A metagenomic approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems
The aim of this study was to determine the soil microbiome throughout mass sequencing in coffee plantations managed with either an organic (OAM; i.e., bio-fertilizers Azospirillum brasilense and Glomus intraradices) or a conventional (CAM; i.e., traditional NPK-fertilization) agronomic systems. Soil...
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| Veröffentlicht in: | Emirates Journal of Food and Agriculture 2020-04, Vol.32 (4), p.263-270 |
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| creator | Rodríguez, Alejandra Cabrera Calzada, Ricardo Trejo Peña, Cristina García-De la Ávila, Jesús G. Arreola Reyna, Erika Nava Paniagua, Felipe Vaca Velásquez, Clara Díaz Herrera, César A. Meza |
| description | The aim of this study was to determine the soil microbiome throughout mass sequencing in coffee plantations managed with either an organic (OAM; i.e., bio-fertilizers Azospirillum brasilense and Glomus intraradices) or a conventional (CAM; i.e., traditional NPK-fertilization) agronomic systems. Soil microbiome samples were collected in tropical eastern Mexico (Veracruz, 19°28’ N & 96° 52’ W), with annual average temperature and rainfall of 24.8° C, and 882.6 mm, respectively. Upon DNA soil-microbiome extraction, the V3-V4 16S rRNA region was amplified, and sequenced (Illumina). Results were analyzed with QIIME based on the EzBioCloud reference. Diverse phyla (n=16), classes (n=40), orders (n=90), families (n=135) and genera (n=333) were identified. The diversity index values were similar in both treatments, with Shannon's being 9.7 and Simpson's 0.99. While the phylum Proteobacteria was more abundant in CAM-soils and classified as copiotrophic, the phylum Acidobacteria was more abundant in OAM-soils and classified as oligotrophic. This classification may be related to the application of microorganisms and their effect on the soil´s state of organic matter and carbon fractions. Our research outcomes indicate that the application of bio-fertilizers promoted an increased presence of Acidobacteria, a phylum positively correlated with organic matter while significantly involved in carbon sequestration. Undisputable, metagenomics emerges as an interesting up-to-date genomic technology for unveiling the hidden content of the soil microbiome black box. |
| doi_str_mv | 10.9755/ejfa.2020.v32.i4.2092 |
| format | Article |
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Arreola ; Reyna, Erika Nava ; Paniagua, Felipe Vaca ; Velásquez, Clara Díaz ; Herrera, César A. Meza</creator><creatorcontrib>Rodríguez, Alejandra Cabrera ; Calzada, Ricardo Trejo ; Peña, Cristina García-De la ; Ávila, Jesús G. Arreola ; Reyna, Erika Nava ; Paniagua, Felipe Vaca ; Velásquez, Clara Díaz ; Herrera, César A. Meza</creatorcontrib><description>The aim of this study was to determine the soil microbiome throughout mass sequencing in coffee plantations managed with either an organic (OAM; i.e., bio-fertilizers Azospirillum brasilense and Glomus intraradices) or a conventional (CAM; i.e., traditional NPK-fertilization) agronomic systems. Soil microbiome samples were collected in tropical eastern Mexico (Veracruz, 19°28’ N & 96° 52’ W), with annual average temperature and rainfall of 24.8° C, and 882.6 mm, respectively. Upon DNA soil-microbiome extraction, the V3-V4 16S rRNA region was amplified, and sequenced (Illumina). Results were analyzed with QIIME based on the EzBioCloud reference. Diverse phyla (n=16), classes (n=40), orders (n=90), families (n=135) and genera (n=333) were identified. The diversity index values were similar in both treatments, with Shannon's being 9.7 and Simpson's 0.99. While the phylum Proteobacteria was more abundant in CAM-soils and classified as copiotrophic, the phylum Acidobacteria was more abundant in OAM-soils and classified as oligotrophic. This classification may be related to the application of microorganisms and their effect on the soil´s state of organic matter and carbon fractions. Our research outcomes indicate that the application of bio-fertilizers promoted an increased presence of Acidobacteria, a phylum positively correlated with organic matter while significantly involved in carbon sequestration. Undisputable, metagenomics emerges as an interesting up-to-date genomic technology for unveiling the hidden content of the soil microbiome black box.</description><identifier>ISSN: 2079-052X</identifier><identifier>EISSN: 2079-0538</identifier><identifier>DOI: 10.9755/ejfa.2020.v32.i4.2092</identifier><language>eng</language><publisher>Sofia: College of Food & Agriculture, United Arab Emirates University</publisher><subject>Acidobacteria ; Agricultural ecosystems ; Agricultural management ; Agricultural production ; Agroecosystems ; Agronomy ; Annual rainfall ; Bacteria ; Biofertilizers ; Carbon sequestration ; Coffee ; Coffee (Plant) ; Compound fertilizers ; Crops ; Deoxyribonucleic acid ; DNA ; Environmental aspects ; Evaluation ; Fertilization ; Fertilizers ; GDP ; Genera ; Genetic aspects ; Genomics ; Gross Domestic Product ; Management ; Methods ; Microbiomes ; Microorganisms ; Nucleotide sequence ; Organic matter ; Organic soils ; Plant growth ; Plantations ; Probiotics ; Production management ; Production processes ; rRNA 16S ; Soil classification ; Soil fertility ; Soil microbiology ; Soils</subject><ispartof>Emirates Journal of Food and Agriculture, 2020-04, Vol.32 (4), p.263-270</ispartof><rights>COPYRIGHT 2020 College of Food & Agriculture, United Arab Emirates University</rights><rights>2020. 