Detection and distribution of insertion sequence 1 (IS1)-containing bacteria in the freshwater environment

The distribution of insertion sequence 1 (IS1)-containing bacteria was inve stigated in Windermere (Cumbria, UK), a freshwater body impacted by treated sewage discharge and run-off from the surrounding catchment. Culturable IS 1-containing bacteria were recovered from the water column at three depths in Windermere North Basin (WNB) and South Basin (WSB), and from sediment at both sites (at the sediment sur face in WSB and to a depth of 12-13 cm in WNB). Polymerase chain reaction amplification of IS1 and the Escherichia co lil Shigella sp. specific gene uidA, from community DNA from shallow sedime nts, extended the detection limit beyond that of culture at both sites. Thi s detection was extended further into deep sediment extracted from WNB as I S1 and uidA were detected in sub-samples to a depth of 4.7 and 2.3 m respec tively. Analysis of a representative subset of 90 IS1-carrying isolates rec overed from water and sediment at both sites demonstrated 21 heterogeneous IS1 profiles with estimated copy numbers ranging from 1 to 16. Identificati on of the host bacteria showed that the element was confined mainly to Ente robacter spp, However, this study showed IS1 to be present in Citrobacter f reundii for the first time. Plasmids were carried by 75.3% of enterobacteri al isolates and four plasmids (2.6%) carried IS1. DNA sequence analysis of five IS1 clones demonstrated that IS1 isoforms from this study were similar (> 89% nucleolide identity) to known IS1 isoforms. Two isoforms of IS1 fro m a single Enterobacter cloacae isolate differed by 6.7% at the nucleotide level suggesting that they had been acquired independently. (C) 2000 Federa tion of European Microbiological Societies. Published by Elsevier Science B .V. All rights reserved.