Using Diatom Assemblages to Assess Urban Stream Conditions

We characterized changes in diatom assemblages along an urban-to-rural gradient to assess impacts of urbanization on stream conditions. Diatoms, water chemistry, and physical variables of riffles at 19 urban and 28 rural stream sites were sampled and assessed during the summer base flow period. Near stream land use was characterized using GIS. In addition, one urban and one rural site were sampled monthly throughout a year to assess temporal variation of diatom assemblages between the urban and rural stream sites. Canonical correspondence analysis (CCA) showed that the 1st ordination axis distinctly separated rural and urban sites. This axis was correlated with conductivity (r = 0.75) and % near-stream commercial/industrial land use (r = 0.55). TWINSPAN classified all sites into four groups based on diatom assemblages. These diatom-based site groups were significantly different in water chemistry (e.g., conductivity, dissolved nutrients), physical habitat (e.g., % stream substrate as fines), and near-stream land use. CCA on the temporal diatom data set showed that diatom assemblages had high seasonal variation along the 2nd axis in both urban and rural sites, however, rural and urban sites were well separated along the 1st ordination axis. Our results suggest that changes in diatom assemblages respond to urban impacts on stream conditions.     

Diatom species–environment relationships and inference models from Isachsen, Ellef Ringnes Island, Canadian High Arctic

Surface sediment diatom assemblages were examined from 26 freshwater sites near Isachsen (78°47N, 103°32W), Ellef Ringnes Island, a region of diverse and atypical water chemistry for high arctic sites. One hundred and sixty eight diatom taxa were identified from these samples, over 50% of which had not previously been recorded in the Canadian High Arctic. Variations in diatom assemblages were related to changes in measured environmental variables using multivariate techniques. Canonical correspondence analysis (CCA) indicated that five variables contributed significantly to explaining patterns of diatom variation (i.e., COND, DIC, Mn, TPF, TPU). The first CCA axis (=0.44) was primarily controlled by conductivity-related variables, while CCA axis 2 (=0.21) was related to particulate concentrations. Diatom-based inference models were generated for the reconstruction of conductivity (RMSEP_jack=0.32, r²_jack=0.76) and pH (RMSEP_jack=0.40, r²_jack=0.69). The strengths of these models indicate that it will be possible to reliably infer past trends in conductivity and pH from diatom assemblages preserved in dated sediment cores from the Isachsen region.     

Diatoms from Indonesian mangroves and their suitability as sea-level indicators for tropical environments

We collected modern diatom samples from two mangrove environments of Sulawesi, Indonesia to provide a much needed dataset for the reconstruction of sea level from tropical environments. The diatom assemblages are dominated by mesohalobous species (e.g. Amphora coffeaeformis, Amphora turgida, Achnanthes delicatula, Nitzschia sigma and Tryblionella balatonis) and oligohalobous (e.g. Amphora veneta, Diploneis ovalis and Progonoia didiomatia) taxa. Both study sites show strong vertical zonations, which suggests that duration and frequency of intertidal exposure are important factors in controlling the relative abundance of diatoms. The assemblages can be generally divided into a mixed assemblage of mesohalobous, oligohalobous–halophilous and oligohalobous-indifferent diatoms that are found from the dense mangrove vegetation towards the landward edge of the transects, and mesohalobous diatom assemblages that are located within the fringing Rhizophora and tidal flat environments. We subsequently developed a diatom-based transfer function, which is a quantitative approach to sea-level reconstruction. The relationship between observed and diatom-predicted elevations suggests accurate and precise reconstructions are possible. The error estimate (± 0.15 m) is comparable to diatom-based transfer functions from temperate marshes.     

