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\section{Discussion}
\subsection{Biomass Pool Size}
The goal of this study was to evaluate how changes in resource stoichiometry
affected the biomass pool size, membership and structure of planktonic and
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 significant change in algal biomass of the biofilm communities among
resource treatments. The changes in the biomass pool size that did occur were
consistent with changing relationships (commensal to competitive) between the
autotrophic and heterotrophic components of the plankton communities but not
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
shifts in resource C:P affected a) the membership and structure of each
community, and b) the recruitment of plankton during biofilm community
...
understanding the assembly of aquatic biofilms. First, biofilm community
richness was consistently higher than planktonic community richness
(Figure~\ref{fig:rarefaction}). Second, for the control, C:P = 10 and C:P = 100
resource treatments the membership and structure of the bacterial biofilm and
plankton communities were more similar within a lifestyle (plankton
vs. versus
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.
First, it is possible that the planktonic community composition of our flow
through incubators was dynamic in time. In this case the biofilm community
would represent a temporally integrated sample of the planktonic organisms
moving through the reactor resulting in higher apparent alpha diversity (i.e.
mass effects would be the dominant assembly mechanism). Second, the biofilm
environment may disproportionately enrich for the least abundant members of the
of the planktonic community. In this case it is probable that the biofilm would
incorporate the most abundant members from the planktonic 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 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 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 and two lowest C treatments (C:P=10 and C:P=100)
separated completely from biofilm communities in principle coordinate space
(Bray-Curtis distance metric). This suggests that the biofilm community was not
integrating variable bacterioplankton community membership, but rather
selecting for a unique community that was composed of distinct populations when
compared to the most abundant members of the plankton community. As noted
above, in the highest C treatment (C:P = 500) the bacterial biofilm and
plankton community membership had significant overlap at the final timepoint
(Figure~\ref{fig:pcoa}). However, bacterioplankton membership for the highest C
treatment among timepoints (8 and 17 days) were also qualitatively as similar
to each other as any other community. Thus, variable planktonic community
...
of the \textit{in situ} resource conditions were sufficient to alter the
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 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
...
community composition and biofilm formation on glass beads placed for three
weeks in three boreal freshwater streams \citep{22237539}. While that study
system is markedly different than our study, the analyses and questions
addressed in each study were sufficiently similar to merit comparison.
\citet{22237539} concluded that the biofilm community membership was most
likely driven by species sorting over mass effects. This is consistent with
what we report here. However, in the \citet{22237539} study the authors
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conducted in three boreal streams during snow melt when connectivity between
the terrestrial and aquatic habitats was high and potentially highly variable
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
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 \citep{22626459}. While
planktonic communities in lake ecosystems can be linked to soil communities in
the watershed, as residence time of the system slows the relative influence of
species sorting increases. Thus, in headwater ecosystems stream plankton
communities can often be composed primarily of soil organisms \citep{22378536}.
In addition to the diverse source communities the \citet{22237539} study
...
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 integrated planktonic library (Figure~\ref{fig:integ_rarefaction}).
This result is consistent with our conclusion that temporal 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 \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
decrease over time although with only two time points it was unclear how
pronounced this effect was (Figure~\ref{fig:rarefaction}). Since biomass of the
plankton and the biofilm increased with increasing C subsidies the intermediate
peak in OTU richness is consistent with a classic productivity-diversity
relationship that 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 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 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
we did not measure extracellular polymeric substances (EPS), direct microscopy
showed that planktonic cells in the highest C treatment (C:P = 500) were
surrounded by what appeared to be EPS. Because biofilm EPS appeared also to
increase moving from the low to high C treatments (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 flocculating DOC
which has been shown to dominate high DOC environments in nature, we did
measure a 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{Lifestyle (biofilm or planktonic) Enriched OTUs}
There are only a few studies that attempt to compare biofilm community
composition and the 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 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
plankton) but are readily enriched in the biofilm lifestyle. Most of the
biofilm enriched algal OTUs were \textit{Bacillariophyta} although there were
...
the same taxonomic rank \citep{Schloss_2011}. 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 shape of rank
abundance distributions between biofilm and planktonic libraries in our data
(Figure~\ref{fig:rank_abund_shape} to be in contrast to that reported by
\citet{22237539} although this may be an artifact of each study's different
source communities (as discussed above). Carbon amendments did not affect
algal library membership and structure to the same degree as it affected
bacterial library composition. As expected, bacterial OTUs enriched in the
high C amended mesocosm (C:P = 500) include OTUs in classic copiotroph families
such as \textit{Vibrionacaea} and \textit{Pseudomonadaceae}. Interestingly, the
one OTU depleted in the high C treatments is annotated as being in the HTCC2188
order of the \textit{Gammaproteobacteria}. HTCC stands for 'high throughput
culture collection' and is a prefix for strains cultured under low nutrient
conditions \citep{Cho_2004, Connon_2002}.
\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 autotrophic pools and heterotrophic pools responded differently to
amendments of labile C as hypothesized. Notably while C 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 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 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 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 time.