Ed Hall edited Materials_and_Methods.tex  almost 9 years ago

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into the sample. Samples were then frozen and analyzed for organic C  content with a Shimadzu 500 TOC analyzer \citep{Wetzel_2000}. Biomass of all  biofilm samples were measured by difference in pre-(without biofilm) and  post-(with biofilm) weighed GF/F filters after oven drying overnight at $60\,^{\circ}{\rm C}$. 60$\,^{\circ}$C.  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 the  water column of each mesocosm for each treatment. For biofilm samples, all  biofilm was gently removed from the complete area of each coverslip (3  coverslips for each treatment per sampling event) before being placed in a test  tube for extraction with 90-95\% acetone for ~ 32 $\sim$32  hours at $-20\,^{\circ}{\rm C}$ -20$\,^{\circ}$C  and analyzed immediatelyafter  using a Turner 10-AU fluorometer \citep{Wetzel_2000}. Bacterial abundance of the planktonic samples was analyzed using Dapi staining  and direct visualization on a Zeis Axio epifluorescence microscope after the 

Roche B linker and the reverse gene specific primer sequence. The gene specific  primer pair for bacterial SSU rRNA genes was 27F/519R \citep{LANED.J.:1991}.  The primer pair p23SrV\_f1/p23SrV\_r1 was used to target 23S rRNA genes on  plastid genomes \citep{Sherwood_2007}. Amplifications were performed in 25 ul $\mu$l  reactions with Qiagen HotStar Taq master mix (Qiagen Inc, Valencia,  California), 1ul of each 5uM primer, and 1ul 1$\mu$l  of template. Reactions were performed on ABI Veriti thermocyclers (Applied Biosytems, Carlsbad, California)  under the following thermal profile: 95$^{\circ}$C for 5 min, then 35 cycles of  94$^{\circ}$C for 30 sec, 54$^{\circ}$C for 40 sec, 72$^{\circ}$C for 1 min,