Ashley Campbell edited Results & Discussion.tex  about 10 years ago

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\section{Results and Discussion}  \cite{Folsom_2014}  With the rapid advancement and declining costs of high throughput sequencing, it has become increasingly easy to probe microbial communities. In this study, we couple stable-isotope probing with 454 pyrosequencing in order to better understand organic matter decomposition dynamics as a function of soil microbial community C utilization. We ran a temporal series of parallel microcosms and measured the changes in the microbial community as result of the addition of a complex carbon mixture using 454 pyrosequencing of the bulk microbial community and fractions from SIP gradient fractionation (Fig. S1). Overall, changes in microbial community composition over time are consistent with C decomposition being accompanied by a microbial community succession. Analysis of the sequenced bulk community DNA demonstrates (insert taxa here) as the most dominant taxa at days 1, 3, and 7 followed by a transition to a (insert taxa here) dominated community at days 14 and 30. Most abundant OTUs at earlier time points were most closely related to members of Bacteriodetes, Actinomycetes, and Proteobacteria. Abundant OTUs of later time points were most closely related to members of Chloroflexi, Proteobacteria, and Verrucomicrobia. The rank abundance of the community fluctuates minimally over time (Fig S2A) accompanied with temporally associated community shifts (FigS2B).   Twenty fractions from a cesium chloride gradient fractionation for each treatment at each time point were sequenced (Fig. S1). Using NMDS analysis from weighted unifrac distances the relationship between all buoyant densities from all treatments and time points are plotted (Fig 1). \textsuperscript{13}C-labeled organisms are expected be to found in the higher buoyant density fractions. Each point on the NMDS represents the microbial community from a single fraction where the size of the point is representative of the density of that fraction and the colors represent the treatments (Fig1A) or days (Fig1B). The high density fractions (1.73-1.74...figure out exact densities) that are differentiating from the control along NMDS2 correspond to fractions that contain \textsuperscript{13}C-labeled OTUs (herein called 'responders'). The differential separation of high density fractions in the \textsuperscript{13}C-xylose treatment compared to the \textsuperscript{13}C-cellulose treatment is indicative of a difference in the responders for each of the substrates (Fig 1A). This data also presents an observable time signature of responders at days 1,3, and 7 for the xylose treatment and days 14 and 30 for the cellulose treatment (Fig1B). This demonstrates that different microbial community members are responsible for the consumption of these two different substrates and that xylose is consumed quickly, whereas, cellulose decomposition takes longer. This supports the hypothesis of a microbial community succession during the decomposition process. Furthermore, this demonstrates the sensitivity of this technique by being able to detect \textsuperscript{13}C-label incorporation in samples with low C additions (blah mg g\textsuperscript{-1} soil).