Soil Microbial Community Responses to Different Management Strategies in Almond Crop
A comparative study of organic and conventional farming systems was conducted in almond orchards to determine the effect of management practices on their fungal and bacterial communities. Soils from two orchards under organic (OM) and conventional (CM), and nearby nonmanaged (NM) soil were analyzed...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/9/1/95 |
| _version_ | 1797440194925821952 |
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| author | Miguel Camacho-Sanchez Juan F. Herencia Francisco T. Arroyo Nieves Capote |
| author_facet | Miguel Camacho-Sanchez Juan F. Herencia Francisco T. Arroyo Nieves Capote |
| author_sort | Miguel Camacho-Sanchez |
| collection | DOAJ |
| description | A comparative study of organic and conventional farming systems was conducted in almond orchards to determine the effect of management practices on their fungal and bacterial communities. Soils from two orchards under organic (OM) and conventional (CM), and nearby nonmanaged (NM) soil were analyzed and compared. Several biochemical and biological parameters were measured (soil pH, electrical conductivity, total nitrogen, organic material, total phosphorous, total DNA, and fungal and bacterial DNA copies). Massive parallel sequencing of regions from fungal ITS rRNA and bacterial 16 S genes was carried out to characterize their diversity in the soil. We report a larger abundance of bacteria and fungi in soils under OM, with a more balanced fungi:bacteria ratio, compared to bacteria-skewed proportions under CM and NM. The fungal phylum <i>Ascomycota</i> corresponded to around the 75% relative abundance in the soil, whereas for bacteria, the phyla <i>Proteobacteria</i>, <i>Acidobacteriota</i> and <i>Bacteroidota</i> integrated around 50% of their diversity. Alpha diversity was similar across practices, but beta diversity was highly clustered by soil management. Linear discriminant analysis effect size (LEfSE) identified bacterial and fungal taxa associated with each type of soil management. Analyses of fungal functional guilds revealed 3–4 times larger abundance of pathogenic fungi under CM compared to OM and NM treatments. Among them, the genus <i>Cylindrocarpon</i> was more abundant under CM, and <i>Fusarium</i> under OM. |
| first_indexed | 2024-03-09T12:03:36Z |
| format | Article |
| id | doaj.art-5103e5b2cba843a89aa74fb38f43703c |
| institution | Directory Open Access Journal |
| issn | 2309-608X |
| language | English |
| last_indexed | 2024-03-09T12:03:36Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj.art-5103e5b2cba843a89aa74fb38f43703c2023-11-30T23:00:15ZengMDPI AGJournal of Fungi2309-608X2023-01-01919510.3390/jof9010095Soil Microbial Community Responses to Different Management Strategies in Almond CropMiguel Camacho-Sanchez0Juan F. Herencia1Francisco T. Arroyo2Nieves Capote3Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Center Las Torres, Alcalá del Río, 41200 Seville, SpainAndalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Center Las Torres, Alcalá del Río, 41200 Seville, SpainAndalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Center Las Torres, Alcalá del Río, 41200 Seville, SpainAndalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Center Las Torres, Alcalá del Río, 41200 Seville, SpainA comparative study of organic and conventional farming systems was conducted in almond orchards to determine the effect of management practices on their fungal and bacterial communities. Soils from two orchards under organic (OM) and conventional (CM), and nearby nonmanaged (NM) soil were analyzed and compared. Several biochemical and biological parameters were measured (soil pH, electrical conductivity, total nitrogen, organic material, total phosphorous, total DNA, and fungal and bacterial DNA copies). Massive parallel sequencing of regions from fungal ITS rRNA and bacterial 16 S genes was carried out to characterize their diversity in the soil. We report a larger abundance of bacteria and fungi in soils under OM, with a more balanced fungi:bacteria ratio, compared to bacteria-skewed proportions under CM and NM. The fungal phylum <i>Ascomycota</i> corresponded to around the 75% relative abundance in the soil, whereas for bacteria, the phyla <i>Proteobacteria</i>, <i>Acidobacteriota</i> and <i>Bacteroidota</i> integrated around 50% of their diversity. Alpha diversity was similar across practices, but beta diversity was highly clustered by soil management. Linear discriminant analysis effect size (LEfSE) identified bacterial and fungal taxa associated with each type of soil management. Analyses of fungal functional guilds revealed 3–4 times larger abundance of pathogenic fungi under CM compared to OM and NM treatments. Among them, the genus <i>Cylindrocarpon</i> was more abundant under CM, and <i>Fusarium</i> under OM.https://www.mdpi.com/2309-608X/9/1/95<i>Prunus dulcis</i>almond agroecosystemsustainable managementmetabarcodingphytopathogenic fungiorganic farming |
| spellingShingle | Miguel Camacho-Sanchez Juan F. Herencia Francisco T. Arroyo Nieves Capote Soil Microbial Community Responses to Different Management Strategies in Almond Crop Journal of Fungi <i>Prunus dulcis</i> almond agroecosystem sustainable management metabarcoding phytopathogenic fungi organic farming |
| title | Soil Microbial Community Responses to Different Management Strategies in Almond Crop |
| title_full | Soil Microbial Community Responses to Different Management Strategies in Almond Crop |
| title_fullStr | Soil Microbial Community Responses to Different Management Strategies in Almond Crop |
| title_full_unstemmed | Soil Microbial Community Responses to Different Management Strategies in Almond Crop |
| title_short | Soil Microbial Community Responses to Different Management Strategies in Almond Crop |
| title_sort | soil microbial community responses to different management strategies in almond crop |
| topic | <i>Prunus dulcis</i> almond agroecosystem sustainable management metabarcoding phytopathogenic fungi organic farming |
| url | https://www.mdpi.com/2309-608X/9/1/95 |
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