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biofilm communities. Our results suggest that C subsidies increased  bacterial biomass in both plankton and biofilm communities as predicted. Carbon  subsidies also resulted in decreased algal biomass in the plankton community,  but there was no signifcant significant  change in algal biomass of the biofilm communities among resource treatments. The changes in the biomass pool size that did occurr occur  were consistent with changing relationships (commensal to competitive) between  the autotrophic and heterotrophic components of the plankton communities but  not neccessarily necessarily  of the biofilm communities. \subsection{Biofilm and Plankton Alpha and Beta Diversity}   Beyond changes in the biomass pool size of each community we explored how 
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structure of the bacterial biofilm and plankton communities were more similar  within a lifestyle (plankton vs. biofilm) than within a resource treatment.  However, for the bacteria in the highest C:P treatment (C:P = 500) both  membership and structure of biofilm and planktonic communities at day 17 were more similar to each other than to communities from other treatments (Figure~\ref{fig:pcoa}). Third, C subsides acted differently on the algal and bacteria communities. Specifically while the highest level of C subsidies (C:P = 500) resulted in a merging of membership in the bacterioplankton and bacterial biofilm communities the same merging of membership was not observed for the algal biofilm and plankton communities which had distinct membership in all treatments.   We propose two potential mechanisms that could result in the increased  diversity of the biofilm communities relative to the planktonic communities. 
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community (i.e. mass effects) but also select and enrich (i.e. species sorting)   the lease abundant members of the planktonic community resulting in a higher level  of detectable alpha diversity.  The second mechanism would result if the biofilm enivronment environment  represented a more diverse habitat including sharply delineated oxygen, nutrient and pH gradients  that are not present in the planktonic environment. In this case the more  diverse habitat would be able to support a more diverse community due to an  abundance of additional environmental habitats (i.e. niches). We evaluated the  first mechanism by comparing membership among the plankton samples taken 9 days  apart (t=8 and t=17). While bacterioplankton communities were not indentical identical  between the time points (Figure~\ref{fig:pcoa}), communities within a treatment  were more similar to each other between timepoints than any other  bacterioplankton community (treatment or timepoint). In addition, the control 
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relative abundance of the populations within each community. Second, an  analysis of the OTU relative abundance in biofilm and planktonic libraries  where OTUs are sorted by planktonic sample rank (Figure~\ref{fig:rank_abund}) shows  that the least abundant members of the plankton community were rountinely routinely  highly abundant within the biofilm community. This was true for both algal and  bacterial communities, at all treatment levels and both timepoints. While we  did not (could not) specifically measure niche diversity within the biofilm 
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reported that planktonic diversity was significantly higher relative to biofilm  diversity (the opposite of what we found in our study). Given the differences  in the source of the planktonic community among studies, this result is not  suprising. surprising.  While biofilm communities were establishsed established  on glass beads in \citet{22237539} and glass slides (this study) over a similar time period (~21  days, \citet{22237539} and ~17 days this study) the origin of the planktonic  community in each study was very different. The \citet{22237539} study was 
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depending on how hydrologic pathways differed among precipitation events. In  this study the source community was a marine intake located approximately  200m from the shore during July when communities are more stable over the 17  day perios period  of the incubation. A separate study conducted in alpine and sub-alpine streams of the Rocky Mountains clearly showed that stream plankton  communities reflected localized precipitation events and could be traced  largely to sources of soil communities of drainages within the watershed 
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appears, however, that sample-wise bacterial biofilm rarefaction curves may  exceed the integrated planktonic curve upon extrapolation and most exceed the  integrated planktonic curve at sampling depths where data is present for the  biofilm and itegrated integrated  planktonic library (Figure~\ref{fig:integ_rarefaction}). This result is consistent with our conclusion that temporal heterogenetity heterogeneity  in the plankton was not sufficient to  explain the higher diversity in the biofilm sample but would explain the  relative differences between planktonic and biofilm diversity found in Besemer  et al. (2012) \citet{22237539}}  compared to this study. In addition, for this study, it is important to note that biofilm community  richness peaked at the intermediate treatment (C:P = 100) and appeared to 
