Universal Amplicon Sequences (mixed 16S/18S) from GEOTRACES Cruises GA03 and GP13
Citation
MGnify (2021). Universal Amplicon Sequences (mixed 16S/18S) from GEOTRACES Cruises GA03 and GP13. Sampling event dataset https://doi.org/10.15468/6hv9td accessed via GBIF.org on 2024-08-23.Description
Dedicated sampling campaigns such as JGOFS, CLIVAR, and GEOTRACES have quantified critical oceanic biogeochemical processes on a global scale. Integrating these measurements with microbial community composition data is highly desirable because it would allow hypotheses about biogeographic distributions to be tested or perhaps lead to the discovery of organisms responsible for a particular biogeochemical process. A promising strategy to generate this microbial community composition data comes from high-throughput sequencing of PCR amplicons generated with the 515Y/926R universal 16S/18S primer set. The two key advantages of the 515Y/926R primers are 1) their comprehensiveness - recovering amplicons from the entire cellular microbial community - and 2) their quantitative nature - recovering gene copy abundances as shown previously with microbial community standards. Compared to metagenomes, amplicons additionally have the advantage of more easily detecting rare community members that may be biogeochemically significant (e.g. diazotrophs). In this study, we applied the 515Y/926R primers to DNA from the recently published bioGEOTRACES metagenomic dataset, and use these results to describe microbial community composition across a longitudinal transect of the southern Pacific Ocean from Australia to Tahiti (GEOTRACES section GP13) and a longitudinal transect of the northern Atlantic from Massachusetts to the Canary Islands (GEOTRACES section GA03). In addition, we conducted intercomparisons with metagenomic taxa abundances and show the two techniques correspond strongly to one another for most samples (average R^2=0.97).Sampling Description
Sampling
Dedicated sampling campaigns such as JGOFS, CLIVAR, and GEOTRACES have quantified critical oceanic biogeochemical processes on a global scale. Integrating these measurements with microbial community composition data is highly desirable because it would allow hypotheses about biogeographic distributions to be tested or perhaps lead to the discovery of organisms responsible for a particular biogeochemical process. A promising strategy to generate this microbial community composition data comes from high-throughput sequencing of PCR amplicons generated with the 515Y/926R universal 16S/18S primer set. The two key advantages of the 515Y/926R primers are 1) their comprehensiveness - recovering amplicons from the entire cellular microbial community - and 2) their quantitative nature - recovering gene copy abundances as shown previously with microbial community standards. Compared to metagenomes, amplicons additionally have the advantage of more easily detecting rare community members that may be biogeochemically significant (e.g. diazotrophs). In this study, we applied the 515Y/926R primers to DNA from the recently published bioGEOTRACES metagenomic dataset, and use these results to describe microbial community composition across a longitudinal transect of the southern Pacific Ocean from Australia to Tahiti (GEOTRACES section GP13) and a longitudinal transect of the northern Atlantic from Massachusetts to the Canary Islands (GEOTRACES section GA03). In addition, we conducted intercomparisons with metagenomic taxa abundances and show the two techniques correspond strongly to one another for most samples (average R^2=0.97).Method steps
- Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/5.0
Taxonomic Coverages
Geographic Coverages
Bibliographic Citations
- McNichol J, Berube PM, Biller SJ, Fuhrman JA. 2021. Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys. mSystems vol. 6 - DOI:10.1128/msystems.00565-21
Contacts
originatorUniversity of Southern California
metadata author
University of Southern California
administrative point of contact
University of Southern California