Relative Abundance and Community Similiarity of Conditionally Rare Taxa¶

Summary¶

This is an non-metric multidimensional scaling (NMDS) plot used to visualize the relationship between communities based on a chosen distance metric (i.e., Bray-Curtis, Unifrac, etc.).
DCM = Deep Chlorophyll Maximum Layer; MES = Mesopelagic Zone; MIX = Marine Epipelagic Mixed Layer; SRF = Surface Water Layer

Visualization requires otu table, taxonomy table, and metadata for creating a phyloseq object. Output "OTUdf_cr_excel.txt" requires user to open file in excel to delete first row, first column, then the contents of the first cell. The amended file is saved as "OTUdf_cr_input.txt" and used for the CRT function.

Visualization can be used to compare the similarity of communities that include all taxa and conditionally rare taxa.
Depth is responsible for 35% and 19% of the variance observed in community composition of all taxa and conditionally rare taxa, respectively
Province is responsible for 13% and 15% of the variance observed in community composition of all taxa and conditionally rare taxa, respectively.
Depth may not be as important as other factors in structuring the microbial communities of conditionally rare taxa.