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| Autores principales: | , , , , , |
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| Formato: | Artículo científico |
| Lenguaje: | en |
| Publicado: |
ISME communications
2025
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| Acceso en línea: | https://pubmed.ncbi.nlm.nih.gov/40182061/ |
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| _version_ | 1868266221019856896 |
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| author | Cheung, Shunyan Morando, Michael Magasin, Jonathan Cornejo-Castillo, Francisco M Zehr, Jonathan P Turk-Kubo, Kendra A |
| author_facet | Cheung, Shunyan Morando, Michael Magasin, Jonathan Cornejo-Castillo, Francisco M Zehr, Jonathan P Turk-Kubo, Kendra A Cheung, Shunyan Morando, Michael Magasin, Jonathan Cornejo-Castillo, Francisco M Zehr, Jonathan P Turk-Kubo, Kendra A |
| collection | PubMed - marine biology |
| contents | gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity. Cheung, Shunyan Morando, Michael Magasin, Jonathan Cornejo-Castillo, Francisco M Zehr, Jonathan P Turk-Kubo, Kendra A Exploring the diversity of diazotrophs is key to understanding their role in supplying fixed nitrogen that supports marine productivity. A nested PCR assay using the universal primer set nifH1-nifH4, which targets the nitrogenase () gene, is a widely used approach for studying marine diazotrophs by amplicon sequencing. Metagenomics, direct sequencing of DNA without PCR, has provided complementary views of the diversity of marine diazotrophs. A significant fraction of the metagenome-derived sequences (e.g. - and -affiliated) were reported to have nucleotide mismatches with the nifH1-nifH4 primers, leading to the suggestion that amplicon sequencing does not detect specific diazotrophic taxa and underrepresents diazotroph diversity. Here, we report that these mismatches are mostly located in a single-base at the 5'-end of the nifH4 primer, which does not impact detection of the genes. This is demonstrated by the presence of genes that contain the nucleotide mismatches in a recent compilation of global ocean amplicon datasets, with high relative abundances detected in a variety of samples. While the metagenome- and metatranscriptome-derived genes accounted for 4.4% of the total amplicon sequence variants from the global ocean amplicon database, the corresponding amplicon sequence variants can have high relative abundances (accounting for 47% of the reads in the database). These analyses underscore that amplicon sequencing using the nifH1-nifH4 primers is an important tool for studying diversity of marine diazotrophs, particularly as a complement to metagenomics which can provide taxonomic and metabolic information for some dominant groups. |
| format | Artículo científico |
| id | pubmed_40182061 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | ISME communications |
| record_format | pubmed |
| spellingShingle | gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity. Cheung, Shunyan Morando, Michael Magasin, Jonathan Cornejo-Castillo, Francisco M Zehr, Jonathan P Turk-Kubo, Kendra A gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity. Cheung, Shunyan Morando, Michael Magasin, Jonathan Cornejo-Castillo, Francisco M Zehr, Jonathan P Turk-Kubo, Kendra A Exploring the diversity of diazotrophs is key to understanding their role in supplying fixed nitrogen that supports marine productivity. A nested PCR assay using the universal primer set nifH1-nifH4, which targets the nitrogenase () gene, is a widely used approach for studying marine diazotrophs by amplicon sequencing. Metagenomics, direct sequencing of DNA without PCR, has provided complementary views of the diversity of marine diazotrophs. A significant fraction of the metagenome-derived sequences (e.g. - and -affiliated) were reported to have nucleotide mismatches with the nifH1-nifH4 primers, leading to the suggestion that amplicon sequencing does not detect specific diazotrophic taxa and underrepresents diazotroph diversity. Here, we report that these mismatches are mostly located in a single-base at the 5'-end of the nifH4 primer, which does not impact detection of the genes. This is demonstrated by the presence of genes that contain the nucleotide mismatches in a recent compilation of global ocean amplicon datasets, with high relative abundances detected in a variety of samples. While the metagenome- and metatranscriptome-derived genes accounted for 4.4% of the total amplicon sequence variants from the global ocean amplicon database, the corresponding amplicon sequence variants can have high relative abundances (accounting for 47% of the reads in the database). These analyses underscore that amplicon sequencing using the nifH1-nifH4 primers is an important tool for studying diversity of marine diazotrophs, particularly as a complement to metagenomics which can provide taxonomic and metabolic information for some dominant groups. |
| title | gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity. |
| url | https://pubmed.ncbi.nlm.nih.gov/40182061/ |