Methods:
DNA was isolated from the mat samples using the Puregene Yeast/Bact. Kit (Qiagen Inc.,
Mississauga, Canada). The partial 18S rDNA sequence was amplified using Crimson
Taq DNA Polymerase (NEB, Mississauga, Canada) according to manufacturer’s
recommendations and the primers Euk-A and Euk-B [1]. The resulting product was
sequenced with the Euk-A, Euk-B and Euk-570F primers [2]. The chloroplast partial 16S
rDNA sequence was amplified using Crimson Taq DNA Polymerase (NEB) and the
primers uni-for and uni-rev [3] and the resulting product sequenced with these primers.
The thermal cycler conditions for both PCR reactions were: 95 °C for 2 minutes,
followed by 35 cycles of 95 °C for 20 seconds, 50 °C for 15 seconds and 68 °C for 2
minutes, and a final single 5 minute incubation at 68 °C. The nucleotide sequences determined in this work have been deposited in the GenBank sequence database and assigned accession numbers GQ396799 and GQ396800.
1. Medlin L, Elwood HJ, Stickel S & Sogin ML (1988) The characterization of
enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71: 491-499.
2.Weekers PH, Gast RJ, Fuerst PA & Byers TJ (1994) Sequence variations in smallsubunit
ribosomal RNAs of Hartmannella vermiformis and their phylogenetic
implications. Molecular Biology and Evolution 11: 684-690.
3. Vaisvila R, Morgan RD, Posfai J & Raleigh EA (2001) Discovery and distribution of
super-integrons among Pseudomonads. Molecular Microbiology 42: 587-601.
Results:
The top-scoring matches returned when using the experimental-tank mat diatom 18S
rDNA sequence to search the GenBank database are Nitzschia spp., and phylogenetic
analysis shows it has the closest relationship with species in this genus (Supplementary
figure below). The bootstrap support for most of the branches in the phylogenetic tree is
poor, but this is likely due to the very high level of identity shared by all of these
sequences (>95%). Analysis of the chloroplast 16S rDNA sequence also shows the
closest relationship to sequences from Nitzschia spp. (not shown). The classification of
this diatom in the genera Nitzschia is also supported by its morphological characteristics
(Figure 1C in main text).

Caption to supplementary data figure:
Phylogenetic relationship of mat-forming diatom to known diatom species. The partial
18S rDNA sequence from the microbial mat diatom was aligned with selected highly
similar diatom sequences from the GenBank public sequence database. Phylogenetic
analyses were conducted in MEGA4 [4]. The relationships were inferred using the
Neighbor-Joining method [5], and bootstrap values are shown as percentages based on
10000 replicates next to the branches [6]. Evolutionary distances were computed using
the Maximum Composite Likelihood method [7] and the scale bar indicates the number
of base substitutions per site. The final analysis contained a total of 1597 positions with
complete deletion of positions containing gaps. Accession numbers for the sequences
used are given in brackets.
4. Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary
Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution
24:1596-1599.
5. Saitou N & Nei M (1987) The neighbor-joining method: A new method for
reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.
6. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the
bootstrap. Evolution 39:783-791.
7. Tamura K, Nei M & Kumar S (2004) Prospects for inferring very large phylogenies by
using the neighbor-joining method. Proceedings of the National Academy of Sciences
(USA) 101:11030-11035.