Ashley Campbell phylum section  over 9 years ago

Commit id: 467299112dcdf2c978d5e9aa0d41bbfb6ec3e8e9

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Most xylose responders are found at higher rank abundances than cellulose responders which fall among the rare taxa in the tail of the RA curve (Fig 3B). This demonstrates that many taxa important to C-cycling are present in the rare biosphere and may be difficult or unable to detect in bulk community sequencing efforts. Responders of xylose or cellulose are wide spread across 7 phyla (Fig 4). There are very few OTUs that utilize both cellulose and xylose (should put in a number of how many OTUs utilize both over how many responders total there were), however, at the phyla level many phylum had responders for both xylose and cellulose.  \textbf{Carbon substrate utilization is inconsistent within phylum.} Dynamics patterns of \textsuperscript{13}C-assimilation from xylose and cellulose occur at discrete, fine-scale taxonomic units (Figure 4).  More often than not we see ecological functionality assigned at the phylum level (refs). It has been proposed that the microbial community functionality responsible for soil C cycling appear at the level of phlya rather than species/genera \cite{Schimel_2012}. However, based on our evidence of clade or single taxa level responses for xylose and cellulose utilization, assigning phylum level functionality is not an accurate depiction of soil C utilization. Phylum level assignment conventions could in part be due to limitations in finer scale taxonomic identifications or methodological limitations (ie sequencing depth). In this study, we have identified Actinobacteria responders for both substrates with a peak shift of ~0.036 gmL\textsuperscript{-1} for cellulose and ~x gmL\textsuperscript{-1} for xylose, suggesting a strong substrate specificity (Figures Sx and Sz - the substrate utilization charts). Albeit, there are no OTUs within Actinobacteria that responded to both xylose (Microbacteriaceae, Micrococcaceae, Cellulomonadaceae, Nakamurellaceae, Promicromonosporaceae, and Geodermatophilaceae) and cellulose (Streptomycetaceae and Pseudonocardiaceae). This information may suggest that while Actinobacteria exhibit an ability to utilize an array of carbon substrates, substrate use may be more clade specific and not widespread throughout the phylum (Figure 4). In the same vein, we identified Bacteroidetes responders for both substrates, yet, at a finer taxonomic resolution there is a clear differential response for xylose (Flavobacteriaceae and Chitinophagaceae) and cellulose (Cytophagaceae). Disagreeing correlations of phylum level abundance associated with C availability has been the source of debate for the role of Bacteroidetes in the degradation process \cite{Fierer_2007,Rui_2009,Sharp_2000,L_pez_Lozano_2013,Bastian_2009}. Our results would suggest that both perspectives are correct at a phylum level, but highlights the need of greater resolution to capture the subtleties of substrate utilization.