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has been shown for many ecosystems and communities both microbial and  otherwise. However, as with other experiments with this result our experimental  design did not allow us to tell whether resources drove productivity that drove  changes in diversity or whether resoruces resources  drove diversity which altered productivity. Rather we note that, as diversity decreased in the highest C  treatment bacterioplankton and biofilm membership became increasingly  similar. This suggests that enviornments environments  that contain high amounts of labile C selected for fewer dominant taxa that came to dominate the biofilm  community, overwhelming the species sorting mechanisms that appeared to  dominate biofilm community assembly in all other treatments. Similarly, while 
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(Figure~\ref{fig:microscope}) it is possible that more abundant planktonic  cells were more readily incorporated into biofilms due both to increased  "stickiness" of the planktonic cells as well as the biofilm itself. While we  did not observe floculating flocculating  DOC which has been shown to dominate high DOC environments in nature, we did measure a substanial substantial  increase in DOC in the C:P = 500 treatment which was more than 2-fold higher than any of the other  treatments. Thus additional adhesion of the plankton and the biofilm may also  explain the merging of the planktonic and biofilm bacterial membership in the  highest C treatment.   \subsection{Lifestype \subsection{Lifestyle  (biofilm or planktonic) Enriched OTUs} There are only a few studies that attempt to compare biofilm community  composition and the overlyng overlying  planktonic community \citep{Besemer_2007, 22237539, Jackson_2001, Lyautey_2005}. Those studies illustrate community  composition among the two habitats are unique with very few taxa found in both.  This is consistent with our findings in this experimental system with a natural  marine planktonic source commmunity. community.  In addition, our study also evaluated algal community composition which showed a similar result suggesting that both  the algal and bacterial biofilm communities form from phylogenetically unique  organisms that exist in low abundance in surrounding habitat (i.e. the 
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bacterial OTUs tended to have members in that were enriched in both the  plankton and the biofilm suggesting the phylogenetic coherence of lifestyle is  not captured at the level of Order. It should be noted however that taxonomic  annotations in reference databasees databases  and therefore environmental sequence collections show little equivalency in phylogenetic breadth between groups at  the same taxonomic rank \citep{Schloss_2011}. Unfortunatley, Unfortunately,  at higher taxonomic resolution (e.g. Genus-level), groups did not possess a sufficient  number of OTUs to evaluate coherence between taxonomic annotation and  lifestyle. Similar to the richness results, we found the 
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\subsection{Conclusion}  In summary this study shows mechanistic links between large scale community  level dynamics and the underlying constituent populations that compose them. We  found that autrotrophic autotrophic  pools and heterotrophic pools responded differently to ammendments amendments  of labile C as hypothesized. Notably while C ammendments amendments  altered both pool size and membership of the bacterial communities we did not  see similar dynamics within the algal communities. Planktonic algae decreased  in response to C amendments presumably in response to increased  competition from a larger bacterial community, however there was not a  similar decrease in biofilm algal community. In addition membership of the  algal communities betweeen between  the plankton and biofilm lifestyles did not become more similar in the algae as it did for the bacteria in the highest C  treatment. Consistent with a growing body of work our results suggest that  complex environmental biofilms are a unique microbial community that form from  taxa (both heterotrophs and autotrophs alike) that are found in low abundance  in the neighboring communities. This membership was affected by resource  ammendements amendments  for heterotrophic but not autotrophic microbes and then only in the most extreme resource environment. This suggests that lifestyle is a major  division among environmental microorganisms and although biofilm forming  microbes must travel in planktonic form at some point - reproductive success  and metabolic contributions to biogeohemical biogeochemical  processes comes from those taxa primarily if not exclusively while they are part of a biofilm. Our results point to lifestyle (planktonic or biofilm) as an   important trait that explains a portion of the exceptional diversity found in  snapshots used to characterize environmental microbial communities in space and  diff --git a/figures/HighLow.l2fc/HighLow.l2fc.pdf b/figures/HighLow.l2fc/HighLow.l2fc.pdf  deleted file mode 100644  index fbc7cd9..0000000  Binary files a/figures/HighLow.l2fc/HighLow.l2fc.pdf and /dev/null differ diff --git a/figures/HighLow.l2fc/caption.tex b/figures/HighLow.l2fc/caption.tex  deleted file mode 100644  index 08ef7d3..0000000  --- a/figures/HighLow.l2fc/caption.tex  +++ /dev/null 
