Abstract:

DEEPEND Year 1 16S rRNA amplicon library sequence data of pelagic Gulf of Mexico microbiomes derived cruise DP02 (August 8-21, 2015) can yield further information beyond bacterioplankton species richness and relative abundances. Using the analytical PiCrust algorithm (“phylogenetic investigation of communities by reconstruction of unobserved states"), we have now been able to generate a derivative dataset that points to possible microbial functions based on 16S rRNA taxonomy. The algorithm assigns potential function based on various databases, including the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology, Greengenes 16S rRNA, and Cluster of Orthologous Groups (COGs) databases for ancestral state reconstruction and gene content predictions. The current functional designations cover all three primary KEGG classification levels and will be analyzed for possible significant trends and correlations with oceanographic or biological features. Data was partitioned into two sets – sans or with chloroplast input (with the latter potentially including chloroplast from eukaryotic phytoplankton). Differential abundance analysis of samples at various depth ranges (Surface, Shallow, Medium, Deep and Very Deep), by collection site and site/depth combined. Results are shown with and without chloroplast and p-values are FDR-adjusted for each defined comparison. Mean relative abundances are shown, followed by standard errors, and then Mann-Whitney FDR corrected P-values.

Suggested Citation:

James White. 2018. Functional interpretation of Year 1 16S rRNA data using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), pelagic Gulf of Mexico microbiomes, August 2015. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N79K48MZ

Purpose:

To overlay functional aspects on Gulf of Mexico pelagic bacterioplankton community 16S taxonomic data of DEEPEND cruise DP02.

Data Parameters and Units:

Metadata for each source CTD and collection site for the relevant DP02 cruise and that produced the 16S rRNA data (of R4.x257.228:0001), are included in the first tab of the main PICRUSt data of the attached .XLS file (called "Resphera.Cruise2. PiCrust Results.2016-GRIIDC.xlsx"). SampleID, Cruise number, Date (DD-MMM-YY), Latitude (decimal degrees), Longitude (decimal degrees), Site, Sample depth1 (m), Sample depth2 (sample depth classification surface, shallow, medium, deep, very deep), Site depth c, Description, Unique Site ID, CTD, Site, Relative abundances of Kyoto Encyclopedia of Genes and Genomes level 1, Relative abundance of Kyoto Encyclopedia of Genes and Genomes level 2, and Relative abundance of Kyoto Encyclopedia of Genes and Genomes level 3 with and without chloroplast associated sequences for each sample

Methods:

Passing 16S rRNA sequences (from R4.x257.228:0001) were assigned to a taxonomic lineage using QIIME and analyzed for functional gene content using PICRUSt.

Error Analysis:

Results are shown with and without chloroplast and p-values are FDR-adjusted for each defined comparison.

Individual Files: