Fig 1.
Average relative abundances of bacterial families in the oyster-related microbiomes, classified by different reference databases.
Families with ≥ 1% relative abundance in samples are shown. Shell microbiome consists of shell (live) and shell (only) treatments.
Table 1.
Summary statistics of 16S rRNA gene amplicon sequencing for oyster-related microbiomes.
Fig 2.
Principal coordinate analysis (PCoA) of oyster-related microbiomes.
PCoA based on 16S rRNA gene sequences using Bray-Curtis similarity matrix.
Fig 3.
Predicted average relative abundances of denitrification genes by paprica for oyster-related microbiomes.
Shell microbiome includes shell (live) and shell (only) treatments. Each full circle represents a relative abundance of 26.1%.
Fig 4.
Predicted relative abundances of genes nosZI and nosZII by paprica in oyster-related microbiomes.
Shell microbiome includes both shell (live) and shell (only) treatments.
Fig 5.
N2 flux measurements from oysters, shell only, and sediment treatments using a continuous flow through design.
For each treatment n = 3 and error bars represent ± s.d. (*) significance p < 0.05.
Fig 6.
Average predicted relative abundances of total (A) nosZ, (B) nosZI, and (C) nosZII by paprica for oyster-related microbiomes.
Digestive gland combined with shell (live) to form oyster microbiome. Shell (only) forms shell microbiome. For each treatment n = 3 and error bars represent ± s.d.
Fig 7.
Linear regression comparing predicted and quantified relative abundances of nosZI genes for shell (live), shell (only) and sediment microbiomes.
Predicted relative abundances based on paprica inferred nosZI gene abundances relative to 16S gene abundances. Quantified relative abundances based on qPCR of nosZI gene copy numbers relative to 16S gene copy numbers.