The effects of water abstractions on invertebrate communities in U.K. streams

There are increasing concerns about the ecological effects of water abstraction and in the UK, these concerns have been hightened by the 1976, 1984 and 1988-92 droughts. This paper assesses macroinvertebrate and environmental changes induced by surface and groundwater abstractions on 22 streams throughout the UK.The approach involved comparative research to assess differences between reference and impacted sites.Using a database comprising 204 sets of biological and environmental data (89 taxa and 16 environmental variables) a preliminary ordination using principle components analysis clearly differentiated three types of sites: upland, lowland and an intermediate type. At this scale, any effects of abstractions on invertebrate communities are shown to be insignificant relative to regional controls. A simultaneous ordination of the environmental and faunal differences between pairs of sites was undertaken separately for each of the three regional groups. Differences are considered as vectors having both direction and amplitude and the analysis elucidates common patterns in the faunal and environmental data. Important changes were observed in two situations: upland streams affected by major diversions as part of hydro-power schemes in Scotland and lowland rivers impacted by groundwater abstractions.No strong patterns of change (either in amplitude or orientation) were demonstrated within any of the taxonomic groups. However, within the upland type some rheophilous taxa were shown typically to be reduced in abundance at impacted sites. Within the lowland type, a consistent pattern in the dataset is demonstrated by a group of taxa that are reduced in abundance at the impacted sites.     

THE POTENTIAL INDICATOR VALUE OF RARE TAXA RICHNESS IN DIATOM‐BASED STREAM BIOASSESSMENT1

Despite their recognized contribution to species richness, the importance of rare taxa richness in bioassessment is unclear. This study aimed to characterize the environmental factors affecting the number of rare diatom taxa in western U.S. streams and rivers, and to evaluate whether this number can be used to differentiate streams with contrasting human disturbance. Three different categories of rare taxa were used: satellite (taxa with low occurrence and low abundance), rural (taxa with high occurrence and low abundance), and urban (taxa with low occurrence and high abundance). Common taxa were included as a separate category of core taxa (taxa with high occurrence and high abundance). We analyzed 987 diatom samples collected over the period of 5 years (2000–2004) for the U.S. Environmental Protection Agency’s (EPA) Western Environmental Monitoring and Assessment Program (WEMAP). The results showed that rural taxa richness (number of rural taxa per site) increased along a longitudinal gradient from mountainous, fast‐flowing oligotrophic streams with fewer fine substrates to large, slow‐moving, nutrient‐rich rivers with abundance of fine substrates. Rural taxa richness was the only rarity metric that distinguished least disturbed (reference) sites from the most disturbed (impacted) sites, but it was significantly different only in the mountains ecoregion. Core taxa richness distinguished reference from impacted sites in the West and in each one of the three ecoregions (mountains, plains, and xeric). Our findings revealed that rural taxa richness can be used as an indicator of human disturbance in streams/rivers, especially in the mountains ecoregion, and that rarity definition is important in bioassessment.     

Diatoms as water quality indicators in the upper reaches of the Great Fish River,Eastern Cape,South Africa

This study focused on the spring-fed upper reaches of the economically important Great Fish River with the aim of determining if diatoms could be used for biomonitoring in semi-arid conditions in southern Africa. Five sites were monitored monthly from 2010 to 2012. Of the 269 diatom taxa belonging to 51 genera identified, the dominant taxa were mostly those considered to be pollution-tolerant: Amphora pediculus, Craticula buderi, Fragilaria biceps, Nitzschia frustulum, Nitzschia paleacea, Planothidium lanceolatum and Rhopalodia gibba. A number of diatom-based numerical indices were used to infer water quality, including the generic diatom index, the specific pollution sensitivity index, the biological diatom index, and percentage pollution-tolerant valves, which forms part of the UK trophic diatom index. All index scores showed the Great Fish River to be impacted, and showed significant correlations of diatom species abundance with pH, NO₃-N, electrical conductivity, NH4-N and CaCO_3. Analysis revealed EC and NO3-N as the main environmental drivers affecting diatom community composition, followed by pH and PO4-P. The percentage of diatom deformities at all sites was high, at 3.5%. Diatom indices showed the river to be impacted by decades of agricultural activity, which was confirmed by chemical water analysis. Thus diatom indices can be used for biomonitoring in semi-arid areas.     

