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\section{Results}  To observe C use dynamics by the soil microbial community, we conducted a  nucleic acid SIP experiment wherein xylose or cellulose carried the isotopic  label, and, we assayed SSU rRNA gene content of CsCl gradient fractions using  high-throughput DNA sequencing technology. We set up three soil microcosm series.   Microcosms in each series were were amended with a C substrate mixture  that included cellulose and xylose. The C substrate mixture approximated  freshly degrading plant biomass. The same substrate mixture was added to microcosms  in each series, however, for each series except the control, one substrate  was substituted for its $^{13}$C counterpart. In one series cellulose was  $^{13}$C-labeled in another xylose was $^{13}$C-labeled and in the control  series no sustrates were $^{13}$C labeled. Microcosm amendments are shorthand identified  in the following figures by the following code: "13CXPS" refers to the  amendment with $^{13}$C-xylose (that is $^{13}$\textbf{C} \textbf{X}lose  \textbf{P}lant \textbf{S}imulant), "13CCPS" refers to the $^{13}$C-cellulose  amendment and "12CCPS" refers to the amendment that only contained $^{12}$C  substrates. Xylose or cellulose were chosen to carry the isotopic label to  contrast C assimilation for labile, soluble C (xylose) versus  insoluble, polymeric C (cellulose). 5.3 mg of C substrate mixture per gram  soil was added to each microcosm representing 18\% of the total soil C. The  mixture included 0.42 mg xylose-C and 0.88 mg cellulose-C g soil$^{-1}$.  Microcosms were harvested at days 1, 3, 7, 14 and 30 during a 30 day  incubation. $^{13}$C-xylose assimilation peaked immediately and tapered  over the 30 day incubation whereas $^{13}$C-cellulose assimilation peaked at  two weeks of (Figure~\ref{fig:ord}).  We sequenced SSU rRNA gene amplicons from a total of 277 CsCl gradient fractions from 14   CsCl gradients and 12 bulk microcosm DNA samples. The SSU rRNA gene data set contained 1,376,008   total sequences. The average number of sequences per sample was 3,816 (sd 3,629) and 265 samples   had over 1,000 sequences. We sequenced SSU rRNA gene amplicons from an average of 19.8 fractions  per CsCl gradient (sd 0.57). The average density between fractions was 0.0040 g mL$^{-1}$   The sequencing effort recoverd a total of 5,940 OTUs. 2,943 of the total  5,940 OTUs were observed in bulk samples. We observed 33 unique phylum and 340 unique genus  annotations.  \subsection{Soil microcosm microbial community changes with time}  Changes in the soil microcosm microbial community structure and membership  correlated with incubation time (Figure~\ref{fig:bulk_ord}B, p-value 0.23,  R$^{2}$ 0.63, Adonis test \citet{Anderson2001a}). The $^{13}$C composition  of the C-substrate addition did not significantly correlate with soil microcosm  community structure and membership (p-value 0.35). Additionally, bulk sample  beta diversity was significantly less than gradient fraction beta diversity  (p-value 0.003, \citet{Anderson2006}). Twenty-nine OTUs significantly changed  in relative abundance with time ("BH" adjusted p-value $<$ 0.10,  \citet{YBenjamini1995}). OTUs that significantly increased in relative  abundance with time included OTUs in the \textit{Verrucomicrobia},  \textit{Proteobacteria}, \textit{Planctomycetes}, \textit{Cyanobacteria},  \textit{Chloroflexi} and \textit{Acidobacteria}. OTUs that significantly  decreased in relative abundance with time included OTUs in the  \textit{Proteobacteria}, \textit{Firmicutes}, \textit{Bacteroidetes} and  \textit{Actinobacteria} (Figure~XX). \textit{Proteobacteria} was the only  phylum that had OTUs that significantly increased and OTUs that significantly  decreased in abundance with time. If sequences were grouped by taxonomic  annotations at the class level, only four classes significantly changed in  abundance, \textit{Bacilli} (decreased), \textit{Flavobacteria} (decreased),  \textit{Gammaproteobacteria} (decreased) and \textit{Herpetosiphonales}  (increased) (Figure~XX). Of the 29 OTUs that changed significantly in relative  abundance with time, 14 are labeled substrate responders (Figure~XX).  \subsection{OTUs that assimilated $^{13}$C from xylose}  Isotope incorporation by an OTU is revealed by enrichment of the OTU in heavy  CsCl gradient fractions containing $^{13}$C labeled DNA relative to heavy  fractions from control gradients containing no $^{13}$C labeled DNA. We refer  to OTUs that putatively incorporated $^{13}$C into DNA from an isotopically  labeled substrate as a substrate ``responder''. Within the first 7 days of  incubation 63\% on average of $^{13}$C-xylose was respired and only an  additional 6\% more was respired from day 7 to 30. At the end of the 30 day  incubation 30\% of the $^{13}$C from added xylose remained in the soils. The  $^{13}$C remaining in the soil from $^{13}$C-xylose addition was likely  stabilized by assimilation into microbial biomass and/or microbial conversion  into other forms of organic matter. It is also possible that some  $^{13}$C-xylose remains unavailable to microbes due to abiotic interactions in  soil \citep{Kalbitz_2000}.   At day 1, 84\% of $^{13}$C-xylose responsive OTUs belong to  \textit{Firmicutes}, 11\% to \textit{Proteobacteria} and 5\% to  \textit{Bacteroidetes}. \textit{Firmicutes} responders decreased to from 16  OTUs at day 1 to 1 OTU at day 3 while \textit{Bacteroidetes} responders  increased from 1 OTU at day 1 to 12 OTUs at day 3. The remaining day 3  responders are members of the \textit{Proteobacteria} (26\%) and the  \textit{Verrucomicrobia} (5\%). Day 7 responders were 53\%  \textit{Actinobacteria}, 40\% \textit{Proteobacteria}, and 7\%  \textit{Firmicutes}. The identities of $^{13}$C-xylose responders change with  time. The numerically dominant $^{13}$C-xylose responder phylum shifts from  \textit{Firmicutes} to \textit{Bacteroidetes} and then to  \textit{Actinobacteria} across days 1, 3 and 7 (Figure~\ref{fig:l2fc},  Figure~\ref{fig:xyl_count}).   All of the $^{13}$C-xylose responders in the \textit{Firmicutes} phylum are  closely related (at least 99\% sequence identity) to cultured isolates from  genera that are known to form endospores (Table~\ref{tab:xyl}). Each  $^{13}$C-xylose responder is closely related to isolates annotated as members  of \textit{Bacillus}, \textit{Paenibacillus} or \textit{Lysinibacillus}.  \textit{Bacteroidetes} $^{13}$C-xylose responders are predominantly closely  related to \textit{Flavobacterium} species (5 of 8 total responders)  (Table~\ref{tab:xyl}. Only one \textit{Bacteroidetes} $^{13}$C-xylose  responder is not closely related to a cultured isolate, ``OTU.183'' (closest  LTP BLAST hit, \textit{Chitinophaca sp.}, 89.5\% sequence identity,  Table~\ref{tab:xyl}). OTU.183 shares high sequence identity with environmental  clones derived from rhizosphere samples (accession AM158371, unpublished) and  the skin microbiome (accession JF219881, \citet{Kong_2012}). Other  \textit{Bacteroidetes} responders share high sequence identities with canonical  soil genera including \textit{Dyadobacer}, \textit{Solibius} and  \textit{Terrimonas}. Six of the 8 \textit{Actinobacteria} $^{13}$C-xylose  responders are in the \textit{Micrococcales} order. One $^{13}$C-xylose  responding \textit{Actinobacteria} OTU shares 100\% sequence identity with  \textit{Agromyces ramosus} (Table~\ref{tab:xyl}). \textit{A. ramosus} is a  known predatory bacterium but is not dependent on a host for growth in culture  \citep{16346402}. It is not possible to determine the specific origin of  assimilated $^{13}$C in a DNA-SIP experiment. $^{13}$C can be passed down  through trophic levels although heavy isotope representation in C pools  targeted by cross-feeders and predators would be diluted with depth into the  trophic cascade. It's possible, however, that the $^{13}$C labeled  \textit{Agromyces} OTU was assimilating $^{13}$C primarily by predation if the  \textit{Agromyces} OTU was selective enough with respect to its prey that it  primarily attacked $^{13}$C-xylose assimilating organisms.   \subsection{$^{13}$C-cellulose incorporating OTUs}   Only 2 and 5 OTUs were found to have incorporated $^{13}$C from  $^{13}$C-cellulose at days 3 and 7, respectively. At days 14 and 30, however,  42 and 39 OTUs were found to incorporate $^{13}$C from $^{13}$C-cellulose into  biomass. An average 16\% of the $^{13}$C-cellulose added was respired within  the first 7 days, 38\% by day 14, and 60\% by day 30. A \textit{Cellvibrio}  and \textit{Sandaracinaceae} OTU assimilated $^{13}$C from $^{13}$C-cellulose  at day 3. Day 7 $^{13}$C-cellulose responders included the same  \textit{Cellvibrio} responder as day 3, a \textit{Verrucomicrobia} OTU and  three \textit{Chloroflexi} OTUs. 50\% of Day 14 responders belong to  \textit{Proteobacteria} (66\% Alpha-, 19\% Gamma-, and 14\% Beta-) followed by  17\% \textit{Planctomycetes}, 14\% \textit{Verrucomicrobia}, 10\%  \textit{Chloroflexi}, 7\% \textit{Actinobacteria} and 2\% cyanobacteria.  \textit{Bacteroidetes} OTUs begin to incoporate $^{13}$C from cellulose at day  30 (13\% of day 30 responders). Other day 30 responding phyla include  \textit{Proteobacteria} (30\% of day 30 responders; 42\% Alpha-, 42\% Delta,  8\% Gamma-, and 8\% Beta-), \textit{Planctomycetes} (20\%),  \textit{Verrucomicrobia} (20\%), \textit{Chloroflexi} (13\%) and cyanobacteria  (3\%). \textit{Proteobacteria}, \textit{Verrucomicrobia}, and  \textit{Chloroflexi} had relatively high numbers of responders with  strong response across multiple time points (Figure~\ref{fig:l2fc}).  \par\textit{Proteobacteria} represent 46\% of all $^{13}$C-cellulose responding  OTUs identified. \textit{Cellvibrio} accounted for 3\% of all proteobacterial  $^{13}$C-cellulose responding OTUs detected. \textit{Cellvibrio} was one of the  first identified cellulose degrading bacteria and was originally described by  Winogradsky in 1929 who named it for its cellulose degrading abilities  \citep{boone2001bergeys}. All $^{13}$C-cellulose responding  \textit{Proteobacteria} share high sequence identity with 16S rRNA genes from  sequenced cultured isolates (Table~\ref{tab:cell}) except for ``OTU.442'' (best  cultured isolate match 92\% sequence identity in the \textit{Chrondomyces}  genus, Table~\ref{tab:cell}) and ``OTU.663'' (best cultured isolate match  outside \textit{Proteobacteria} entirely, \textit{Clostridium} genus, 89\%  sequence identity, Table~\ref{tab:cell}). Some \textit{Proteobacteria}  responders share high sequence identity with type strains for genera known to  possess cellulose degraders including \textit{Rhizobium}, \textit{Devosia},  \textit{Stenotrophomonas} and \textit{Cellvibrio}. One \textit{Proteobacteria}  OTU shares high sequence identity with a \textit{Brevundimonas} cultured  isolate. \textit{Brevundimonas} has not previously been identified as a  cellulose degrader, but has been shown to degrade cellouronic acid, an oxidized  form of cellulose \citep{Tavernier_2008}.