Ashley Campbell Fleshing out KDE  almost 10 years ago

Commit id: bed592c03e5e623f29fcab59e885a46710b103ca

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For the \textsuperscript{13}C-cellulose treatment only one Proteobacteria passes the 'responder' criteria at day 3 and two OTUs (Proteobacteria and Chloroflexi) at day 7. By day 14, responders are detected in Proteobacteria, Verrucomicrobia, Chloroflexi, Planctomycetes, and Actinobacteria. The same responders are detected at day 30 with the exception of Actinobacteria and the addition of Bacteriodetes. These trends are more readily observable in the bulk community abundances than discerned with xylose responders. This is likely due to the low abundance of these phlya, where changes in bulk community abundance are easier to discern. Comparatively, phlya of consistently high abundance mask response changes unless they present changes of grand proportions.   Kernel density estimates (KDE) of the CsCl density shifts measured for responders  in \textsuperscript{13}C-xylose were compared to KDE those  of \textsuperscript{13}C-cellulose responders  (Fig 3A). In general, xylose An organism with 100\% 13C-labeling of DNA would exhibit a density shift of 0.04gmL\textsuperscript{-1}. Xylose  utilizers have a smaller density shift (<0.02 mg/L) gmL\textsuperscript{-1})  than cellulose utilizers (0.005-0.03), (0.005-0.03 gmL\textsuperscript{-1}),  with few exceptions. This suggests a greater substrate specificity among cellulose degraders than xylose degraders. Partial 13C-labeling (<0.04gmL\textsuperscript{-1} density shift) could be a result of various lifestyles ('trophic strategy' better word choice?) such as assimilation of C from multiple substrates (both \textsuperscript{12}C and \textsuperscript{13}C in this instance) or 13C-label dilution as it cascades through trophic levels via consumption of 13C-labeled organisms or their waste products.  The vast majority of xylose degraders are found at a lower rank abundance than cellulose degraders; which fall among the rare taxa in the tail of the rank abundance curve (Fig 3B). This suggests that taxa important to C-cycling may be difficult or unable to detect in bulk community sequencing efforts. This supports evidence of functionally important taxa being in the rare biosphere. Phylogenetic tree demonstrates responders in our data set for both xylose and cellulose (Fig 4). Depicts the there are very few OTUs that utilize both cellulose and xylose.