Development of a diatom-based transfer function for lakes and streams severely impacted by secondary salinity in the south-west region of Western Australia

The association of diatom assemblages to salinity was studied in 95 lakes and streams ranging from freshwater to hypersaline in the south-west of Western Australia. The relationship between environmental variables and species composition was explored using canonical correspondence analysis (CCA) and partial CCA. Salinity was shown to account for a significant and independent amount of variation in the diatom data, enabling a transfer function to be developed based on the final dataset, which consisted of 89 sites and 150 diatom taxa. The most successful model was derived using tolerance-downweighted weighted averaging. Summary statistics showed that the transfer function performed very well with a high coefficient of determination and low prediction errors that remained high after the cross-validation method of jackknifing (r _apparent² = 0.97 and r _jackknifed² = 0.89). This suggests that salinity can be accurately predicted using relative abundances of diatoms, and the model can now be applied to paleolimnological reconstructions. However, the transfer function also provides the basis for use in future biomonitoring studies to detect increases in salinity for lakes and streams most at risk, as well as to evaluate the success of remediation measures implemented to secondary salinised systems. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Guest Editors: J. John & B. Timms Salt Lake Research: Biodiversity and Conservation—Selected papers from the 9th Conference of the International Society for Salt Lake Research     

Comparison of Freshwater Diatom Assemblages from a High Arctic Oasis to Nearby Polar Desert Sites and Their Application to Environmental Inference Models

Arctic oases are regions of atypical warmth and relatively high biological production and diversity. They are small in area (<5 km²) and uncommon in occurrence, yet they are relatively well studied due to the abundance of plant and animal life contained within them. A notable exception is the lack of research on freshwater ecosystems within polar oases. Here, we aim to increase our understanding of freshwater diatom ecology in polar oases. Diatoms were identified and enumerated from modern sediments collected in 23 lakes and ponds contained within the Lake Hazen oasis on Ellesmere Island, and compared with diatom assemblages from 29 sites located outside of the oasis across the northern portion of the island. There were significant differences in water chemistry variables between oasis and northern sites, with oasis sites having higher conductivity and greater concentrations of nutrients and related variables such as dissolved organic carbon (DOC). Taxa across all sites were typical of those recorded in Arctic freshwaters, with species from the genera Achnanthes sensu lato, Fragilaria sensu lato, and Nitzschia dominating the assemblages. A correspondence analysis (CA) ordination showed that oasis sites generally plotted separately from the northern sites, although the sites also appear to plot separately based on whether they were lakes or ponds. Canonical correspondence analysis (CCA) identified specific conductivity, DOC, and SiO₂ as explaining significant (P < 0.05) and additional amounts of variation in the diatom data set. The most robust diatom‐based inference model was generated for DOC, which will provide useful reconstructions on long‐term changes in paleo‐optics of high Arctic lakes.     

Distribution of benthic diatoms in U.S. rivers in relation to conductivity and ionic composition

• 1 We quantified the relationships between diatom relative abundance and water conductivity and ionic composition, using a dataset of 3239 benthic diatom samples collected from 1109 river sites throughout the U.S.A. [U.S. Geological Survey National Water‐Quality Assessment (NAWQA) Program dataset]. This dataset provided a unique opportunity to explore the autecology of freshwater diatoms over a broad range of environmental conditions.
• 2 Conductivity ranged from 10 to 14 500 μS cm^?1, but most of the rivers had moderate conductivity (interquartile range 180–618 μS cm^?1). Calcium and bicarbonate were the dominant ions. Ionic composition, however, varied greatly because of the influence of natural and anthropogenic factors.
• 3 Canonical correspondence analysis (CCA) and Monte Carlo permutation tests showed that conductivity and abundances of major ions (HCO + CO, Cl^?, SO, Ca²⁺, Mg²⁺, Na⁺, K⁺) all explained a statistically significant amount of the variation in assemblage composition of benthic diatoms. Concentrations of HCO + CO and Ca²⁺ were the most significant sources of environmental variance.
• 4 The CCA showed that the gradient of ionic composition explaining most variation in diatom assemblage structure ranged from waters dominated by Ca²⁺ and HCO + CO to waters with higher proportions of Na⁺, K⁺, and Cl^?. The CCA also revealed that the distributions of some diatoms correlated strongly with proportions of individual cations and anions, and with the ratio of monovalent to divalent cations.
• 5 We present species indicator values (optima) for conductivity, major ions and proportions of those ions. We also identify diatom taxa characteristic of specific major‐ion chemistries. These species optima may be useful in future interpretations of diatom ecology and as indicator values in water‐quality assessment.

