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10.3390/genes15070824
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Article

Soil Microbial Communities in Lemon Orchards Affected by Citrus Mal Secco Disease

by
Alexandros Mosca
1,†,
Giulio Dimaria
1,†,
Daniele Nicotra
1,
Francesco Modica
1,‡,
Maria Elena Massimino
1,
Antonino F. Catara
2,
Giuseppe Scuderi
2,
Marcella Russo
2 and
Vittoria Catara
1,*
1
Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
2
Agrobiotech Soc. Coop., 95121 Catania, Italy
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
‡
Present address: Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy.
Genes 2024, 15(7), 824; https://doi.org/10.3390/genes15070824
Submission received: 25 April 2024 / Revised: 17 June 2024 / Accepted: 18 June 2024 / Published: 21 June 2024
(This article belongs to the Special Issue Microbiome Analysis Techniques and Discovery)
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Highlights

What are the main findings?
  • In the soil of lemon orchards in which symptoms of the citrus mal secco disease had been observed, Plenodomus tracheiphilus (Pt) was detected using qPCR and a metagenomic approach.
  • The lemon orchards location and the presence of Pt affected the composition and β-diversity of the microbial communities.
  • In samples in which Pt was more abundant, microbial taxa that might play a putative role of biocontrol agents resulted significantly enriched. Some of these taxa were also core members of the microbial communities and showed a negative correlation with the pathogen.
What is the implication of the main finding?
  • Soil could represent a reservoir for Pt inoculum for root infections, whereas infected plant materials in the canopy may serve as a source.
  • This study identifies a promising sustainable approach for managing citrus mal secco disease through the use of microorganisms capable of effectively reducing pathogen inoculum levels.

Abstract

Mal secco is a vascular disease of citrus caused by the mitosporic fungus Plenodomus tracheiphilus. Soil containing infected plant material constitutes an inoculum source for root infections. In this study, the soil bacterial and fungal communities of five lemon orchards located in Syracuse Province (Sicily, Italy) affected by mal secco were analyzed. Soil samples were collected under lemon tree canopies and subjected to total genomic DNA extraction. The fungal DNA was detected through qPCR in all orchards, with variable concentrations. Bacterial and fungal communities were profiled using 16S and ITS amplicon-based high-throughput sequencing, respectively. According to our results, the relative abundances of the most represented bacterial phyla (e.g., Proteobacteria, Actinobacteriota, Acidobacteriota) changed across the orchards, while in the fungal community, the phylum Ascomycota was dominant, with Basidiomycota and Mortierellomycota abundances fluctuating. On the whole, β diversity analysis showed significant variation in the composition of the soil microbial communities across the orchards. This result was confirmed by the analysis of the core community (taxa present at ≥ 75% of total samples), where putative beneficial bacteria resulted in significantly enriched fungus-infected soil samples, suggesting complex microbial interactions. Our findings shed light on the composition and diversity of the soil microbiome in lemon orchards with the occurrence of mal secco infections.
Keywords: Citrus limon; Plenodomus tracheiphilus; soil microbiome; qPCR; bacterial and fungal communities; amplicon-based metagenomics Citrus limon; Plenodomus tracheiphilus; soil microbiome; qPCR; bacterial and fungal communities; amplicon-based metagenomics

Share and Cite

MDPI and ACS Style

Mosca, A.; Dimaria, G.; Nicotra, D.; Modica, F.; Massimino, M.E.; Catara, A.F.; Scuderi, G.; Russo, M.; Catara, V. Soil Microbial Communities in Lemon Orchards Affected by Citrus Mal Secco Disease. Genes 2024, 15, 824. https://doi.org/10.3390/genes15070824

AMA Style

Mosca A, Dimaria G, Nicotra D, Modica F, Massimino ME, Catara AF, Scuderi G, Russo M, Catara V. Soil Microbial Communities in Lemon Orchards Affected by Citrus Mal Secco Disease. Genes. 2024; 15(7):824. https://doi.org/10.3390/genes15070824

Chicago/Turabian Style

Mosca, Alexandros, Giulio Dimaria, Daniele Nicotra, Francesco Modica, Maria Elena Massimino, Antonino F. Catara, Giuseppe Scuderi, Marcella Russo, and Vittoria Catara. 2024. "Soil Microbial Communities in Lemon Orchards Affected by Citrus Mal Secco Disease" Genes 15, no. 7: 824. https://doi.org/10.3390/genes15070824

APA Style

Mosca, A., Dimaria, G., Nicotra, D., Modica, F., Massimino, M. E., Catara, A. F., Scuderi, G., Russo, M., & Catara, V. (2024). Soil Microbial Communities in Lemon Orchards Affected by Citrus Mal Secco Disease. Genes, 15(7), 824. https://doi.org/10.3390/genes15070824

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