Epiphytic diatoms in two freshwater maritime Antarctic lakes

SUMMARY.

• 1 An ecological study of two small maritime Antarctic lakes on Signy Island, South Orkney Islands, was undertaken from January 1986 to March 1987. Analysis of diatom counts from the lakes provided examples of oligotrophic and mesotrophic ecosystems.
• 2 A diverse community of 104 epiphytic taxa was identified. Twenty-eight taxa had a percentage abundance greater than 1% in both lakes. Distinctive dominant taxa were identified from each lake.
• 3 A variety of ordination techniques was performed on the abundance data and a principal components analysis demonstrated differences in the diatom assemblages between the two lakes. Clear separations of sites and species were evident between the lakes, and accounted for the greatest percentage variance.
• 4 Species composition varied with depth within each lake and was also important in influencing changes in assemblage composition between sites.
• 5 A redundancy analysis indicated that species composition was correlated to concentrations of nitrogen and phosphorus but the total variance accounted for by the four physical and chemical factors measured was low (24%).

     

Diatom community response to an acid mine drainage gradient

Acid mine drainage (AMD) is a significant environmental issue worldwide. On the West Coast of the South Island, New Zealand, many AMD-affected streams occur within close proximity to naturally acidic streams, enabling us to compare the response of communities in naturally and anthropogenic acidified systems. We investigated epiphytic diatom communities in 39 streams along an AMD gradient that included naturally acidic and circum-neutral reference streams. There was a wide range in taxonomic richness in reference streams and those moderately impacted by AMD (8–33 taxa). Taxonomic richness was greatly reduced in severely impacted streams (1–5 taxa) at a threshold of pH 3.4 and was dominated by Pinnularia cf. acidophila (69–100% relative abundance). Community composition differed between circum-neutral reference streams and moderately and severely impacted streams. However, naturally acidic and moderately impacted streams had similar diatom communities primarily composed of Eunotia and Frustulia species. Our results indicate that diatom communities are strongly structured by pH and able to tolerate moderate conductivity and metal concentrations. This is a challenge for researchers and water managers attempting to incorporate diatoms into AMD monitoring in regions with naturally acidic streams.     

Phylogenetic balance and ecological evenness

The frequency distribution of numbers of species in taxonomic groups, where many species belong to a few very diverse higher taxa, is mirrored by that of species in most communities, where many individuals belong to a few very abundant species. Various hypotheses mechanistically link a species' community abundance with the diversity of the higher level taxon (genus, family, order) to which it belongs, but empirical data are equivocal about general trends in the relation between rank-taxon diversity and mean abundance. One reason for this inconclusive result may be the effect of the semisubjective nature of rank-based classification. We assessed the relationship between clade diversity and mean species abundance for two diverse tropical tree communities, using both traditional rank-based analysis and two new phylogenetic analyses (based on the ratio of individuals to taxa at each node in the phylogeny). Both rank-based and phylogenetic analyses using taxonomic ranks above the species level as terminal taxa detected a trend associating common species with species-rich families. In contrast, phylogenetic analyses using species as terminal taxa could not distinguish the observed distribution of species abundances from a random distribution with respect to clade diversity. The difference between these results might be due to (1) the absence of a real phylogeny-wide relationship between clade abundance and diversity, (2) the influence of poor phylogenetic resolution within families in our phylogenies, or (3) insufficient sensitivity of our metrics to subtle tree-wide effects. Further development and application of phylogeny-based methods for testing abundance-diversity relationships is needed.     