     

Total phosphorus inference models and indices for coastal plain streams based on benthic diatom assemblages from artificial substrates

We investigated the potential for using diatoms to monitor and assess nutrient enrichment in coastal plain streams using weighted-averaging inference models and diatom trophic indices. Samples were collected from low-gradient, clay- to sand-bottom streams in New Jersey (NJ), USA, using artificial substrates (diatometers). Multivariate analysis showed that conductivity was overall the most important explanatory variable. Total phosphorus (TP) explained a significant proportion of the variation in diatom species composition. There was statistical justification for development of inference models for TP but not for total nitrogen (TN). We developed and tested models for inferring TP using weighted-averaging (WA) and weighted-averaging partial least squares (WA-PLS) regression and calibration techniques. We also created a diatom TP index by rescaling the inferred TP values. WA-PLS provided the best model (n = 38), which showed moderate predictive ability (r _boot² = 0.43; RMSEP_boot = 0.30 log₁₀ μg l⁻¹ TP); it performed best at lower TP concentrations and tended to underestimate values above 100 μg l⁻¹. The TP index performed well; it assigned the majority of the index scores to the correct nutrient category. TP models and indices developed for the Coastal Plain had lower predictive ability than those developed for northern NJ and streams in other comparable geographic regions of the US. This lower performance can be attributed primarily to a data gap in the TP gradient in the calibration dataset (lack of sites with TP concentrations between 240 and 560 μg l⁻¹), and a smaller number of samples. We conclude that diatom-based TP inference models and artificial substrate sampling are useful for assessing and monitoring nutrient enrichment in coastal plain streams. Given the worldwide distribution of streams similar to those in this study, these tools should be widely applicable. Handling editor: D. Ryder     

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.     

The construction of a diatom-based chlorophyll a transfer function and its application at three lakes on Signy Island (maritime Antarctic) subject to differing degrees of nutrient enrichment

1. Canonical correspondence analysis of a diatom and water chemistry dataset from fifty-nine maritime Antarctic lakes situated on Signy and Livingston Islands showed that nutrients and functions of nutrients (NH₄⁺, chlorophyll a) accounted for a significant fraction of the variance in the diatom data. 2. Weighted averaging regression was used to construct a diatom-based transfer function for inferring chlorophyll a concentrations from sediment core diatom assemblages. 3. The transfer function was applied to ²¹⁰Pb-dated sediment cores from three lakes (Moss, Sombre and Heywood) receiving different levels of nutrient input from fur seal populations, i.e. low, medium and high, respectively. 4. Moss Lake showed relatively stable reconstructed chlorophyll a values, and no evidence of recent eutrophication, agreeing with measured chlorophyll a concentrations at the site. 5. Changes in diatom assemblages and results of chlorophyll a reconstructions at Sombre Lake suggested that nutrient enrichment had occurred, which could be clearly linked to fluctuations in the measured water chemistry over the last 10–14 years. 6. Despite recorded increases in recent nutrient inputs there was no apparent diatom response at Heywood Lake.     

Influence of ionic strength and conductivity on benthic diatom communities in a tropical river (Monjolinho), S?o Carlos-SP, Brazil

