Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in Egypt
Plants especially in their natural habitat are considered part of a rich ecosystem that includes many various microorganisms in the soil. The current study aimed to identify the bacterial profile of agriculture-related soil samples using the metabarcoding technique to compare and explore relevant rh...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/12/10/2543 |
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| author | Mohamed Hassan Korkar Mahmoud Magdy Samah Mohamed Rizk Yosur Gamal Fiteha Aiman Hanafy Atta Mohamed Abdel-Salam Rashed |
| author_facet | Mohamed Hassan Korkar Mahmoud Magdy Samah Mohamed Rizk Yosur Gamal Fiteha Aiman Hanafy Atta Mohamed Abdel-Salam Rashed |
| author_sort | Mohamed Hassan Korkar |
| collection | DOAJ |
| description | Plants especially in their natural habitat are considered part of a rich ecosystem that includes many various microorganisms in the soil. The current study aimed to identify the bacterial profile of agriculture-related soil samples using the metabarcoding technique to compare and explore relevant rhizosphere bacteria associated with plant cultivations in newly reclaimed land and habitual cultivated ones. The total environmental DNA was extracted from rhizosphere and noncultivated samples derived from three land types in Egypt. The bacterial 16S rDNA was amplified and sequenced by NGS technology to profile each sample. The microbial profile was characterized by statistical and literature-based methods. Among all samples, the most identified phyla were Actinobacteriota (28%), followed by Proteobacteriota (26%), Firmicutes (14%), Acidobacteriota and Chloroflexi (7%), Gemmatimonadota (5%), Bacteriodota and Crenarchaeota (3%), and Myxococcota (2%), in addition to 37 other phyla with <1% counts. A total of 74 OTUs were unique to the plant rhizosphere area and classified as Bacteriodota (5.1%:0.3%), Firmicutes (2.4%:0.1%), and Proteobacteria (3.5%:2%) phyla in agricultural and reclaimed lands, respectively. Moreover, the rhizosphere profile included a large portion of uncultured and unidentified bacterial species, which opened a window to further analysis. Our analysis provides a key knowledge about the rhizosphere microbiome and highlights its possible use to create microbial-based biofertilizers targeting plant performance in contrast to traditional fertilizers and their side effect on the agriculture sector. |
| first_indexed | 2024-03-09T20:52:51Z |
| format | Article |
| id | doaj.art-b3a62837a0c7489489e32e6098c978c6 |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-09T20:52:51Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-b3a62837a0c7489489e32e6098c978c62023-11-23T22:29:01ZengMDPI AGAgronomy2073-43952022-10-011210254310.3390/agronomy12102543Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in EgyptMohamed Hassan Korkar0Mahmoud Magdy1Samah Mohamed Rizk2Yosur Gamal Fiteha3Aiman Hanafy Atta4Mohamed Abdel-Salam Rashed5Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, EgyptGenetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, EgyptGenetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, EgyptGenetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, EgyptGenetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, EgyptGenetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, EgyptPlants especially in their natural habitat are considered part of a rich ecosystem that includes many various microorganisms in the soil. The current study aimed to identify the bacterial profile of agriculture-related soil samples using the metabarcoding technique to compare and explore relevant rhizosphere bacteria associated with plant cultivations in newly reclaimed land and habitual cultivated ones. The total environmental DNA was extracted from rhizosphere and noncultivated samples derived from three land types in Egypt. The bacterial 16S rDNA was amplified and sequenced by NGS technology to profile each sample. The microbial profile was characterized by statistical and literature-based methods. Among all samples, the most identified phyla were Actinobacteriota (28%), followed by Proteobacteriota (26%), Firmicutes (14%), Acidobacteriota and Chloroflexi (7%), Gemmatimonadota (5%), Bacteriodota and Crenarchaeota (3%), and Myxococcota (2%), in addition to 37 other phyla with <1% counts. A total of 74 OTUs were unique to the plant rhizosphere area and classified as Bacteriodota (5.1%:0.3%), Firmicutes (2.4%:0.1%), and Proteobacteria (3.5%:2%) phyla in agricultural and reclaimed lands, respectively. Moreover, the rhizosphere profile included a large portion of uncultured and unidentified bacterial species, which opened a window to further analysis. Our analysis provides a key knowledge about the rhizosphere microbiome and highlights its possible use to create microbial-based biofertilizers targeting plant performance in contrast to traditional fertilizers and their side effect on the agriculture sector.https://www.mdpi.com/2073-4395/12/10/254316S rDNA metabarcodingmicrobial communitynewly reclaimed landsexophytasoil microbiota |
| spellingShingle | Mohamed Hassan Korkar Mahmoud Magdy Samah Mohamed Rizk Yosur Gamal Fiteha Aiman Hanafy Atta Mohamed Abdel-Salam Rashed Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in Egypt Agronomy 16S rDNA metabarcoding microbial community newly reclaimed lands exophyta soil microbiota |
| title | Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in Egypt |
| title_full | Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in Egypt |
| title_fullStr | Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in Egypt |
| title_full_unstemmed | Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in Egypt |
| title_short | Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in Egypt |
| title_sort | rhizosphere associated microbiome profile of agricultural reclaimed lands in egypt |
| topic | 16S rDNA metabarcoding microbial community newly reclaimed lands exophyta soil microbiota |
| url | https://www.mdpi.com/2073-4395/12/10/2543 |
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