ý.,,: V. ý ýý . - Nottingham eTheses - University of Nottingham

can help to predict the types of bacteria that will be found there (van Wintzin, -, erode er
al., 1997). During the current study a detailed analysis of the environment from which the
communities were isolated was performed (Chapter 3). The main assessment of these
analyses is that the communities were dominated by Gram-negative rods which were
psychrotrophic or psychrophilic and halotolerant. Characterisation of the AFP active
isolates using ARDRA and molecular sequencing (Chapter 5) also provided information
on what types of bacteria were present in the community. Therefore DGGE was
performed using nucleic acid extraction techniques and PCR universal primers (Section
2.9.5.3) that would select for these bacterial communities, i. e. cold. saline, aquatic
ecosystem communities (Ovreäs et al., 1997; Bosshard et al., 1999, Schäfer er al., 2001).
6.3.2.2 -
Sample isolation and maintenance
The second step where bias can occur is during sample collection and
maintenance of the samples until analysis (Amann et al., 1995; Hugenholtz et al., 1998).
Certain environments, especially extreme ecosystems contain bacterial communities that
are specifically adapted to that environment, therefore, changing that environment, i. e.
changing the salinity, pressure, temperature in which a community is maintained, can
cause the enrichment of certain bacterial groups within the community, thus changing the
abundance ratios of the groups within the community or more drastically changing the
composition of the community so that it no longer reflects the original structure (Rochelle
et al., 1994). During the current study water samples were taken directly from the lake
and stored in a thermally insulated `cool box', to prevent them from freezing, for
transportation back to the laboratory, where they were immediately processed and then
frozen. It was necessary to prevent the samples from initially freezing so that the bacteria
were kept viable. It is likely that the temperature of the water samples did change from
the point of their isolation to when they were processed. However. because during
transportation (