Freshwater diatom biogeography in the Canadian Arctic Archipelago

Aim Document the biogeographical distributions of diatoms in the Canadian Arctic in relation to environmental factors. Location The Canadian Arctic Archipelago. Methods Diatoms were extracted from lake sediments and treated using standard methods. Rarefaction‐estimated species richness, diatom concentrations (valves cc^?1), and diatom abundance were mapped using a Geographic Information System. The physical and chemical parameters of the lakes were measured. Results A total of 326 taxa from 63 genera were found in 62 lakes of the study area. Up to 85 and as low as eight taxa were identified in any one lake, and rarefaction‐estimated species richness correlated with lake size. Nearby lakes could have greatly different diatom assemblages. Many taxa showed limited distributions. Response surfaces and ordination techniques indicate that a large number of taxa prefer colder regions of the Arctic while the abundance of others was influenced by lake water chemical parameters such as TKN and SiO₂. Main conclusions Although many taxa were common and found across the study area, diatom assemblages showed regional differences in the Arctic. Some taxa were not found in either the northern or southern parts of the Archipelago and others were restricted to particular regions. Newly delineated genera showed interpretable geographical patterns and could be related to environmental factors, suggesting that this more natural grouping may enhance our understanding of diatom ecology. Geographical, physical, and chemical factors are needed to explain diatom distributions in the Arctic.     

Effects of a simulated upwelling event on the littoral epilithic diatom community of an ancient tropical lake (Lake Matano,Sulawesi Island,Indonesia)

Currently accepted paradigms in ecology dictate that disturbances at all temporal scales exert a significant influence on community structure and ecosystem stability. Microbial community resistance and resilience to perturbations are largely dependent on the physiological flexibility and taxonomic richness of the pre-perturbation community. Can a microbial community dominated by late-successional endemic taxa exhibit resistance and/or functional redundancy? In this study, intact littoral epilithic diatom communities from an ancient, tropical lake were exposed to oxygenated, filtered hypolimnetic water to simulate a lake upwelling event. Filtered lake surface water was used as a control. Discriminant function models based on changes in density and relative abundance of taxa after both treatments assigned samples to their correct treatment groups 100% of the time. A change in relative abundance of taxa between the two treatments indicated that competitive outcomes varied with a shift in the water chemistry, with different taxa exhibiting positive, negative, or neutral numerical responses. These results suggest that highly endemic diatom communities can maintain community function through shifts in competitive dynamics. We conclude that condition-specific competition models can be invoked to explain diatom community dynamics despite the inability of diatoms to use behavior to respond to changes in the abiotic environment.     

Assemblage diversity,cell density and within-slide variability: Implications for quality assurance/quality control and uncertainty assessment in diatom-based monitoring

This study was undertaken to evaluate the variability associated with the microscope analysis step in the application of the Eastern Canadian Diatom Index (IDEC: Indice Diatomées de l’Est du Canada), with the general objective of developing a suitable quality assurance/quality control (QA/QC) program for this biological index. For this purpose, we estimated within-slide variability (replicability) and inter-analysts variability (reproducibility), as a function of diatom assemblage diversity and slide cell density. Overall, our results show that variability associated with diatom assemblage characterization is low, which ensures that IDEC scores reflect environmental changes rather than variability at the microscope analysis step. The main recommendations ensuing from this study are (for the IDEC in particular but also for diatom-based monitoring in general):

• (1)An error term of ±2 IDEC units corresponding to the within-slide variability (replicability) should accompany all reported IDEC scores.
• (2)A deviation of ±3 points from the audit's IDEC scores should be considered as an acceptable difference. Considering the above-mentioned estimated error term of ±2 associated with all IDEC scores, an overall deviation of 7 would still be satisfactory.
• (3)Samples showing low diversity (Hill's N2 ≤5) should automatically be submitted for QA/QC.
• (4)A Bray–Curtis (analyst vs audit) similarity of ≥60% should also be included as a QA/QC criterion, and should increase to ≥70% for poorly diversified assemblages (Hill's N2 ≤5).
• (5)A diatom valve density of ≤15 per field of view should be targeted in order to reduce variability at the enumeration step.

The results of this study illustrate how a relatively simple and straightforward approach to QA/QC can greatly strengthen the reliability of ecological inferences from an index based on a group of organisms with a high taxonomical diversity. It also highlights the importance of regular communication between analysts in order to maintain a high degree of concordance within taxonomical identification.     

Should only live diatoms be used in the bioassessment of small mountain streams?

It is unclear whether differentiating live and dead diatoms would enhance the accuracy and precision of diatom-based stream bioassessment. We collected benthic diatom samples from 25 stream sites in the Northern Oregon Coast ecoregion. We counted live diatoms (cells with visible chloroplasts) and then compared the counts with those generated using the conventional method (clean counts). Non-metric multidimensional scaling (NMDS) showed that the diatom assemblages generated from the two counts were overall similar. The relationships between the two diatom assemblages (summarized as NMDS ordination axes) and the environmental variables were also similar. Both assemblages correlated well with in-stream physical habitat conditions (e.g., channel dimensions, substrate types, and canopy cover). The conventional diatom method provides taxonomic confidence while the live diatom count offers ecological reliability. Both methods can be used in bioassessment based on specific assessment objectives. Handling editor: J. Saros     

Defining ecological thresholds to determine class boundaries in a bioassessment tool: The case of the Eastern Canadian Diatom Index (IDEC)

Most bioassessment tools are based on the Reference Condition Approach (RCA), where the biological integrity of a site is defined by the “distance” between current conditions and its reference condition status. Among them, the Eastern Canadian Diatom Index (IDEC) was developed to evaluate the ecological integrity of streams along an alteration gradient, as a function of the dissimilarity of their diatom community from their suitable reference communities. In the first version of the IDEC, the alteration gradient was arbitrarily divided, like most traditional approaches, into five classes of equal size representing the qualitative statuses of the site. In this article, we propose a remodeling of those classes by introducing ecologically meaningful thresholds, reducing the subjectivity in the determination of the number and the range (widths) of classes. We developed a new approach which uses biotypes issued from a classification technique (Self-Organizing Maps) to determine thresholds between integrity classes of the IDEC. These biotypes represent relatively homogenous ecological entities composed of taxa adapted to a particular biological integrity status. Based on these biotypes, four classes were established. The new limits between classes are now based on the maximum ecological distance between diatom groups, and the transition from one class to another may be related to major ecological thresholds that induce important shifts in community structure. The proposed biotype-based approach allows for the identification of ecologically meaningful differences among biological communities and provides a more relevant interpretation of the community changes along the alteration gradient.     

Structure of Benthic Diatom Assemblages from a Mangrove Environment in a Mexican Subtropical Lagoon1

The taxonomic list and the structure of benthic diatom assemblages occurring in fine sediments (silt and sand) from the mangrove forest of the Balandra lagoon in Baja California Sur, Mexico was determined based on seasonal samplings for one year. Assemblage structure was analyzed using several ecological indices for estimating diversity (H'), dominance (REDI), equitability, and similarity. A total of 230 diatom taxa were identified and include 109 new records for the Baja California peninsula coast. Taxa representative of highly productive and hypersaline environments were common. Assemblages were characterized by a few abundant species and many uncommon or rare taxa. High diatom diversity estimates at all sampling sites during all seasons suggest that diatom assemblages in sediments of the Balandra lagoon represent a quasi-pristine environment.     

Identifying reference benthic diatom communities in an agricultural watershed (Guadiana River,SW Spain)

Determining the ecological status of river ecosystems should be based on reference (near-natural) conditions and on the use of their biological communities. Identifying reference conditions is particularly difficult in largely disturbed watersheds, such as those of agricultural landscapes. Ecotype reference sites and their characteristic diatom communities were identified in the Guadiana watershed. Three different ecotypes were defined: rivers with siliceous bedrocks, upper watershed calcareous rivers, and mainland watercourses. Thirteen key stressors divided in four categories (channel alteration, hydrological pressure, pollution pressure, and river habitat pressure) were used to select reference sites in each ecotype. Multivariate techniques were used to describe type-specific reference diatom community in each ecotype. Because of the difficulty to define reference sites in the mainland watercourses, some sites were selected under the criterion of minimum impacted sites. Diatoms inhabiting sites included species tolerant to high nutrient concentration and mineralized waters, like Nitzschia inconspicua, Gomphonema parvulum, and Navicula veneta. These taxa defined the best condition (near-to-reference) in an ecotype highly impacted by human activities, the best possible in the long-lasting impaired conditions in the large river watercourses in agricultural landscapes.     