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\textbf{Figure 7}  diff --git a/figures/HighLow.l2fc/size.tex b/figures/HighLow.l2fc/size.tex  deleted file mode 100644  index c5f9d92..0000000  --- a/figures/HighLow.l2fc/size.tex  +++ /dev/null 
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Principal coordinates ordination of bray-curtis distances for 23S rRNA plastid libraries and 16S rRNA gene libraries. OTU points are weighted pricipal coordinate averages (weights are relative abundace values in each sample) and the variance along each pricipal axis is expanded to match the site variance. Point annotations denote the amended C:P ratio for the mesocosm from which each sample was derived.  diff --git a/figures/biplot_combined/biplot_combined.pdf b/figures/biplot_combined/biplot_combined.pdf  deleted file mode 100644  index b3c5ae5..0000000  Binary files a/figures/biplot_combined/biplot_combined.pdf and /dev/null differ diff --git a/figures/biplot_combined/size.tex b/figures/biplot_combined/size.tex  deleted file mode 100644  index 5d07749..0000000  --- a/figures/biplot_combined/size.tex  +++ /dev/null 
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\textbf{Figure 5 }Principal Principal  coordinates ordination of bray-curtis distances for 23S rRNA plastid libraries and 16S rRNA gene libraries. OTU points are weighted pricipal principal  coordinate averages (weights are relative abundace abundance  values in each sample) and the variance along each pricipal principal  axis is expanded to match the site variance. Point annotations denote the amended C:P ratio for the mesocosm from which each sample was derived.test  diff --git a/figures/combined_rarefaction/caption.tex b/figures/combined_rarefaction/caption.tex  deleted file mode 100644  index 9588827..0000000  --- a/figures/combined_rarefaction/caption.tex  +++ /dev/null 
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Rarefaction curves for each biofilm versus planktonic sequence library (SSU rRNA genes for bacteria, LSU rRNA plastid genes for algae). Samples from the same time and treatment are shown in the same panel. Panel strip text at top denotes time (15 or 24 days) and whether the column is for bacterial or algal sequence libraries. Panel strip text on the right denotes the amended C:P ratio for the mesocosm.   diff --git a/figures/combined_rarefaction/combined_rarefaction.pdf b/figures/combined_rarefaction/combined_rarefaction.pdf  deleted file mode 100644  index c8dbac1..0000000  Binary files a/figures/combined_rarefaction/combined_rarefaction.pdf and /dev/null differ diff --git a/figures/combined_rarefaction/combined_rarefaction.png b/figures/combined_rarefaction/combined_rarefaction.png  deleted file mode 100644  index 6870901..0000000  Binary files a/figures/combined_rarefaction/combined_rarefaction.png and /dev/null differ diff --git a/figures/combined_rarefaction/size.tex b/figures/combined_rarefaction/size.tex  deleted file mode 100644  index c5f9d92..0000000  --- a/figures/combined_rarefaction/size.tex  +++ /dev/null 
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\textbf{Figure 4}  diff --git a/figures/combined_rarefaction1/combined_rarefaction1.pdf b/figures/combined_rarefaction1/combined_rarefaction1.pdf  deleted file mode 100644  index c8dbac1..0000000  Binary files a/figures/combined_rarefaction1/combined_rarefaction1.pdf and /dev/null differ diff --git a/figures/combined_rarefaction1/size.tex b/figures/combined_rarefaction1/size.tex  deleted file mode 100644  index 5d07749..0000000  --- a/figures/combined_rarefaction1/size.tex  +++ /dev/null 
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\textbf{Figure 4}  diff --git a/figures/combined_rarefaction2/combined_rarefaction2.pdf b/figures/combined_rarefaction2/combined_rarefaction2.pdf  deleted file mode 100644  index 4cc0668..0000000  Binary files a/figures/combined_rarefaction2/combined_rarefaction2.pdf and /dev/null differ diff --git a/figures/combined_rarefaction2/size.tex b/figures/combined_rarefaction2/size.tex  deleted file mode 100644  index 240a5d7..0000000  --- a/figures/combined_rarefaction2/size.tex  +++ /dev/null 
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Rarefaction curves for all biofilm versus plankton libraries. Each panel represents a single C:P treament treatment  and time point. Richness is greater for all planktonic communities when compared to corresponding biofilm communities. diff --git a/figures/conceptualmodel/caption.tex b/figures/conceptualmodel/caption.tex  index 600bc36..818bd2e 100644  --- a/figures/conceptualmodel/caption.tex  +++ b/figures/conceptualmodel/caption.tex 
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\textbf{Figure 1} Carbon subsidies in the form of glucose alleviate the dependence of heterotrophic bactria bacteria  on algal derived carbon C  (C) exudates. This should result in an increase in resource space and biomass for bacteria and a decrease in resource space and biomass for algae due to increased competition for phosphorus (P). We hypothesized that this predicted change in biomass pool size of these two grouops groups  will result in changes in the plankton community composition of both groups that will propogate propagate  to to the composition of biofilm communities for both groups. diff --git a/figures/integrated_rarefaction/caption.tex b/figures/integrated_rarefaction/caption.tex  index 01ecdf4..c22a934 100644  --- a/figures/integrated_rarefaction/caption.tex  +++ b/figures/integrated_rarefaction/caption.tex 