Benthic diatoms are important indicators of ecological conditions in lotic systems. The objective of this study was to elucidate the confounding effects of eutrophication, organic pollution and ionic strength and conductivity on benthic diatom communities. Benthic diatoms and water quality sampling was done at 10 sites during summer base flow period (2008 and 2009). Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to determine environmental gradients along which species vary with respect to ionic strength and conductivity and other environmental variables. Using variance partitioning, we assessed the individual importance of a set of environmental variables (eutrophication and organic pollution) versus ionic strength and conductivity on diatom community structure. The effects of ionic strength and conductivity and organic pollution, eutrophication and other environmental variables were integrated into overall resultant benthic diatom communities. Through partial CCA, we partitioned the variance in diatom data between two sets of exploratory variables, i.e. ionic strength and conductivity (26.9%); other variables, particularly eutrophication and organic pollution (23.0%); shared variance (11.3%) and unexplained variance (38.8%). Due to the interaction of the effects of ionic strength and conductivity and other variables in this study, laboratory experiments must be performed to confirm the observed effects of ionic strength and conductivity.     

Benthic diatom communities in boreal streams: community structure in relation to environmental and spatial gradients

An important goal for community ecology is the characterization and prediction of changes in community patterns along environmental gradients. We aimed to identify the major environmental correlates of diatom distribution patterns in boreal running waters. We classified 197 stream sites based on their diatom flora. Direct ordination methods were then used to identify the key environmental determinants of this diatom-based stream typology. Finally, we tested whether a regional classification scheme based on terrestrial landscapes (ecoregions) provides a reasonable framework for a regional grouping of streams based on their diatom flora. Two-way indicator species analysis produced 13 site groups, which were primarily separated by chemical variables, mainly conductivity, total P and water colour. In partial CCA, the environmental and spatial factors accounted for 38% and 24%, respectively, of explained variation in community composition. A high proportion (almost 40%) of variation explained by the combined effect (spatially-structured environmental) indicated that diatom communities of boreal streams incorporate a strong spatial component. At the level of subecoregions, classification strength was almost equally strong for all sites as for near-pristine reference sites only. Procrustes analysis indicated that spatial factors and patterns in diatom community structure were strongly concordant. Our data support the argument that diatom communities are strongly spatially structured, with distinctly different communities in different parts of the country. Because of the strong spatial patterns of community composition, bioassessment programs utilising lotic diatoms would clearly benefit from regional stratification. A combination of regional stratification and the prediction of assemblage structure from local environmental features might provide the most robust framework for diatom-based assessment of the biological integrity of boreal streams.     

Development of a diatom index of biotic integrity for acid mine drainage impacted streams

Acid mine drainage (AMD) resulting from extensive coal mining throughout Appalachia since the 1800s has caused a legacy of severe acid and dissolved metal loads to thousands of stream miles, which has critically impacted aquatic life and ecological attributes. Relationships of diatoms and macroinvertebrates with AMD have been established, but no index specifically designed to quantify AMD impacts using diatoms has been created, nor have the response of multiple organism groups been compared for their utility as indices assessing AMD severity.For the purpose of developing an effective assessment and management strategy for AMD impacted streams, this study created and tested a multi-metric AMD-diatom index of biotic integrity (AMD-DIBI) and compared its response to AMD severity with an already established multi-metric macroinvertebrate community index (ICI). In 2006, 41 sites in southeast Ohio were sampled that represented an AMD impact gradient and non-AMD impacted reference sites. Metrics comprising the AMD-DIBI were selected based on their responsiveness to AMD and nutrient impacts. In the following year, the AMD-DIBI and its metrics were tested on a validation dataset consisting of 18 sites in an AMD impacted watershed. Results indicated a significant correlation between AMD-DIBI and ICI scores, and both indices and all metrics were strongly correlated with water chemistry variables indicative of AMD pollution (P < 0.05). Stepwise multiple regression selected alkalinity and conductivity as most influential to AMD-DIBI (adjusted r² = 0.70) and ICI scores (adjusted r² = 0.66). Narrative classes (e.g., Poor, Fair, Good, and Excellent) defined by index scores provided effective classifications of AMD severity. When tested on the watershed scale, AMD-DIBI and its metrics very successfully quantified AMD gradients and coal mining impacts as indicated by canonical correspondence analysis. This newly developed AMD-DIBI will be very useful for assessing impairment, sensitivity, and recovery of diatom communities in streams damaged or threatened by coal mining activities. In addition, because the AMD-DIBI was very responsive to a gradient of AMD pollution, it could be used in future studies measuring the long-term status of streams and effectiveness of various remediation methods. This study highlights the responsive power of diatom-based metrics.     