Biodiversity shortcuts in biomonitoring of novel ecosystems

Hydropower reservoirs are novel ecosystems that present different challenges for the design of biomonitoring programs. To ensure long-term programs and wide spatial coverage, it is important to test the reliability of different cost-saving strategies that have been widely evaluated among researchers, such as taxonomic sufficiency, numerical sufficiency and surrogate groups. Using data on zooplankton composition, our objective was to test whether these strategies could be applied to increase the efficiency of biomonitoring programs in reservoirs. Zooplankton data were collected at the Santo Antônio do Jari Hydroelectric Plant, which is located between the states of Pará and Amapá (Amazon region, Brazil), over 23 months between 2012 and 2015. The data were organized in different taxonomic groups (cladocerans, copepods, rotifers and testate amoebae) and matrices by decreasing the taxonomic resolution (from species to genera and families) and the numerical resolution (from species abundance to species presence/absence) of the data. The ordination patterns obtained with Principal Coordinate Analysis for the different matrices were compared using Procrustes analyses. Our results suggest that ordination patterns using genus-level data were similar to those obtained with species-level data. However, analyses based on family-level data were often unable to reproduce results based on species-level data. Ordination patterns using presence/absence data were similar to those obtained from abundance data. We also found that the strengths of the relationships between ordinations derived from different taxonomic groups (e.g., rotifers and cladocerans) were low and often not significant. We conclude that the use of zooplankton genera and presence/absence data may be a reliable strategy to monitor reservoirs. However, our results highlight the need to monitor different zooplankton groups, as the ordination patterns depicted by a given group were poorly related to those generated by a second zooplankton group.     

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

DNA metabarcoding is a promising approach for rapidly surveying biodiversity and is likely to become an important tool for measuring ecosystem responses to environmental change. Metabarcoding markers need sufficient taxonomic coverage to detect groups of interest, sufficient sequence divergence to resolve species, and will ideally indicate relative abundance of taxa present. We characterized zooplankton assemblages with three different metabarcoding markers (nuclear 18S rDNA, mitochondrial COI, and mitochondrial 16S rDNA) to compare their performance in terms of taxonomic coverage, taxonomic resolution, and correspondence between morphology‐ and DNA‐based identification. COI amplicons sequenced on separate runs showed that operational taxonomic units representing >0.1% of reads per sample were highly reproducible, although slightly more taxa were detected using a lower annealing temperature. Mitochondrial COI and nuclear 18S showed similar taxonomic coverage across zooplankton phyla. However, mitochondrial COI resolved up to threefold more taxa to species compared to 18S. All markers revealed similar patterns of beta‐diversity, although different taxa were identified as the greatest contributors to these patterns for 18S. For calanoid copepod families, all markers displayed a positive relationship between biomass and sequence reads, although the relationship was typically strongest for 18S. The use of COI for metabarcoding has been questioned due to lack of conserved primer‐binding sites. However, our results show the taxonomic coverage and resolution provided by degenerate COI primers, combined with a comparatively well‐developed reference sequence database, make them valuable metabarcoding markers for biodiversity assessment.     

INFECTION,GROWTH, AND COMMUNITY-LEVEL CONSEQUENCES OF A DIATOM PATHOGEN IN A SONORAN DESERT STREAM1

We describe effect of a pathogen that spread through a dense, rapidly growing, benthic diatom community during two infection periods (February and mid-April 1991) in Sycamore Creek, Arizona. Infected areas appeared as gray rings within a matrix of healthy diatom growth and spread rapidly, eventually covering all benthic substrata and causing algal sloughing (within 2 wk in February and 1 wk in April). Examination of algal material with transmission electron microscopy revealed the presence of invasive bacteria within diatom cells from infected areas, suggesting a pathogenic bacterium as the most probable cause of this phenomenon. Infected area supported lower chlorophyll a concentrations and contained higher percentages of diatom cells with fragmented or reduced chloroplasts than uninfected areas. Spread of the pathogen appeared to be linked most strongly with diatom densities. The infection spread most rapidly in April, when cell densities were highest, and decimated all diatom species populations. The February infection was more species-specific in its action, affecting large motile and rosetteforming taxa more strongly than small, adnate diatoms. This latter group likely resided at the base of communities and may have been buffered from pathogen transfer by mucilage and/or dentrital particles. Consequently, relative abundance of small, adnate diatom taxa increased in algal communities as a result of the February infection. Pathogen-induced alteration of diatom species composition and abundance should influence primary production in this ecosystem and affect the dynamics of organisms that exploit algae as a resource.     

