2011.seqs
Epilimnion samples in 2006-08 were pooled from 0, 1 and 2 m depths and in 2009-10 from 0 and 1 m depths. Metalimnion samples in 2006-08 were pooled from 3 and 4 m depths, and in 2009-10 from 2 and 3 m depths. Hypolimnion samples in 2006 were from 5 m depth, in 2007-08 pooled from 5 and 6 m depths and in 2009-10 pooled from 4, 5 and 6 m depths. Water was passed through a 50 µm sieve to remove larger zooplankton. Pooled water was transported to the laboratory and kept at +4 C ° until it was concentrated with tangential flow filtration (Durapore cassette, pore size 0.22 µm, Millipore) within 6 hours of sampling. Concentrated water samples were frozen and freeze dried with Alpha 1-4 LD plus (Christ, Osterode, Germany). DNA was extracted by phenol-chloroform extraction (Griffits, et al., 2000) from 0.4 mg of freeze-dried material. Amplification of bacterial 16S rRNA genes (E. coli positions 341 to 805) was conducted using general bacteria primers 341F (5’-CCTACGGGNGGCWGCAG-3’) and 805R (5’-GACTACHVGGGTATCTAATCC-3’) (Herlemann et al. 2011). PCR and amplicon processing prior to sequencing was performed as described in Eiler et al. (2011), except for purification  of PCR products  with Agencourt AMPure XP purification system (Beckman Coulter, Danvers, USA) and amplicon quantification with SYBR Green in a Qubit fluorometer (Invitrogen Corporation, Carlsbad, USA). Amplicons were sequenced with Titanium chemistry from adaptor A, using a 454 GS-FLX system (454 Life Sciences, Branford, CT) at the Institute of Biotechnology hosted by University of Helsinki, Finland. The resulting reads carried the sample-specific molecular barcode and covered the entire V4 region of the 16S rRNA gene as well as flanking regions.  Barcodes resemble samples as given:      Run GYQXXNK04  barcode ATCAT H081007  barcode ATGAC H100406  barcode ATGCA M081119_b  barcode ACATC E090818  barcode ACACA M100622  barcode ACAGT E100406  barcode ACTAT E100622  barcode ACTGA M071009  barcode ACGAG H070924  barcode AGATG E100503  barcode AGAGA M100406  barcode AGTAC M090818  barcode AGTGT H090818  barcode AGCTA H100503  barcode TATCA M090915  barcode TACAC H090915  barcode TACTA H091020  barcode TACGT M091020  barcode TAGAG E091020  barcode TAGTC H100622  barcode TCTGT E090311  barcode TGACA H091215  barcode TGAGT M100503  barcode TGTAG H081119_b  barcode TGTCT E100825  barcode TGTGA M080617  barcode TGCAT E080715  barcode TGCTG M091215  barcode CATAC M080812  barcode CATCT H080715  barcode CATGA M100825  barcode CACAT E090915  barcode CAGTA H100825  barcode CAGCG E091215    Run F6THLXZ01  barcode AGATG H090519  barcode AGTCA M090519   barcode AGCTA E060520  barcode AGCGC M060520  barcode TATAT H060520  barcode TATCA E061020  barcode TATGC M061020  barcode TACAC H061020  barcode TACTA E070423   barcode TACGT M070423   barcode TAGAG H070423   barcode TAGTC E070522   barcode TAGCT M070522   barcode TCATA H070522   barcode TCACT E070603  barcode TCAGC M070603   barcode TCTAC H070603   barcode TCGTG H070619   barcode TCGCA E070703_a   barcode TGATC M070703   barcode TGACA H070703    barcode TGAGT E070716   barcode TGTAG M070716  barcode TGTCT H070716  barcode TGTGA E070731   barcode TGCAT M070731  barcode TGCTG H070731  barcode CATAC E070814   barcode CATCT M070814   barcode CATGA E070828   barcode CACAT M070828    barcode CACTC H070828   barcode CAGTA E070911   barcode CAGCG M070911  barcode CTATC H070911   barcode CTACA E090616     run F6THLXZ02   barcode ATATA E071009       barcode ATCAT M071022       barcode ATCTC E071022      barcode ATCGA H071022      barcode ATGAC E080505       barcode ATGTG M080505      barcode ATGCA H080505      barcode ACATC E080520       barcode ACACA M080520       barcode ACAGT H080520       barcode ACTAT E080603       barcode ACTCG M080603      barcode ACTGA H080603      barcode ACGAG E080617      barcode ACGCT H080617       barcode AGATG E080701       barcode AGAGA M080701       barcode AGTAC H080701       barcode AGTGT M080715       barcode AGCTA E070924  barcode AGCGC M090616  barcode TATAT H090616  barcode TATCA E090714       barcode TATGC M090714       barcode TACAC H090714       barcode TACTA E080729       barcode TACGT M080729      barcode TAGAG H080729      barcode TAGTC E080812       barcode TAGCT E070703_b       barcode TCATA H080812  barcode TCACT E080826       barcode TCAGC M080826       barcode TCTAC H080826      barcode TCTGT E080910       barcode TCGAT M080910       barcode TCGTG H080910       barcode TCGCA E080923  barcode TGATC M080923  barcode TGACA H080923      barcode TGAGT E081007  barcode TGTAG M081007  barcode TGTGA E081029  barcode TGCAT M081029  barcode TGCTG H081029  barcode CATAC E081119_a  barcode CATCT M081119_a  barcode CATGA H081119_a  barcode CACAT M070924  barcode CAGTA E090505  barcode CAGCG M090505  barcode CTATC H090505      barcode CTACA E090519
Uppsala University, Department of Ecology and Gene
F6THLXZ01