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Diatoms are major contributors to global carbon fixation and constitute a significant portion of biofilms found in lotic ecosystems. Despite their widespread abundance and the fact that extensive studies have been performed on morphological features of frustules, molecular tools for the identification of diatoms are not commonly available. This study focuses on the development of oligonucleotide probes for the detection of diatom species relevant to water quality assessment. The selected panel of diatoms covers all the species found in water of varying quality from the rivers of central-East Apennine (Italy). Small subunit rRNA-targeted probes were applied to a microarray platform as well as to a new technique termed Primer-Probe, with the aim of obtaining a molecular tool suitable for accurate identification of both single and mixed species diatom populations. The Primer-Probe technique together with dot-blot assays proved to be ideal for the preliminary screening of a large set of DNA oligonucleotides designed by ARB software. It was shown that microarrays, as a promising technology for rapid and simultaneous detection of a wide range of species-specific genetic markers, can be adapted to monitor changes within a diatom community. It is suggested that microarrays will provide a molecular basis for microbial identification to support standard microscopy techniques used by ecologists and environmental scientists for monitoring water quality. [ABSTRACT FROM AUTHOR]

The purpose of this study was to test the applicability of different methods of river habitat assessment and their respective indices in a series of sample sites in Italy. These investigations were carried out within the EU AQEM project with the aim of combining the macroinvertebrate information with that achieved by investigating the hydromorphological characteristics of the river ecosystem as well as the surrounding landscape features. The River Habitat Survey (including the derived indices Habitat Modification Score and Habitat Quality Assessment) from U.K., and three Italian indices (Index of Fluvial Functioning, Buffer Strip Index and Wild State Index) were applied at 33 AQEM sites distributed in three different Italian river types. The obtained results indicate the overall ability of the applied indices to detect the degradation gradient, including river morphology and habitat, in the studied riverine ecosystems. Index of Fluvial Functioning seems useful to promptly describe the ecological quality of rivers as suggested by the good correlation with the AQEM multimetric biotic index. The Buffer Strip Index, showing a clear affinity with the Habitat Quality Assessment, seems suitable to assess richness and quality of the physical structure of a riverine site. The Habitat Modification Score recorded efficiently the morphological impact where present (e.g., North Apennine river sites), while the Italian indices appear to be not appropriate for differentiating this impact type from the general degradation of rivers. [ABSTRACT FROM AUTHOR]