Supplementary information.
Detailed below is data gathered from Opanuku Stream (Lat. 36o53’43”S, Long. 174o35’44”E) from
samples gathered and processed in the same manner as described for Oakley Creek.
Quantity and quality of DNA from various extraction methods. Yields of DNA extracted from Opanuku
Stream biofilm were less using commercially-available extraction kits (methods D, E and F) compared to
any other method used (Table S1). Again, a NanoDrop (Thermo Scientific Ltd., Auckland, NZ) assay
revealed methods A and B to yield the purest extracts of DNA, as assessed from absorption ratios, while
methods D and E yielded the least pure DNA extracts. However, neither the concentration nor purity of
the DNA significantly influenced the concentration of DNA amplified by PCR.
Table S1: Details of the quantity and quality of biofilm DNA extracted from
Opanuku Stream, using six different procedures (A to F; see Table 1). For
consistency, all DNA extracts were suspended in 100 l of the eluent
solution
DNA
Extraction
Method
Concentration of
DNA Extracted
(ng μl-1)
* Ratio
260/280
§ Ratio
260/230
Concentration of
DNA Amplified
(ng μl-1) ∆
A
220  65
2.06  0.02
2.22  0.08
33.5  1.38
B
390  116
2.12  0.01
2.24  0.04
51.8  15.7
C
321  104
2.03  0.02
1.67  0.14
32.1  7.29
D
46  2
0.94  0.03
0.35  0.00
37.0  3.71
E
17  5
1.39  0.13
0.26  0.02
22.2  2.49
F
15  2
2.01  0.08
1.00  0.12
41.1  2.30
* Ratio of absorbance at 260 nm and 280 nm. A ratio of ~1.8 is generally accepted as
‘pure’ for DNA.
§ Ratio of absorbance at 260 nm and 230 nm. A ratio in the range of 2.0-2.2 is generally
accepted as pure for DNA
∆ DNA amplified using ARISA PCR primers LDBact and SDBact (Ranjard et al., 2001)
Comparison of bacterial community structure between samples. Multivariate analysis revealed
significant differences (pairwise PERMANOVAs, all p ≤ 0.05) among bacterial ARISA data obtained using
each extraction technique (Figure S2). The greatest variability between each of the five stream sections
was again observed for DNA extracted using the commercially-available kits (methods D, E and F), which
yielded multivariate dispersion values of 1.3, 1.3 and 1.1, respectively. Methods A, B and C yielded
multivariate dispersion values of only 0.9, 0.8 and 0.9, respectively.
Figure S2. Differences in bacterial ARISA
profiles from rocks sampled from different
sections of Opanuku Stream. Plot is nonmetric multidimensional scaling of ARISA
data, derived from a Bray-Curtis matrix of
samples. Letters refer to the DNA
extraction protocol used (see Table 1). 2D
stress = 0.19