The Impact of Different Planting Systems on the Bacterial Diversity of Rice Cultivated in Saline Soil Based on 16S rRNA Gene-Based Metagenomic Insights
Soil salinity is considered to be a major impediment to the production of rice among other abiotic stresses. In this study, 16S rRNA Illumina amplicon sequencing was performed to characterise the halophilic communities entrapped in rice rhizosphere soil cultivated in different planting systems (conv...
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MDPI AG
2022-10-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/12/10/1624 |
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| author | Pugazhenthi Davidson Rokins Nellaiappan Olaganathan Gopal Rangasamy Anandham Ramasamy Saraswathi |
| author_facet | Pugazhenthi Davidson Rokins Nellaiappan Olaganathan Gopal Rangasamy Anandham Ramasamy Saraswathi |
| author_sort | Pugazhenthi Davidson Rokins |
| collection | DOAJ |
| description | Soil salinity is considered to be a major impediment to the production of rice among other abiotic stresses. In this study, 16S rRNA Illumina amplicon sequencing was performed to characterise the halophilic communities entrapped in rice rhizosphere soil cultivated in different planting systems (conventional, aerobic and System of Rice Intensification (SRI)) under saline conditions. The physicochemical properties and urease, soil dehydrogenase, alkaline phosphatase and arylsulphatase activity of soil samples were evaluated to understand their influence on the bacterial communities of the soil. Electrical conductivity (EC) of soil was lower in SRI soil samples, while the available major soil nutrients (nitrogen, phosphorous and potassium) content and soil enzyme activities such as dehydrogenase, alkaline phosphatase, urease and arylsulphatase were higher. A total of 2,516,700 reads were generated by amplicon sequencing of the hypervariable V3–V4 regions of bacterial 16S rRNA gene and were clustered into 273,447 OTU operational taxonomic units. The total number of Operational Taxonomic Units (OTUs) was higher in the conventional soil samples compared to the SRI and aerobic soil samples. Metagenomic analysis revealed that Proteobacteria was the most dominant phyla in all the planting systems followed by Actinobacteria, Firmicutes and Chloroflexi. The alpha diversity index was higher in conventional soil samples compared to other samples and more species diversity was found in SRI soil samples. KEGG analysis revealed that bacterial communities in different soil samples showed varied functional properties. The bacterial diversity of saline soil in this study can be utilised to identify microbial communities with biotechnological potential that can be employed for plant growth promotion in saline environments. |
| first_indexed | 2024-03-09T20:55:44Z |
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| id | doaj.art-b153bf83b7e345d7837f60d3f8e3b5e4 |
| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-09T20:55:44Z |
| publishDate | 2022-10-01 |
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| series | Agriculture |
| spelling | doaj.art-b153bf83b7e345d7837f60d3f8e3b5e42023-11-23T22:21:24ZengMDPI AGAgriculture2077-04722022-10-011210162410.3390/agriculture12101624The Impact of Different Planting Systems on the Bacterial Diversity of Rice Cultivated in Saline Soil Based on 16S rRNA Gene-Based Metagenomic InsightsPugazhenthi Davidson Rokins0Nellaiappan Olaganathan Gopal1Rangasamy Anandham2Ramasamy Saraswathi3Department of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU), Coimbatore 641003, IndiaDepartment of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU), Coimbatore 641003, IndiaDepartment of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU), Coimbatore 641003, IndiaDepartment of Plant Genetic Resources, Tamil Nadu Agricultural University (TNAU), Coimbatore 641003, IndiaSoil salinity is considered to be a major impediment to the production of rice among other abiotic stresses. In this study, 16S rRNA Illumina amplicon sequencing was performed to characterise the halophilic communities entrapped in rice rhizosphere soil cultivated in different planting systems (conventional, aerobic and System of Rice Intensification (SRI)) under saline conditions. The physicochemical properties and urease, soil dehydrogenase, alkaline phosphatase and arylsulphatase activity of soil samples were evaluated to understand their influence on the bacterial communities of the soil. Electrical conductivity (EC) of soil was lower in SRI soil samples, while the available major soil nutrients (nitrogen, phosphorous and potassium) content and soil enzyme activities such as dehydrogenase, alkaline phosphatase, urease and arylsulphatase were higher. A total of 2,516,700 reads were generated by amplicon sequencing of the hypervariable V3–V4 regions of bacterial 16S rRNA gene and were clustered into 273,447 OTU operational taxonomic units. The total number of Operational Taxonomic Units (OTUs) was higher in the conventional soil samples compared to the SRI and aerobic soil samples. Metagenomic analysis revealed that Proteobacteria was the most dominant phyla in all the planting systems followed by Actinobacteria, Firmicutes and Chloroflexi. The alpha diversity index was higher in conventional soil samples compared to other samples and more species diversity was found in SRI soil samples. KEGG analysis revealed that bacterial communities in different soil samples showed varied functional properties. The bacterial diversity of saline soil in this study can be utilised to identify microbial communities with biotechnological potential that can be employed for plant growth promotion in saline environments.https://www.mdpi.com/2077-0472/12/10/1624ricerhizosphere soilsalinityplanting systembacterial diversityproteobacteria |
| spellingShingle | Pugazhenthi Davidson Rokins Nellaiappan Olaganathan Gopal Rangasamy Anandham Ramasamy Saraswathi The Impact of Different Planting Systems on the Bacterial Diversity of Rice Cultivated in Saline Soil Based on 16S rRNA Gene-Based Metagenomic Insights Agriculture rice rhizosphere soil salinity planting system bacterial diversity proteobacteria |
| title | The Impact of Different Planting Systems on the Bacterial Diversity of Rice Cultivated in Saline Soil Based on 16S rRNA Gene-Based Metagenomic Insights |
| title_full | The Impact of Different Planting Systems on the Bacterial Diversity of Rice Cultivated in Saline Soil Based on 16S rRNA Gene-Based Metagenomic Insights |
| title_fullStr | The Impact of Different Planting Systems on the Bacterial Diversity of Rice Cultivated in Saline Soil Based on 16S rRNA Gene-Based Metagenomic Insights |
| title_full_unstemmed | The Impact of Different Planting Systems on the Bacterial Diversity of Rice Cultivated in Saline Soil Based on 16S rRNA Gene-Based Metagenomic Insights |
| title_short | The Impact of Different Planting Systems on the Bacterial Diversity of Rice Cultivated in Saline Soil Based on 16S rRNA Gene-Based Metagenomic Insights |
| title_sort | impact of different planting systems on the bacterial diversity of rice cultivated in saline soil based on 16s rrna gene based metagenomic insights |
| topic | rice rhizosphere soil salinity planting system bacterial diversity proteobacteria |
| url | https://www.mdpi.com/2077-0472/12/10/1624 |
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