Terminal restriction fragment length polymorphism (T-RFLP) is increasingly being used to examine microbial community structure and accordingly, a range of approaches have been used to analyze data sets. A number of published reports have included data and results that were statistically flawed or lacked rigorous statistical testing. A range of simple, yet powerful techniques are available to examine community data, however their use is seldom, if ever, discussed in microbial literature. We describe an approach that overcomes some of the problems associated with analyzing community datasets and offer an approach that makes data interpretation simple and effective. The Bray-Curtis coefficient is suggested as an ideal coefficient to be used for the construction of similarity matrices. Its strengths include its ability to deal with data sets containing multiple blocks of zeros in a meaningful manner. Non-metric multi-dimensional scaling is described as a powerful, yet easily interpreted method to examine community patterns based on T-RFLP data. Importantly, we describe the use of significance testing of data sets to allow quantitative assessment of similarity, removing subjectivity in comparing complex data sets. Finally, we introduce a quantitative measure of sample dispersion and suggest its usefulness in describing site heterogeneity.
Terminal restriction fragment length polymorphism ͑T-RFLP͒ is increasingly being used to examine microbial community structure and accordingly, a range of approaches have been used to analyze data sets. A number of published reports have included data and results that were statistically flawed or lacked rigorous statistical testing. A range of simple, yet powerful techniques are available to examine community data, however their use is seldom, if ever, discussed in microbial literature. We describe an approach that overcomes some of the problems associated with analyzing community datasets and offer an approach that makes data interpretation simple and effective. The Bray-Curtis coefficient is suggested as an ideal coefficient to be used for the construction of similarity matrices. Its strengths include its ability to deal with data sets containing multiple blocks of zeros in a meaningful manner. Non-metric multi-dimensional scaling is described as a powerful, yet easily interpreted method to examine community patterns based on T-RFLP data. Importantly, we describe the use of significance testing of data sets to allow quantitative assessment of similarity, removing subjectivity in comparing complex data sets. Finally, we introduce a quantitative measure of sample dispersion and suggest its usefulness in describing site heterogeneity.Abbreviations: T-RFLP -Terminal restriction fragment length polymorphism; MDS -non-metric multidimensional scaling; ANOSIM -analysis of similarity; SIMPER -similarity percentage Antonie van Leeuwenhoek 86: 339-347, 2004.
Floodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi-arid floodplain would transition towards comprising mainly dry-soil specialist species with increasing drought severity. Here, we used 18S rRNA amplicon pyrosequencing to measure the eukaryote community composition in soils that had been depleted of water to varying degrees to confirm that reproducible transitional changes occur in eukaryotic biodiversity on this floodplain. Interflood community structures (3 years post-flood) were dominated by persistent rather than either aquatic or dry-specialist organisms. Only 2% of taxa were unique to dry locations by 8 years post-flood, and 10% were restricted to wet locations (inundated a year to 2 weeks post-flood). Almost half (48%) of the total soil biota were detected in both these environments. The discovery of a large suite of organisms able to survive nearly a decade of drought, and up to a year submerged supports the concept of inherent resilience of Australian semi-arid floodplain soil communities under increasing pressure from climatic induced changes in water availability.
Microfaunal samples were collected from within the channels of three rivers in north eastern Victoria, Australia (the Murray, Ovens and Broken Rivers) as a component of a study examining the effects of flow on the biota of lowland rivers in Australia. Samples were collected from the water column of the river channel and slackwaters and from the layer of water immediately above the bottom sediment of the slackwaters. There was no connectivity between the river channel and the floodplain wetlands for all three rivers during the sampling period. Substantial numbers of microfauna were resident in the slackwaters of all three rivers, with the greatest densities occurring close to the bottom sediment, with densities often exceeding 1000 animals l )1 whereas in the plankton samples densities were usually less than 500 animals l )1 . The presence of large and diverse microfaunal communities and the lack of connectivity between the river channel and associated floodplain wetland indicate that these communities are capable of persisting and recruiting within riverine channel slackwaters.
Non-flowing, slackwater habitats in lowland rivers support diverse and abundant benthic microfaunal communities; however, there is little information on how these communities respond to changes in hydrology. In this study, we tested two hypotheses: (1) microfaunal richness and density will be higher in slackwater habitats compared to flowing habitats; (2) altering the hydrology of a habitat will result in changes in the richness and density of microfauna over time so that communities will become similar to those found in a habitat with the same flow characteristics. Flowing and slackwater habitats were manipulated by constructing barriers to redirect flows, either away from flowing habitats and creating slackwater habitats, or towards a slackwater creating a flowing habitat. The resultant epibenthic microfaunal communities were compared to those in unmodified slackwaters and flowing habitats. Over a 4-month period, epibenthic microfaunal samples were collected from the four experimental treatments. Analysis of variance indicates that there was no difference in rotifer richness or abundance between habitat types, but significant differences in the richness and abundance of microcrustacean occurred with higher richness and densities occurring in the slackwater habitats compared to flowing habitats. Within four weeks of the treatments being applied, there was little difference in the microfaunal communities between the natural and created flowing habitats or between the natural and created slackwater habitats. As the hydrology of a river varies, slackwater habitats will be scoured and new habitats created. The microfauna populations associated with these habitats appear to have strategies that enable them to cope with the disturbance and to recolonise newly created slackwater areas.
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