16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors
Nitrifying bacteria and archaea are ubiquitous and can transform ammonia locked up in soil or manure into nitrate, a more soluble form of nitrogen. However, nitrifying bacteria and archaea inhabiting maize rhizosphere have not been fully explored. This study evaluates the diversity and abundance of...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-08-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/12/9/1328 |
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| author | Oluwatobi Esther Ayiti Ayansina Segun Ayangbenro Olubukola Oluranti Babalola |
| author_facet | Oluwatobi Esther Ayiti Ayansina Segun Ayangbenro Olubukola Oluranti Babalola |
| author_sort | Oluwatobi Esther Ayiti |
| collection | DOAJ |
| description | Nitrifying bacteria and archaea are ubiquitous and can transform ammonia locked up in soil or manure into nitrate, a more soluble form of nitrogen. However, nitrifying bacteria and archaea inhabiting maize rhizosphere have not been fully explored. This study evaluates the diversity and abundance of nitrifying bacteria and archaea across different growth stages of maize using 16S amplicon sequencing. Moreover, the influence of environmental factors (soil physical and chemical properties) on the nitrifying communities was evaluated. Rhizosphere soil DNA was extracted using Nucleospin Soil DNA extraction kit and sequenced on Illumina Miseq platform. MG-RAST was used to analyze the raw sequences. The physical and chemical properties of the soil were measured using standard procedure. The results revealed 9 genera of nitrifying bacteria; <i>Nitrospira</i>, <i>Nitrosospira</i>, <i>Nitrobacter</i>, <i>Nitrosovibrio</i>, <i>Nitrosomonas</i>, <i>Nitrosococcus</i>, <i>Nitrococcus</i>, unclassified (derived from Nitrosomonadales), unclassified (derived from Nitrosomonadaceae) and 1 archaeon <i>Candidatus Nitrososphaera</i>. The Nitrospirae phyla group, which had the most nitrifying bacteria, was more abundant at the tasselling stage (67.94%). Alpha diversity showed no significant difference. However, the Beta diversity showed significant difference (<i>p</i> = 0.01, R = 0.58) across the growth stages. The growth stages had no significant effect on the diversity of nitrifying bacteria and archaea, but the tasselling stage had the most abundant nitrifying bacteria. A correlation was observed between some of the chemical properties and some nitrifying bacteria. The research outcome can be put into consideration while carrying out a biotechnological process that involves nitrifying bacteria and archaea. |
| first_indexed | 2024-03-10T01:02:21Z |
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| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-10T01:02:21Z |
| publishDate | 2022-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj.art-31c2a5bca2e24806aee49b76be99220c2023-11-23T14:32:08ZengMDPI AGAgriculture2077-04722022-08-01129132810.3390/agriculture1209132816S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental FactorsOluwatobi Esther Ayiti0Ayansina Segun Ayangbenro1Olubukola Oluranti Babalola2Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho 2735, South AfricaFood Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho 2735, South AfricaFood Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho 2735, South AfricaNitrifying bacteria and archaea are ubiquitous and can transform ammonia locked up in soil or manure into nitrate, a more soluble form of nitrogen. However, nitrifying bacteria and archaea inhabiting maize rhizosphere have not been fully explored. This study evaluates the diversity and abundance of nitrifying bacteria and archaea across different growth stages of maize using 16S amplicon sequencing. Moreover, the influence of environmental factors (soil physical and chemical properties) on the nitrifying communities was evaluated. Rhizosphere soil DNA was extracted using Nucleospin Soil DNA extraction kit and sequenced on Illumina Miseq platform. MG-RAST was used to analyze the raw sequences. The physical and chemical properties of the soil were measured using standard procedure. The results revealed 9 genera of nitrifying bacteria; <i>Nitrospira</i>, <i>Nitrosospira</i>, <i>Nitrobacter</i>, <i>Nitrosovibrio</i>, <i>Nitrosomonas</i>, <i>Nitrosococcus</i>, <i>Nitrococcus</i>, unclassified (derived from Nitrosomonadales), unclassified (derived from Nitrosomonadaceae) and 1 archaeon <i>Candidatus Nitrososphaera</i>. The Nitrospirae phyla group, which had the most nitrifying bacteria, was more abundant at the tasselling stage (67.94%). Alpha diversity showed no significant difference. However, the Beta diversity showed significant difference (<i>p</i> = 0.01, R = 0.58) across the growth stages. The growth stages had no significant effect on the diversity of nitrifying bacteria and archaea, but the tasselling stage had the most abundant nitrifying bacteria. A correlation was observed between some of the chemical properties and some nitrifying bacteria. The research outcome can be put into consideration while carrying out a biotechnological process that involves nitrifying bacteria and archaea.https://www.mdpi.com/2077-0472/12/9/1328Nitrospiraebiotechnologynitratemaize growth stagesnucleospinammonia |
| spellingShingle | Oluwatobi Esther Ayiti Ayansina Segun Ayangbenro Olubukola Oluranti Babalola 16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors Agriculture Nitrospirae biotechnology nitrate maize growth stages nucleospin ammonia |
| title | 16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors |
| title_full | 16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors |
| title_fullStr | 16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors |
| title_full_unstemmed | 16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors |
| title_short | 16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors |
| title_sort | 16s amplicon sequencing of nitrifying bacteria and archaea inhabiting maize rhizosphere and the influencing environmental factors |
| topic | Nitrospirae biotechnology nitrate maize growth stages nucleospin ammonia |
| url | https://www.mdpi.com/2077-0472/12/9/1328 |
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