Ashley Campbell phylum level section  over 9 years ago

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\textbf{Carbon substrate utilization is inconsistent within phylum.} 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 to lack of sequencing resolution as seen here with many responders present in the rarer ranks (Figure 3B).   In this study, we have identifiedBacteroidetes responders for both xylose and cellulosedifferential response of taxa within Bacteroidetes could be the cause of debate between the correlation of phylum level abundance associated with C availability \cite{Fierer_2007,Rui_2009,Sharp_2000,L_pez_Lozano_2013,Bastian_2009}. For Actinobacteria, genomic analysis has revealed the ability to utilize a diverse array of polysaccharides which has been attributed to their resilience to stressful soil conditions \cite{Trivedi_2013}. Despite this versatile ability, they have also been demonstrated to possess high affinity transporters for specific substrates \cite{Trivedi_2013}. In this study,  Actinobacteriahad  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. cellulose (Streptomycetaceae and Pseudonocardiaceae).  This information may suggest that while Actinobacteria exhibit an ability to utilize an array of carbon substrates, substrate specificity use  may be more clade specificfor certain substrates  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). could be the cause of debate between the correlation of phylum level abundance associated with C availability \cite{Fierer_2007,Rui_2009,Sharp_2000,L_pez_Lozano_2013,Bastian_2009}.  Whole phylum responses were not detected for xylose or cellulose yet utilization of these substrates spanned many phylogenetically diverse groups. However, substrate utilization within each phylum was demonstrated at the clade or single taxa level. In a study that amended forest soils with single C substrates in the presence of 3-bromodeoxyuridine (BrdU), they determined that more than 500 taxa responded to labile C but occured predominantly in two phlya, Proteobacteria and Actinobacteria \cite{Goldfarb_2011}. On the other hand, the soils amended with more recalcitrant C such as cellulose and lignin were noted for spanning eight phyla, but were limited to a small number of taxa within each of those phyla that were responders \cite{Goldfarb_2011}. It has previously been suggested that all taxa within a phylum are unlikely to share ecological characteristics \cite{Fierer_2007}, and furthermore, within a species population \cite{Choudoir_2012,Preheim_2011,Hunt_2008}. Habitat traits of coastal Vibrio isolates were mapped onto microbial phylogeny revealing discrete ecological populations based on seasonal occurrence and particulate size fractionation \cite{Preheim_2011,Hunt_2008}. These data would suggest that portraying the response of a few OTUs or clades as a phylum level response would be overreaching.