Chuck Pepe-Ranney edited Results.tex  almost 10 years ago

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\subsubsection{Alpha diversity}  Alpha diversity in all treatments for both the plankton and the biofilm communities was visualized using rarefaction curves. Rarefaction curves show bacterial OTU richness in the 16S rRNA gene sequence surveys was consistently higher than planktonic counterparts. This trend was also true for the 23S libraries (Figure 1). The biofilm communities with the highest C:P treatment (500) had fewer total OTUs than any of the other treatments (F1).  \subsubsection{Community membership: membership,  biofilm versus plankton} Membership between the bacterial plankton and biofilm communities was notably different for all treatments except for the highest carbon treatment where the plankton and biofilm communities were more similar to each other than any other community and begin to resemble each other more over time (F2, F3). Algal plankton and biofilm communities were also composed of different taxa with no comparable similarities among algal communities in the highest carbon treatment as was observed for the bacterial communities(F2).  In bacterial libraries, sequences were distributed into 636 total OTUs. 57\% of quality controlled sequences fell into the top 25 OTUs in order of decreasing sum of relative abundance across all samples. The most differentially abundant OTUs between biofilm and planktonic bacterial 16S libraries fell into the Actinobacteria, Bacteroidetes and Proteobacteria. Highest absolute log$_{2}$ fold change ratios were found in planktonic versus biofilm comparisons which is consistent with the increased alpha diversity in biofilm samples. Sequence counts are spread across greater diversty in biofilm libraries as comparted to planktonic. Of the top five OTUs ordered by absolute log$_{2}$ fold change for planktonic versus comparison one is annotated as in the Bacteroidetes, two Gammaproteobacteria, one Betaproteobacteria and one Alphaproteobacteria. Only three OTU centroid sequences for highly differentially abundant bacterial 16S OTUs among the top 20 OTUS ordered by absolute log$_{2}$ fold change in biofilm versus planctonic samples share high sequence identity with cultured isolates (Table 1).  The biofilm versus planktonic grouping is statistically significant by the adonis test \cite{Anderson_2001} for both the bacterial and algal libraries(p-values 0.006 and 0.001, respectively). The environment type (biofilm or plankton) vector represents 18\% and 36\% of variance for pairwise sample distances in bacterial and algal libraries, respectively.   \subsubsection(Community membership: high carbon)  pass