Characterization of Freshwater Diatom Communities: Comparing Taxonomic and Genetic‐Fingerprinting Approaches

Benthic diatom assemblages from five sampling sites located on two rivers were characterized simultaneously by means of traditional microscopic observations and PCR‐DGGE fingerprinting with primers specifically designed for Bacillariophyceae. Community structure, richness, and diversity assessed by both methods were compared. Diatom lists obtained from morphological identification were separated into subsets, depending on (i) the taxonomic level considered (genus, species, variety) and, for each of them, (ii) the relative abundance (RA) of each component (the whole data set, RA > 1%, RA > 2%). These data were then compared to genetic fingerprinting data. Clusters based on taxonomic composition and DGGE banding patterns were very similar, showing good correspondence of community structure between the two methods. Data were compared by linear regressions between indices (richness, diversity) and by Mantel tests on dissimilarity matrices generated for each community composition data set. Statistical analysis indicated that the most reliable correlations with fingerprinting were obtained for genera representing more than 1% RA or species representing more than 2% RA. The results reveal that the PCR‐DGGE protocol described here offers a satisfactory alternative for performing preliminary screening of coarse differences in diatom global community structure between samples. It can be regarded as a good complement to taxonomic analyses, which still remain necessary to detect precise changes in richness and diversity, especially when considering species with low abundance in natural assemblages.     

Taxonomy‐free molecular diatom index for high‐throughput eDNA biomonitoring

Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution. Here, we investigate the possibility to overcome these limitations using a taxonomy‐free approach that allows the computing of a molecular index directly from eDNA data without any reference to morphotaxonomy. As a case study, we use the benthic diatoms index, commonly used for monitoring the biological quality of rivers and streams. We analysed 87 epilithic samples from Swiss rivers, the ecological status of which was established based on the microscopic identification of diatom species. We compared the diatom index derived from eDNA data obtained with or without taxonomic assignment. Our taxonomy‐free approach yields promising results by providing a correct assessment for 77% of examined sites. The main advantage of this method is that almost 95% of OTUs could be used for index calculation, compared to 35% in the case of the taxonomic assignment approach. Its main limitations are under‐sampling and the need to calibrate the index based on the microscopic assessment of diatoms communities. However, once calibrated, the taxonomy‐free molecular index can be easily standardized and applied in routine biomonitoring, as a complementary tool allowing fast and cost‐effective assessment of the biological quality of watercourses.     

Plastid Genome Phylogeny and a Model of Amino Acid Substitution for Proteins Encoded by Chloroplast DNA

Maximum likelihood (ML) phylogenies based on 9,957 amino acid (AA) sites of 45 proteins encoded in the plastid genomes of Cyanophora, a diatom, a rhodophyte (red algae), a euglenophyte, and five land plants are compared with respect to several properties of the data, including between-site rate variation and aberrant amino acid composition in individual species. Neighbor-joining trees from AA LogDet distances and ML analyses are seen to be congruent when site rate variability was taken into account. Four feasible trees are identified in these analyses, one of which is preferred, and one of which is almost excluded by statistical criteria. A transition probability matrix for the general reversible Markov model of amino acid substitutions is estimated from the data, assuming each of these four trees. In all cases, the tree with diatom and rhodophyte as sister taxa was clearly favored. The new transition matrix based on the best tree, called cpREV, takes into account distinct substitution patterns in plastid-encoded proteins and should be useful in future ML inferences using such data. A second rate matrix, called cpREV*, based on a weighted sum of rate matrices from different trees, is also considered. Received: 3 June 1999 / Accepted: 26 November 1999