Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study
Abstract Background The soil microbiota has a direct impact on plant development and other metabolic systems, such as the degradation of organic matter and the availability of microelements and metabolites. In the context of agricultural soils, microbial activity is crucial for maintaining soil heal...
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | Environmental Microbiome |
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| Online Access: | https://doi.org/10.1186/s40793-023-00519-4 |
| _version_ | 1797556315127545856 |
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| author | Dámaris Núñez-Gómez Pablo Melgarejo Juan José Martínez-Nicolás Francisca Hernández Rafael Martínez-Font Vicente Lidón Pilar Legua |
| author_facet | Dámaris Núñez-Gómez Pablo Melgarejo Juan José Martínez-Nicolás Francisca Hernández Rafael Martínez-Font Vicente Lidón Pilar Legua |
| author_sort | Dámaris Núñez-Gómez |
| collection | DOAJ |
| description | Abstract Background The soil microbiota has a direct impact on plant development and other metabolic systems, such as the degradation of organic matter and the availability of microelements and metabolites. In the context of agricultural soils, microbial activity is crucial for maintaining soil health and productivity. Thus, the present study aimed to identify, characterize, and quantify the microbial communities of four types of substrates with varying proportions of marine port sediment used for cultivating lemons. By investigating microbial diversity and relative abundance, the work aimed to highlight the importance of soil microbial communities in agriculture when alternative culture media was used. Results The composition and structure of the sampled microbial communities were assessed through the amplification and sequencing of the V3-V4 variable regions of the 16 S rRNA gene The results revealed a diverse microbial community composition in all substrate samples, with a total of 41 phyla, 113 classes, 266 orders, 405 families, 715 genera, and 1513 species identified. Among these, Proteobacteria, Bacteroidota, Planctomycetota, Patescibacteria, Chloroflexi, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, and Gemmatimonadota accounted for over 90% of the bacterial reads, indicating their dominance in the substrates. Conclusions The impact of the substrate origin on the diversity and relative abundace of the microbiota was confirmed. The higher content of beneficial bacterial communities for plant development identified in peat could explain why is considered an ideal agricultural substrate. Development of “beneficial for plants” bacterial communities in alternative agricultural substrates, regardless of the edaphic characteristics, opens the possibility of studying the forced and specific inoculation of these culture media aiming to be agriculturally ideals. |
| first_indexed | 2024-03-10T17:01:06Z |
| format | Article |
| id | doaj.art-9da3e0eb0893477bba4bf60029d95df9 |
| institution | Directory Open Access Journal |
| issn | 2524-6372 |
| language | English |
| last_indexed | 2024-03-10T17:01:06Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Environmental Microbiome |
| spelling | doaj.art-9da3e0eb0893477bba4bf60029d95df92023-11-20T10:58:45ZengBMCEnvironmental Microbiome2524-63722023-08-0118111410.1186/s40793-023-00519-4Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing studyDámaris Núñez-Gómez0Pablo Melgarejo1Juan José Martínez-Nicolás2Francisca Hernández3Rafael Martínez-Font4Vicente Lidón5Pilar Legua6Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez UniversityCentro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez UniversityCentro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez UniversityCentro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez UniversityCentro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez UniversityCentro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez UniversityCentro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Miguel Hernandez UniversityAbstract Background The soil microbiota has a direct impact on plant development and other metabolic systems, such as the degradation of organic matter and the availability of microelements and metabolites. In the context of agricultural soils, microbial activity is crucial for maintaining soil health and productivity. Thus, the present study aimed to identify, characterize, and quantify the microbial communities of four types of substrates with varying proportions of marine port sediment used for cultivating lemons. By investigating microbial diversity and relative abundance, the work aimed to highlight the importance of soil microbial communities in agriculture when alternative culture media was used. Results The composition and structure of the sampled microbial communities were assessed through the amplification and sequencing of the V3-V4 variable regions of the 16 S rRNA gene The results revealed a diverse microbial community composition in all substrate samples, with a total of 41 phyla, 113 classes, 266 orders, 405 families, 715 genera, and 1513 species identified. Among these, Proteobacteria, Bacteroidota, Planctomycetota, Patescibacteria, Chloroflexi, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, and Gemmatimonadota accounted for over 90% of the bacterial reads, indicating their dominance in the substrates. Conclusions The impact of the substrate origin on the diversity and relative abundace of the microbiota was confirmed. The higher content of beneficial bacterial communities for plant development identified in peat could explain why is considered an ideal agricultural substrate. Development of “beneficial for plants” bacterial communities in alternative agricultural substrates, regardless of the edaphic characteristics, opens the possibility of studying the forced and specific inoculation of these culture media aiming to be agriculturally ideals.https://doi.org/10.1186/s40793-023-00519-4Microbiome16S rRNAMarine sedimentAgricultural substrateWaste reuseFunctional inferences |
| spellingShingle | Dámaris Núñez-Gómez Pablo Melgarejo Juan José Martínez-Nicolás Francisca Hernández Rafael Martínez-Font Vicente Lidón Pilar Legua Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study Environmental Microbiome Microbiome 16S rRNA Marine sediment Agricultural substrate Waste reuse Functional inferences |
| title | Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study |
| title_full | Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study |
| title_fullStr | Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study |
| title_full_unstemmed | Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study |
| title_short | Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study |
| title_sort | effects of marine sediment as agricultural substrate on soil microbial diversity an amplicon sequencing study |
| topic | Microbiome 16S rRNA Marine sediment Agricultural substrate Waste reuse Functional inferences |
| url | https://doi.org/10.1186/s40793-023-00519-4 |
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