Environmental effects on biofilm bacterial communities: a comparison of natural and anthropogenic factors in New Zealand streams

Abstract

Summary We investigated the resident bacterial communities within the biofilm of 252 streams in New Zealand with the aim of assessing the community variation associated with natural and anthropogenic‐influenced environmental characteristics. This work is part of a larger project investigating the use of bacterial communities as biological indicators, and here we assess how predictable the variation in bacterial community is in response to environmental influences. Samples of epilithic biofilm were collected in the Austral Summer of 2010, and bacterial communities were characterised using the DNA‐fingerprinting technique automated ribosomal intergenic spacer analysis (ARISA). Multivariate analysis of the ARISA data revealed that geographical location (region) was a better predictor of bacterial community structure than land use. Our finding that taxon richness varied with geographical location, decreasing along a north to south (increasing latitude) gradient, and that land use had no significant effect on taxon richness suggests that bacterial communities have great potential to act as biological indicators of stream health. In particular, the maintenance of taxon richness at impacted sites is a key advantage since the local extinction of many traditional indicator organisms, such as fish or macroinvertebrates, often precludes their further use. Our conceptual model of bacterial community structure proposes that stream biofilm communities are comprised of four broad groups of bacteria: ubiquitous bacteria (found at all sites), region‐specific bacteria (those representative of geographical areas), natural‐state bacteria (those associated with unmodified systems) and impact‐related bacteria (those associated with human activities). The proportion of these four groups at a particular sample site would provide the basis of a novel bacterial community index of stream health.

Identifying congruence in stream assemblage thresholds in response to nutrient and sediment gradients for limit setting

“…Details of the DNA extraction method and ARISA were previously described by Washington et al. (). Briefly, this method determines the relative abundance of the different intergenic spacer fragment lengths of the 16S to 23S ribosomal RNA genes.…”

Relationships between molecular bacterial diversity and chemistry of groundwater in the Wairarapa Valley, New Zealand

“…It is hard to argue that one molecular profiling tool is better than the others as each technique has its own advantages and drawbacks. For example, the automated ribosomal intergenic spacer analysis (ARISA) approach is another popular molecular tool that can be effectively used in microbial community analyses Washington et al 2013). But one of the issues in the ARISA methodology is that it is possible to produce PCR products with same length for different species.…”

Advances in Watershed Science and Assessment

“…assemblages [150][151][152]. One emerging strategy is in the use of prokaryote assemblages, which has historically been limited because many prokaryotes are not readily cultured in the laboratory.…”

“…One emerging strategy is in the use of prokaryote assemblages, which has historically been limited because many prokaryotes are not readily cultured in the laboratory. However, emerging technologies that allow for quantification of assemblage composition through DNA sequencing have largely removed this limitation, making prokaryote assemblage assessments an emerging new option for bioassessment of aquatic systems [152,153]. Rapidly evolving DNA sequencing methods have the potential to greatly enhance not only bioassessments using prokaryotes but also those using assemblages that have traditionally been evaluated by identification of specimens based on morphological characteristics [154][155][156][157].…”