Relationships Between Environmental Variables and Benthic Diatom Assemblages in California Central Valley Streams (USA)

This study examines distributional patterns of benthic diatom assemblages in relation to environmental characteristics in streams and rivers in the California Central Valley ecoregion. Benthic diatoms, water quality, and physical habitat conditions were characterized from 53 randomly selected sites. The stream sites were characterized by low mid-channel canopy cover and high channel substrate embeddedness. The waters at these sites were enriched with minerals and turbidity varied from 1.3 to 185.0 NTU with an average of 13.5 NTU. A total of 249 diatom taxa were identified. Average taxa richness was 41 with a range of 7–76. The assemblages were dominated by Staurosira construens (11%), Epithemia sorex (8%), Cocconeis placentula (7%), and Nitzschia amphibia (6%). Multivariate analyses (cluster analysis, classification tree analysis, and canonical correspondence analysis) all showed that benthic diatom assemblages were mainly affected by channel morphology, in-stream habitat, and riparian conditions. The 1st CCA axis negatively correlated with mean wetted channel width (r = −0.66) and thalweg depth (r = −0.65) (Table 4). The 2nd axis correlated with % coarse substrates (r=0.60). Our results suggest that benthic diatoms can be used for assessing physical habitat alterations in streams.     

Stream diatom assemblages as predictors of climate

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BENTHIC DIATOM AUTECOLOGY AND INFERENCE MODEL DEVELOPMENT FROM THE CANADIAN HIGH ARCTIC ARCHIPELAGO1

Diatom assemblages were analyzed from 64 lakes and ponds from Alert, Ellesmere Island and Mould Bay, Prince Patrick Island in the Canadian High Arctic Archipelago. Diverse water chemistry conditions and diatom communities were present in these sites. Small benthic taxa typically dominated diatom communities; however, assemblages were markedly different between Alert and Mould Bay sites in response to disparate water chemistry characteristics in the two regions. The most abundant taxa belonged to the genera Navicula, Cymbella, Achnanthes, Nitzschia, and Pinnularia. Canonical correspondence analysis indicated that pH, specific conductivity, dissolved organic carbon, and total phosphorus were the most important limnological variables in determining species composition. Diatom inference models were developed for pH, specific conductivity, and dissolved organic carbon using weighted averaging and weighted averaging partial least squares techniques; these had root mean square error of prediction/r²_boot values of 0.40/0.77, 0.28/0.70, and 0.24/0.55, respectively. These models are applicable to sites with large ranges of taxonomic and limnological variation and will allow the reconstruction of past changes of climate‐related limnological parameters from biostratigraphic records in future paleolimnological studies.     

Environmental controls of diatom species in northeast Pacific sediments

Non-linear, unimodal techniques are suitable for estimation of environmental properties in the northeast (NE) Pacific based on fossil diatom taxa (species and/or species groups) found in modern (core-top) sediments. Canonical Correspondence Analysis (CCA), a constrained ordination technique, discerned best-fit relationships among two multivariate datasets (the floral and the environmental) and thus yielded insight into the environmental variables that best explain the species variance within diatom populations. Based on these insights, we developed predictive functions for annual Primary Productivity (PP) and seasonal range of sea Sea-Surface Temperature using unimodal models and cross validation techniques. Estimates of annual PP (r²_jack = 0.92; RMSEP = 91.94 gC/m²/y) explained the highest percentage of variance in the core-top diatom record (22.1%).     