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\textbf{Figure 8} Rarefaction plots for all samples. Planktonic libraries have been integrated such that the count for each OTU is the sum of counts across all samples. diff --git a/figures/l2fc_pval_all/caption.tex b/figures/l2fc_pval_all/caption.tex  deleted file mode 100644  index e5fabcf..0000000  --- a/figures/l2fc_pval_all/caption.tex  +++ /dev/null 
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\textbf{Figure 6}  diff --git a/figures/l2fc_pval_all/l2fc_pval_all.pdf b/figures/l2fc_pval_all/l2fc_pval_all.pdf  deleted file mode 100644  index d95553c..0000000  Binary files a/figures/l2fc_pval_all/l2fc_pval_all.pdf and /dev/null differ diff --git a/figures/l2fc_pval_all/size.tex b/figures/l2fc_pval_all/size.tex  deleted file mode 100644  index 6b423c5..0000000  --- a/figures/l2fc_pval_all/size.tex  +++ /dev/null 
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\textbf{Figure 6} $log_2$ of environment type lifestyle  OTU proportion  mean ratios (bioflm (biofilm  or plankton) and corresponding, adjusted p-values. Each point represents one OTU proportion  mean ratio and points are grouped along the x-axis by Order. Outlined points have adjusted p-values below a false discovery rate of 0.10. diff --git a/figures/lightmicroscopy.002/caption.tex b/figures/lightmicroscopy.002/caption.tex  index a8b67ed..83b3197 100644  --- a/figures/lightmicroscopy.002/caption.tex  +++ b/figures/lightmicroscopy.002/caption.tex 
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\textbf{Figure 3} The structure (density of cells and thickness of biofilm) and the amount of EPS (cloudy material) increased with increasing carbon C  subsidies from the control to the highest carbon C  treatment (C:P=500). diff --git a/figures/pool size/caption.tex b/figures/pool size/caption.tex  deleted file mode 100644  index 1079641..0000000  --- a/figures/pool size/caption.tex  +++ /dev/null 
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\textbf{Figure 2} Increases in carbon resulted in decreases in A) planktonic algal biomass (estiated as Chl \textit{a} but B) not algal biomass present in the biofilm \textit{a} in each. In contrast both C) biofilm total biomass and D) number of planktonic bacterial cells increased with increasing carbon subsidies. Responses in treatments separated by different letters were statistically different from one another (p<0.05) as was the highest C:P treatment for planktonic bacterial abundance compared to the the control or the C:P = 10 treatment (p<0.05). The bacterial abudance sample for the C:P = 100 treatment was lost before analysis and is therfore not reported in panel d.  diff --git a/figures/pool size/size.tex b/figures/pool size/size.tex  deleted file mode 100644  index 2fcf78b..0000000  --- a/figures/pool size/size.tex  +++ /dev/null 
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Increases in C resulted in decreases in A) planktonic algal biomass (estimated  as Chl \textit{a} but B) not algal biomass present in the biofilm \textit{a} in  each. In contrast both C) biofilm total biomass and D) number of planktonic  bacterial cells increased with increasing C subsidies. Responses in treatments  separated by different letters were statistically different from one another  (p<0.05) as was the highest C:P treatment for planktonic bacterial abundance  compared to the control or the C:P = 10 treatment (p<0.05). The bacterial  abundance sample for the C:P = 100 treatment was lost before analysis and is  therefore not reported in panel d.  diff --git a/figures/combined_rarefaction4/size.tex b/figures/pool_size/size.tex  similarity index 100%  rename from figures/combined_rarefaction4/size.tex  rename to figures/pool_size/size.tex  diff --git a/figures/rank_abund/caption.tex b/figures/rank_abund/caption.tex  deleted file mode 100644  index 08ef7d3..0000000  --- a/figures/rank_abund/caption.tex  +++ /dev/null 
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\textbf{Figure 7} Rank abundance plots. Each panel represents a single time point and C:P. The "rank" of each OTU is based on planktonic sample relative abundance. Each position along the x-axis represents a single OTU. Both the x and y axes are scaled logarithmically.test  diff --git a/figures/rank_abund_shape/caption.tex b/figures/rank_abund_shape/caption.tex  index 60baa8a..3a5fb74 100644  --- a/figures/rank_abund_shape/caption.tex  +++ b/figures/rank_abund_shape/caption.tex 
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\textbf{Figure 9} Rank abundance plots for all date-amendment combinations. diff --git a/figures/rank_abund_shape1/caption.tex b/figures/rank_abund_shape1/caption.tex  deleted file mode 100644  index a8a1b0c..0000000  --- a/figures/rank_abund_shape1/caption.tex  +++ /dev/null 
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\textbf{Table 1}  diff --git a/figures/table1/size.tex b/figures/table1/size.tex  deleted file mode 100644  index 2fcf78b..0000000  --- a/figures/table1/size.tex  +++ /dev/null 
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