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Sediment samples from the coastal lagoons and estuaries of New York and New Jersey were used to investigate the influence of contaminants on diatom assemblages. Multivariate analyses demonstrated correspondence between composition of diatom assemblages and concentrations of several metals and total PAH. The effects of the individual contaminants were difficult to disentangle because of the considerable correlations between their concentrations. The most conspicuous trend was the increase in the relative abundance of small centric planktonic diatoms in response to contamination and the corresponding decrease in the benthic flora. The high relative abundance of planktonic species on contaminated sediments apparently resulted not so much from their tolerance to pollution, but from the paucity of benthic species. A comparison of the assemblages on the surface and at the depth of approximately 8–10 cm revealed a statistically significant temporal change in community composition towards planktonic diatoms. [ABSTRACT FROM AUTHOR]

Abstract: Diatoms from the genus Achnanthidium are abundant in rivers, streams, and springs of the Appalachian Mountains. They inhabit clean and polluted waters, including those affected by acid mine drainage. The identification of Achnanthidium taxa is difficult due to their small cell size and insufficient information in the diatom floras. We studied the taxonomy and ecology of Achnanthidium in Appalachian rivers by analyzing a data set of benthic diatom samples and corresponding water chemistry data collected during several water-quality surveys from 181 sampling sites. Ten species were identified using scanning electron and light microscopy: A. alpestre (Lowe & Kociolek) Lowe & Kociolek, A. atomus (Hustedt) Monnier, Lange-Bertalot, & Ector, A. deflexum (Reimer) Kingston, A. duthii (Sreenivasa) Edlund, A. eutrophilum (Lange-Bertalot) Lange-Bertalot, A. cf. gracillimum (Meister) Lange-Bertalot, A. cf. latecephalum Kobayasi, A. minutissimum (Kützing) Czarnecki (sensu lato), A. reimeri (Camburn) comb. nov., and A. rivulare Potapova & Ponader. The distribution of common taxa in relation to water chemistry was studied by fitting non-parametric regression models (generalized additive models, GAM, and non-parametric multiplicative regression models, NPMR) to species relative abundances. Studied Achnanthidium species differed considerably in their responses to water chemistry. These results suggest that species-level identifications will lead to more accurate bioassessments. [Copyright &y& Elsevier]

Abstract: Two major arguments in favor of using diatoms in water-quality assessments are that their distributions are cosmopolitan and their ecology is well studied. If these assumptions are true, diatom-based monitoring tools could be considered universal and used in any geographic area. Indeed, some diatom metrics based on species indicator values developed in Europe are often used in North America and many other parts of the world. There is considerable evidence, however, that diatom metrics are less useful when applied in a geographic area other than where species relations with environmental characteristics were originally studied to construct the metrics. We used U.S. Geological Survey National Water-Quality Assessment program data to create diatom metrics for monitoring eutrophication, and show here that these metrics provide better assessments in U.S. rivers than similar metrics developed for European inland waters. We also demonstrate that metrics developed by studying diatom–nutrient relationships on the continental-scale can be further refined if combined with regional-scale studies. [Copyright &y& Elsevier]

• DNA metabarcoding is an emergent tool for biodiversity assessments. • Benthic eukaryotic assemblages were characterized using18S-V9 rDNA. • Diatoms, water molds, holozoans, green algae, fungi responded to stream impairment. • This approach may be recommended for biomonitoring of stream eukaryotic biota. DNA metabarcoding is rapidly expanding as a new approach to biodiversity assessments and biomonitoring and is especially valuable for characterizing microbial communities in aquatic habitats. When applied to eukaryotic organisms, metabarcoding is usually targeting specific taxonomic groups, such as macroinvertebrates, fungi, diatoms, or other protists. The goal of this study was to explore the potential use of metabarcoding of entire biofilm eukaryotic assemblages for the purpose of stream biomonitoring. We sampled 14 stream sites in New Jersey, USA along an impairment gradient and characterized rock biofilm assemblages using Illumina Mi-Seq sequencing of the V9 hypervariable region of 18S rDNA following the Earth Microbiome Project (EMP) protocol. We also enumerated diatoms from the same samples to compare DNA metabarcoding results with morphological assessments. Among the 5866 unique rDNA sequence variants, the fungal and holozoan sequences were the most diverse, while diatom sequences were the most abundant in most sites. Among-site variability of assemblage composition was significantly higher than within-site variability of field and lab replicates, which indicates an acceptable level of reproducibility of the method. Different taxonomic groups of eukaryotes exhibited similar, but not identical patterns of assemblage variation in response to underlying environmental gradients. Both morphological and metabarcoding approaches recovered strong relationships between diatom assemblage composition and water quality impairment. Several other groups of eukaryotes, such as fungi, peronosporomycetes, green algae, and holozoans had only slightly weaker response to water quality impairment than diatoms. These findings suggest that molecular characterization of biofilm eukaryotic assemblages can be an effective tool for monitoring stream biota and its responses to disturbance even if the taxonomic assignments of sequences are only partially resolved. [ABSTRACT FROM AUTHOR]