. [Google Scholar]
- Wang, S.; Wang, J.; Zhou, Y.; Huang, Y.; Tang, X. Prospecting the Plant Growth–Promoting Activities of Endophytic Bacteria Franconibacter Sp. YSD YN2 Isolated from Cyperus esculentus L. Var. Sativus Leaves. Ann. Microbiol. 2022, 72, 1. [Google Scholar] [CrossRef]
- Santoyo, G.; Orozco-Mosqueda, M.D.C.; Govindappa, M. Mechanisms of Biocontrol and Plant Growth-Promoting Activity in Soil Bacterial Species of Bacillus and Pseudomonas: A Review. Biocontrol. Sci. Technol. 2012, 22, 855–872. [Google Scholar] [CrossRef]
- Donn, S.; Kirkegaard, J.A.; Perera, G.; Richardson, A.E.; Watt, M. Evolution of Bacterial Communities in the Wheat Crop Rhizosphere. Environ. Microbiol. 2015, 17, 610–621. [Google Scholar] [CrossRef] [PubMed]
- Ofek, M.; Hadar, Y.; Minz, D. Ecology of Root Colonizing Massilia (Oxalobacteraceae). PLoS ONE 2012, 7, e40117. [Google Scholar] [CrossRef] [PubMed]
- Raaijmakers, J.M.; Paulitz, T.C.; Steinberg, C.; Alabouvette, C.; Moënne-Loccoz, Y. The Rhizosphere: A Playground and Battlefield for Soilborne Pathogens and Beneficial Microorganisms. Plant Soil 2009, 321, 341–361. [Google Scholar] [CrossRef] [Green Version]
- Bejarano-Bolívar, A.A.; Lamelas, A.; Aguirre von Wobeser, E.; Sánchez-Rangel, D.; Méndez-Bravo, A.; Eskalen, A.; Reverchon, F. Shifts in the Structure of Rhizosphere Bacterial Communities of Avocado after Fusarium Dieback. Rhizosphere 2021, 18, 100333. [Google Scholar] [CrossRef]
- Venkateshwaran, M.; Jayaraman, D.; Chabaud, M.; Genre, A.; Balloon, A.J.; Maeda, J.; Forshey, K.; den Os, D.; Kwiecien, N.W.; Coon, J.J.; et al. A Role for the Mevalonate Pathway in Early Plant Symbiotic Signaling. Proc. Natl. Acad. Sci. USA 2015, 112, 9781–9786. [Google Scholar] [CrossRef] [Green Version]
- Harris, J.A. Measurements of the Soil Microbial Community for Estimating the Success of Restoration. Eur. J. Soil Sci. 2003, 54, 801–808. [Google Scholar] [CrossRef]
- Wu, Z.; Hao, Z.; Sun, Y.; Guo, L.; Huang, L.; Zeng, Y.; Wang, Y.; Yang, L.; Chen, B. Comparison on the Structure and Function of the Rhizosphere Microbial Community between Healthy and Root-Rot Panax Notoginseng. Appl. Soil Ecol. 2016, 107, 99–107. [Google Scholar] [CrossRef]
- Siles, J.A.; García-Sánchez, M.; Gómez-Brandón, M. Studying Microbial Communities through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review. Microorganisms 2021, 9, 1165. [Google Scholar] [CrossRef]
- Campos, J.A.; Peco, J.D.; García-Noguero, E. Antigerminative Comparison between Naturally Occurring Naphthoquinones and Commercial Pesticides. Soil Dehydrogenase Activity Used as Bioindicator to Test Soil Toxicity. Sci. Total Environ. 2019, 694, 133672. [Google Scholar] [CrossRef]
- Paz-Ferreiro, J.; Fu, S. Biological Indices for Soil Quality Evaluation: Perspectives and Limitations. Land Degrad. Dev. 2016, 27, 14–25. [Google Scholar] [CrossRef]
- Aspray, T.; Gluszek, A.; Carvalho, D. Effect of Nitrogen Amendment on Respiration and Respiratory Quotient (RQ) in Three Hydrocarbon Contaminated Soils of Different Type. Chemosphere 2008, 72, 947–951. [Google Scholar] [CrossRef] [PubMed]
- Dotaniya, M.L.; Aparna, K.; Dotaniya, C.K.; Singh, M.; Regar, K.L. Role of Soil Enzymes in Sustainable Crop Production. In Enzymes in Food Biotechnology; Elsevier: Amsterdam, The Netherlands, 2019; pp. 569–589. [Google Scholar]
- Wolinska, A.; Stepniewsk, Z. Dehydrogenase Activity in the Soil Environment. In Dehydrogenases; InTech: London, UK, 2012. [Google Scholar]
- Wiatrowska, K.; Komisarek, J.; Olejnik, J. Variations in Organic Carbon Content and Dehydrogenases Activity in Post-Agriculture Forest Soils: A Case Study in South-Western Pomerania. Forests 2021, 12, 459. [Google Scholar] [CrossRef]
- Dukare, A.; Paul, S. Effect of Chitinolytic Biocontrol Bacterial Inoculation on Soil Microbiological Activities and Fusarium Population in Rhizophere of Pigeon Pea (Cajanus cajan). Ann. Plant Prot. Sci. 2018, 26, 98. [Google Scholar] [CrossRef]
- Posas, M.B.; Toyota, K.; Islam, T.M. Inhibition of Bacterial Wilt of Tomato Caused by Ralstonia Solanacearum by Sugars and Amino Acids. Microbes Environ. 2007, 22, 290–296. [Google Scholar] [CrossRef]
ZB1 | ZB2 | ZB3 | ZB5 | ZB6 | ZB7 | ZF1 | ZF2 | ZF3 | ZF4 | |
---|---|---|---|---|---|---|---|---|---|---|
Taxa_S | 1454 | 1283 | 1141 | 1309 | 958 | 1345 | 1155 | 1270 | 2078 | 1440 |
Individuals (Richness ASVs level) | 36,299 | 32,009 | 27,465 | 28,502 | 19,823 | 27,429 | 25,296 | 25,719 | 54,646 | 33,625 |
Shannon_H | 6.657 | 6.538 | 6.41 | 6.594 | 6.281 | 6.657 | 6.501 | 6.587 | 6.994 | 6.761 |
Evenness_e^H/S | 0.5354 | 0.5385 | 0.5329 | 0.5583 | 0.5577 | 0.5788 | 0.5765 | 0.5711 | 0.5248 | 0.5996 |
Chao-1 | 1455 | 1285 | 1142 | 1310 | 958.7 | 1347 | 1156 | 1271 | 2080 | 1444 |
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Farda, B.; Djebaili, R.; Bernardi, M.; Pace, L.; Del Gallo, M.; Pellegrini, M. Bacterial Microbiota and Soil Fertility of Crocus sativus L. Rhizosphere in the Presence and Absence of Fusarium spp. Land 2022, 11, 2048. https://doi.org/10.3390/land11112048
Farda B, Djebaili R, Bernardi M, Pace L, Del Gallo M, Pellegrini M. Bacterial Microbiota and Soil Fertility of Crocus sativus L. Rhizosphere in the Presence and Absence of Fusarium spp. Land. 2022; 11(11):2048. https://doi.org/10.3390/land11112048
Chicago/Turabian StyleFarda, Beatrice, Rihab Djebaili, Matteo Bernardi, Loretta Pace, Maddalena Del Gallo, and Marika Pellegrini. 2022. "Bacterial Microbiota and Soil Fertility of Crocus sativus L. Rhizosphere in the Presence and Absence of Fusarium spp." Land 11, no. 11: 2048. https://doi.org/10.3390/land11112048