Testing of the applicability of European diatom indices in the tropical rift valley lake,Lake Hawassa,in Ethiopia

Quantitative ecological monitoring of African lakes is needed to understand growing human pressures on ecosystems. Diatom-based indices are routinely used for this purpose elsewhere in the world, but have not yet been produced for the flora of African freshwater lakes. Here we tested the applicability of the European diatom indices on the biomonitoring system of Lake Hawassa, Ethiopia. Physico-chemical and benthic diatom sampling was done at nine sites with different degrees of human disturbance along the lakeshore area from February to November 2015 and 2016. A percentage disturbance score (PDS) was calculated at each site and categorised from no evident disturbance (0–25%) to high disturbance (75–100%). Based on this criterion and selected physico-chemical parameters, the sampling sites categorized into minimal, moderate and high disturbance. Seventeen diatom indices were calculated using Omnidia software version 5.3. Out of a total of 17 indices that were calculated using the Omnidia software, six were selected as potential metrics. The diatom indices had a high discrimination efficiency and were significantly correlated with most the environmental parameters (r > 0.6; p < 0.05). Among these, the trophic diatom index (TDI) and generic diatom index (IDG) showed the best potential to discriminate the three clustered sites, based on their ecological classification. Accordingly, although robust locally based indices are needed, the TDI and IDG diatom indices could be used in monitoring of water quality in tropical African rift lakes.     

Laurentian Great Lakes Phytoplankton and Their Water Quality Characteristics,Including a Diatom-Based Model for Paleoreconstruction of Phosphorus

Recent shifts in water quality and food web characteristics driven by anthropogenic impacts on the Laurentian Great Lakes warranted an examination of pelagic primary producers as tracers of environmental change. The distributions of the 263 common phytoplankton taxa were related to water quality variables to determine taxon-specific responses that may be useful in indicator models. A detailed checklist of taxa and their environmental optima are provided. Multivariate analyses indicated a strong relationship between total phosphorus (TP) and patterns in the diatom assemblages across the Great Lakes. Of the 118 common diatom taxa, 90 (76%) had a directional response along the TP gradient. We further evaluated a diatom-based transfer function for TP based on the weighted-average abundance of taxa, assuming unimodal distributions along the TP gradient. The r² between observed and inferred TP in the training dataset was 0.79. Substantial spatial and environmental autocorrelation within the training set of samples justified the need for further model validation. A randomization procedure indicated that the actual transfer function consistently performed better than functions based on reshuffled environmental data. Further, TP was minimally confounded by other environmental variables, as indicated by the relatively large amount of unique variance in the diatoms explained by TP. We demonstrated the effectiveness of the transfer function by hindcasting TP concentrations using fossil diatom assemblages in a Lake Superior sediment core. Passive, multivariate analysis of the fossil samples against the training set indicated that phosphorus was a strong determinant of historical diatom assemblages, verifying that the transfer function was suited to reconstruct past TP in Lake Superior. Collectively, these results showed that phytoplankton coefficients for water quality can be robust indicators of Great Lakes pelagic condition. The diatom-based transfer function can be used in lake management when retrospective data are needed for tracking long-term degradation, remediation and trajectories.     

Determinants of Benthic Diatom Community Structurein Boreal Streams: the Role of Environmental and Spatial Factors at Different Scales

Benthic diatoms were sampled at 197 sites in Finnish boreal streams. The diatom distribution patterns were related to environmental and spatial factors at three spatial scales using Canonical Correspondence Analysis (CCA). The results emphasized the predominance of chemical‐constituent concentration and ion composition on structuring benthic diatom communities in running waters. Within a river system, physical factors had notable influence on diatom community structure reflecting mainly only minor changes in water chemistry within a watershed. Partial CCA revealed that pure spatial component explained ca. 20% of explainable variation in diatom data at each of the three scales. Environmental factors captured 53–78% of explained variation in species data at ecoregion and river system level. According to Procrustean Randomization Test, spatial coordinates of the study sites and patterns in diatom community structure were strongly concordant (m² = 0.862, p = 0.001) across the largest spatial scale. Similarly, at smaller spatial scales in southern and central Finland, congruence was significant. These data support the view that diatom communities exhibit a rather strong spatial component especially at largest, national scale.