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Arreola</creatorcontrib><creatorcontrib>Reyna, Erika Nava</creatorcontrib><creatorcontrib>Paniagua, Felipe Vaca</creatorcontrib><creatorcontrib>Velásquez, Clara Díaz</creatorcontrib><creatorcontrib>Herrera, César A. Meza</creatorcontrib><title>A metagenomic approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems</title><title>Emirates Journal of Food and Agriculture</title><description>The aim of this study was to determine the soil microbiome throughout mass sequencing in coffee plantations managed with either an organic (OAM; i.e., bio-fertilizers Azospirillum brasilense and Glomus intraradices) or a conventional (CAM; i.e., traditional NPK-fertilization) agronomic systems. Soil microbiome samples were collected in tropical eastern Mexico (Veracruz, 19°28’ N & 96° 52’ W), with annual average temperature and rainfall of 24.8° C, and 882.6 mm, respectively. Upon DNA soil-microbiome extraction, the V3-V4 16S rRNA region was amplified, and sequenced (Illumina). Results were analyzed with QIIME based on the EzBioCloud reference. Diverse phyla (n=16), classes (n=40), orders (n=90), families (n=135) and genera (n=333) were identified. The diversity index values were similar in both treatments, with Shannon's being 9.7 and Simpson's 0.99. While the phylum Proteobacteria was more abundant in CAM-soils and classified as copiotrophic, the phylum Acidobacteria was more abundant in OAM-soils and classified as oligotrophic. This classification may be related to the application of microorganisms and their effect on the soil´s state of organic matter and carbon fractions. Our research outcomes indicate that the application of bio-fertilizers promoted an increased presence of Acidobacteria, a phylum positively correlated with organic matter while significantly involved in carbon sequestration. 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Arreola</au><au>Reyna, Erika Nava</au><au>Paniagua, Felipe Vaca</au><au>Velásquez, Clara Díaz</au><au>Herrera, César A. Meza</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A metagenomic approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems</atitle><jtitle>Emirates Journal of Food and Agriculture</jtitle><date>2020-04-01</date><risdate>2020</risdate><volume>32</volume><issue>4</issue><spage>263</spage><epage>270</epage><pages>263-270</pages><issn>2079-052X</issn><eissn>2079-0538</eissn><abstract>The aim of this study was to determine the soil microbiome throughout mass sequencing in coffee plantations managed with either an organic (OAM; i.e., bio-fertilizers Azospirillum brasilense and Glomus intraradices) or a conventional (CAM; i.e., traditional NPK-fertilization) agronomic systems. Soil microbiome samples were collected in tropical eastern Mexico (Veracruz, 19°28’ N & 96° 52’ W), with annual average temperature and rainfall of 24.8° C, and 882.6 mm, respectively. Upon DNA soil-microbiome extraction, the V3-V4 16S rRNA region was amplified, and sequenced (Illumina). Results were analyzed with QIIME based on the EzBioCloud reference. Diverse phyla (n=16), classes (n=40), orders (n=90), families (n=135) and genera (n=333) were identified. The diversity index values were similar in both treatments, with Shannon's being 9.7 and Simpson's 0.99. While the phylum Proteobacteria was more abundant in CAM-soils and classified as copiotrophic, the phylum Acidobacteria was more abundant in OAM-soils and classified as oligotrophic. This classification may be related to the application of microorganisms and their effect on the soil´s state of organic matter and carbon fractions. Our research outcomes indicate that the application of bio-fertilizers promoted an increased presence of Acidobacteria, a phylum positively correlated with organic matter while significantly involved in carbon sequestration. Undisputable, metagenomics emerges as an interesting up-to-date genomic technology for unveiling the hidden content of the soil microbiome black box.</abstract><cop>Sofia</cop><pub>College of Food & Agriculture, United Arab Emirates University</pub><doi>10.9755/ejfa.2020.v32.i4.2092</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Emirates Journal of Food and Agriculture, 2020-04, Vol.32 (4), p.263-270 |
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| subjects | Acidobacteria Agricultural ecosystems Agricultural management Agricultural production Agroecosystems Agronomy Annual rainfall Bacteria Biofertilizers Carbon sequestration Coffee Coffee (Plant) Compound fertilizers Crops Deoxyribonucleic acid DNA Environmental aspects Evaluation Fertilization Fertilizers GDP Genera Genetic aspects Genomics Gross Domestic Product Management Methods Microbiomes Microorganisms Nucleotide sequence Organic matter Organic soils Plant growth Plantations Probiotics Production management Production processes rRNA 16S Soil classification Soil fertility Soil microbiology Soils |
| title | A metagenomic approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems |
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