Chuck Pepe-Ranney edited Material and Methods.tex  almost 10 years ago

Commit id: 885334c900df8c84dda02674bfde59c658af66f6

deletions | additions      

       

\subsubsection{DOC and Chlorophyll Measurements}  To assess the efficacy of the carbon additions we sampled each mesocosm twice daily during the first week of the experiment to evaluate dissolved organic carbon (DOC) content. Six days after the initiation of the experiment we collected plankton on filters to evaluate planktonic Chl a and bacterial abundance. Once it was clear (day 8) that pool size of each community had been altered we filtered plankton onto 0.2 $\mu$m filters and harvested coverslips to assess bacterial and algal community composition (16S and 23S rDNA). In addition all mesoscosms were analyzed a second time (day 17) to assess how community composition of both the plankton and biofilm communities had been altered over time.  Samples for dissolved organic carbon (DOC) analysis were collected in acid washed 50 mL falcon tubes after filtration through a 0.2 polycarbonate membrane filter (Millipore GTTP GTTP02500, Sigma Aldrich P9199) attached to a 60 mL syringe. Syringes and filters were first flushed multiple times with the control sample to prevent leaching of carbon from the syringe or the filter into the sample. Samples were then frozen and analyzed for organic carbon content with a Shimadzu 500 TOC analyzer (Wetzel and Likens 2000). \cite{Wetzel_2000}.  For Chl \textit{a} analysis we collected plankton on GF/F filters (Whatman, Sigma Aldrich Cat. # Z242489) by filtering between 500 mL and 1L from each treatment. For biofilm samples, all biofilm was gently removed from the complete area of each coverslip before being placed in a test tube forxtraction with 90-95% 90-95\%  acetone for ~ 32 hours at -20C -20C  and analyzed immediately after using a Turner 10-AU fluorometer (Wetzel and Likens 2000). \cite{Wetzel_2000}.  We analyzed bacterial abundance of the planktonic samples using Dapi staining and direct visualization on a Zeis Axio epifluorescence microscope after the methods of Porter and Feig (1980). Briefly, 1-3 mL of water was filtered through a 0.2 $\mu$m black polycarbonate membrane filter and post stained with a combination of Dapi and Citifluor mountant media (Ted Pella Redding, Ca) to a final concentration of 1$\mu$ ml-1.  DNA extraction For plankton, cells were collected by filtering between 20 – 30 mL of water onto a 0.2 $\mu$m pore-size polycarbonate filter (Whatman Nucleopore 28417598, Sigma-Aldrich cat# WHA110656). For biofilm communities, biomass from the entire coverslip area of three separate slides were collected and combined in an eppendorf tube by gentle scrapping the slip surface with an ethanol rinsed and flamed razor blade. DNA from both the filter and the biofilm was extracted using a Mobio Power Soil DNA isolation kit (MoBio Cat. # 12888).