On this page, you will find more information on our most abundant greenhouse OTUs. We will first describe our Top 10 Greenhouse OTUs and then we will look into the OTUs present in bromeliads in comparison to Nepenthes pitcher plants.

Top 10 Most Abundant OTUs

Figure 1: Top 10 OTUs SAR Composition


We selected our top 10 OTU’s based on the highest read numbers displayed in our data table. From this table, we noticed that half of our OTU’s are a part of the alveolate group (5), in comparison to the rhizaria (3) and stramenopile group (2). The majority of these alveolates are ciliates.


Figure 2: Greenhouse Top 10 OTUs


These are the top ten OTUs from our samples by occurrence and readnumber. OTU 11 has the highest occurrence (found in 67 samples out of 81) with 39443 reads. It is Viridiraptor sp., an algivore within Rhizaria. OTU 4 has the highest readnumber (131165) with an occurrence of 50. It is a Stichotrichia ciliate.


Figure 3: Readnumber vs. Occurrence of all OTUs


This is a plot of the readnumber and occurrence of all of our OTUs (not yet filtered for possible contamination). The colored dots are our top 10 OTUs by readnumber. The majority of our OTUs have occurrences less than 20 and readnumbers less than 1000.


Figure 4: Presence of Top 10 Greenhouse OTUs

This is the occurrence of each of the top 10 OTUs by readnumber in our pitcher (light green) vs. bromeliad samples (dark green). Certain OTUs dominate in bromeliads vs. pitchers. For example, OTU13 has a much higher presence in pitcher samples compared to bromeliad samples.


Chunk of code used to make bar plot. 
 #Data visualization comparing Pitchers and Bromeliads in one bar plot
 ## Creating new data frame using .csv file 
 Greenhouse_10_OTU <- read_csv("Greenhouse_10_OTU.CSV")
 Code to create bar plot 
 ggplot(data = Greenhouse_10_OTU, mapping = aes(x = reorder(OTU,Occurrences), y = Occurrences, fill = Sample)) +
 theme_classic()+
 xlab("OTU")+
 ylab("Number of Samples")+
 ggtitle(label="Presence of Top 10 OTUs in Greenhouse samples")+
 scale_fill_manual(values = c("#81ae64","#c7e78b"))+
 geom_col()


More Information on Top 10 OTUs


Samples are color-coded based on its SAR composition: stramenopiles (red), alveolates (blue), and rhizaria (yellow). Bmorpho is its morphology based on what’s in GenBank and Tmorpho is its morphology based on it’s placement on the phylogenetic tree. The arrows on these tables point towards the image of the organism that corresponds to each individual OTU.


OTUs in both Bromeliads and Pitchers


Figure 1: SAR Composition of the 153 OTU’s observed (Readnumbers)


After filtering out OTUs with readnumbers less than 100 and occurrences less than 5, we were left with 153 OTUs. Still, alveolates represent the highest proportion of OTUs.


Figure 2: SAR Composition of the 153 OTU’s observed (Occurrences)


By occurrence, alveolates are less dominant compared to stramenopiles and rhizaria than when splitting these clades by readnumber.


Figure 3: Readnumber vs Occurrences (DNA & RNA)

This scatterplot is comparing the read number vs. occurrence values of our OTU’s in log scale. It is also color coded by the type of sample it was found in, DNA (blue) or RNA (red). One main insight from this graph is how the OTU’s found in DNA samples seem to have higher read numbers in comparison to the OTUs found in RNA samples.


Figure 4: Split PCoA of Greenhouse Samples


This is a PCoA split by plant type, colored by month, and with point shape representing molecule type. There is no clear pattern by month or plant type. There are some clusters by molecule.


Chunk of code used to make PCoA. 
ordi <- ordinate(mergedtree, method = "PCoA", distance = "Unifrac", weighted = TRUE)
pcoa_pitcher = plot_ordination(mergedtree, ordi, color = "Month", shape = "Molecule", label = "Names")
facet_wrap(~ Plant_type)
#Print it
pcoa_pitcher + geom_point(size = 3)


Figure 5: PCoA of Greenhouse Samples


This figure is similar to the split PCoA shown above. The only difference is that this PCoA is color-coded by plant type and has its shape represented by molecule type. There does not seem to be any distinct pattern(s) between the different plant types, although, there does seem to be some clustering between the different molecule types.


Chunk of code used to make PCoA. 
ordi <- ordinate(mergedtree, method = "PCoA", distance = "Unifrac", weighted = TRUE)
pcoa_pitcher = plot_ordination(mergedtree, ordi, color = "Plant_type", shape = "Molecule", label = "Names")

#Print it
pcoa_pitcher + geom_point(size = 3)

Figure 6: Heatmap of Bromeliads vs Pitcher Samples


This is a heatmap split on the x-axis by bromeliad samples (red) and pitcher samples (orange), and on the y-axis by OTU readnumber (OTUs with highest readnumber on the bottom, lowest on the top). Most OTUs have low abundance within the samples (1-500 reads). There is also not a clear difference in OTU presence between the bromeliad and pitcher samples.


Chunk of code used to make heatmap. 
heatmap(d_matrix, Rowv=NA, Colv=NA, cexRow=0.5, cexCol=0.5, col= c("#ccffcc", "#66ff66", "#009933", "#3333ff", "#000033"))
legend(x="bottomright", legend=c("1-100", "101-500", "501-1500", "1500-6000",">6001"), fill=c("#ccffcc", "#66ff66", "#009933", "#3333ff", "#000033"))

OTUs in Nepenthes pitcher plants


Figure 1: Pitcher Plant Samples Rank of Abundance Curve


This is a rank abundance curve for only our pitcher samples. The x-axis is the number of OTUs, and the y-axis is the readnumber of each subsequent OTU. Pitcher DNA samples (furthest to the right) have the highest microbe abundance (P3A-DNA).


Figure 2: Pitcher Plant DNA vs RNA Rank of Abundance Curve


Seen more clearly here, the DNA samples (blue) contain the most OTUs and have the highest abundance. After the top 7 DNA samples, however, DNA and RNA show similar patterns of abundance.


OTUs in Bromeliads


Figure 1: Bromeliad Samples Rank of Abundance Curve


This is a rank of abundance curve for our bromeliad samples. The y-axis represents readnumbers while the x-axis represents the number of OTUs present. The sample that stood out to us the most was B2S-DNA since it has the highest abundance of microbes. Most samples only had OTUs with low readnumbers (less than 100 reads) after about 15 OTUs.


Figure 2: Bromeliad DNA vs RNA Rank of Abundance Curve


Similar to the pitcher plant rank of abundance curve, the bromeliad DNA samples (blue) also appear to have a higher abundance of OTUs when compared to the RNA samples.


All figures and tables presented on this website were made by Jailene and Hannah using R/RStudio, Google Sheets, Procreate, and Microsoft Excel.