Structure Of Diatom Assemblages Research Articles

Using DNA metabarcoding to characterize national scale diatom-environment relationships and to develop indicators in streams and rivers of the United States

Recent advancements in DNA techniques, metabarcoding, and bioinformatics could help expand the use of benthic diatoms in monitoring and assessment programs by providing relatively quick and increasingly cost-effective ways to quantify diatom diversity in environmental samples. However, such applications of DNA-based approaches are relatively new, and in the United States, unknowns regarding their applications at large scales exist because only a few small-scale studies have been done. Here, we present results from the first nationwide survey to use DNA metabarcoding (rbcL) of benthic diatoms, which were collected from 1788 streams and rivers across nine ecoregions spanning the conterminous USA. At the national scale, we found that diatom assemblage structure (1) was strongly associated with total phosphorus and total nitrogen concentrations, conductivity, and pH and (2) had clear patterns that corresponded with differences in these variables among the nine ecoregions. These four variables were strong predictors of diatom assemblage structure in ecoregion-specific analyses, but our results also showed that diatom-environment relationships, the importance of environmental variables, and the ranges of these variables within which assemblage changes occurred differed among ecoregions. To further examine how assemblage data could be used for biomonitoring purposes, we used indicator species analysis to identify ecoregion-specific taxa that decreased or increased along each environmental gradient, and we used their relative abundances of gene reads in samples as metrics. These metrics were strongly correlated with their corresponding variable of interest (e.g., low phosphorus diatoms with total phosphorus concentrations), and generalized additive models showed how their relationships compared among ecoregions. These large-scale national patterns and nine sets of ecoregional results demonstrated that diatom DNA metabarcoding is a robust approach that could be useful to monitoring and assessment programs spanning the variety of conditions that exist throughout the conterminous United States.

Composition, structure, and distribution of diatom assemblages in Mediterranean thermal spring ecotones affected by natural and human disturbances

Composition, structure, and distribution of diatom assemblages in Mediterranean thermal spring ecotones affected by natural and human disturbances

Taxonomic diversity and structure of benthic diatom taxocenes (Bacillariophyta) along the Crimean Coast (the Black Sea)

Diversity and structure of benthic diatom assemblages in 16 Crimean nearshore habitats with varying levels of technogenic bottom area pollution at depths range 0.5–50 m were investigated and accessed using Taxonomic Distinctness indices (TaxDI). In total 793 species and intraspecific taxa, belonging to 736 species, 130 genera, 53 families, 27 orders and 3 classes of Bacillariophyta were registered. The structure of diatom assemblages from polluted sites can be described as having low species richness and a large proportion of mono- and oligospecies branches at the family and order levels. In locations under a moderate anthropogenic impact, the structure was characterised by relatively high species richness and an equal ratio of oligo- and poly-species branches closed at genus level, with the presence of monospecies branches converging at family or order level. Taxocenes in pristine sites were distinguished by the highest species richness and a predominance of poly-species branches closed at different hierarchical levels.

Ecological assessment of recent anthropogenic impacts on an estuarine ecosystem based on benthic diatom assemblages

Until recently, Camamu Bay (CB), a tropical estuarine ecosystem of the northeast coast of Brazil, state of Bahia, was considered pristine. However, an explosive regional economic growth is increasingly pressuring CB. We used the structure of diatom assemblages to determine whether this economic growth has impacted this habitat. We sampled water and sediment to determine the structure of diatom assemblages and measure physicochemical variables, including nutrients concentrations, salinity, pH, conductivity, temperature, redox potential, suspended particulate matter, dissolved oxygen, and granulometry at each of 30 sampling stations. We produced the percentage of the 11 eutrophication or organic pollution indicator taxa identified (namely Achnanthes fogedii, Bacillaria paxillifera, Cocconeis placentula, Cyclotella striata, Cyclotella stylorum, Halamphora coffeaeformis, Opephora marina, Paralia sulcata var. coronata, Paralia sulcata var. radiata, Planothidium delicatulum, and Tabullaria waernii) for each sample and we also determined the potential correlations of diatom taxa with the physicochemical variables. Our results revealed five distinct diatom groups determined by different combinations of variables reflecting the influence of natural and anthropic factors along the salinity gradient and that salinity exerted the strongest structuring effect on the assemblages. Higher presences of eutrophication indicator species were found near the central areas of the bay and in intermediate areas of Serinhaém and Maraú rivers. Planktonic taxa (e.g., Paralia sulcata) of occurring in the Marau River’s indicated high nutrients loading and uncommon hydrodynamic conditions. Our results suggest CB is undergoing a degradation process due to the economic activities.

Response of Diatoms to the Changing Water Quality in the Myristica Swamps of the Western Ghats, India

Myristica swamps are one of the rarest wetland ecosystems within the sub-tropical evergreen forests of the Western Ghats, India. As their name indicates, they harbor trees belonging to the ancient family Myristicaceae. Due to the waterlogged conditions and high humic decomposition, these swamps are acidic, harbor rare and endemic biotas, and provide ecosystem services to humans. Monitoring this rare ecosystem is crucial because the swamps that once formed a large hydrological network across the Western Ghats are now confined to isolated patches due to human disturbance such as agricultural interventions, roads, and dam construction. Due to the change in land use, there is also a drastic change in water chemistry and associated biodiversity. Biomonitoring is more precise than physical and chemical monitoring. So, the current study aimed to undertake a comprehensive analysis of the physical, chemical, and biological assessment of these swamps. The diatom assemblages are strongly affected by water chemistry and serve as a powerful indicator of environmental changes in the freshwater aquatic systems. However, there is no information on diatom assemblages in these swamps, and the present study aimed to determine the diatom assemblage structure in the Myristica swamps and their response to changing water quality. Diatom samples were taken at 17 different swamps across the central Western Ghats, and a set of environmental parameters was evaluated. Analysis revealed a total of 91 species of diatoms belonging to 27 genera across the 17 sites, from which 44 diatom species showed restricted distribution to this unique environment. Overall, the dominant diatom genera inside the swamps included, Navicula (19.8%), Gomphonema (16%), Eunotia (13.3%), Ulnaria (9.4%), Achnanthidium (8%), Frustulia (6.2%), Planothidium (5.2%), and Brachysira (2.8%). High diatom species richness was observed in the swamps having less anthropogenic disturbance, and diatom assemblage composition was primarily determined by dissolved oxygen, pH, and conductivity. The significant number of geographically restricted taxa in this study points towards our limited understanding of this tropical biome and calls for a dire need for more studies from here, not only to improve our knowledge concerning the diversity, ecology, and biogeography of these diatoms but to further encourage their use in applied (paleo) environmental sciences. Our results indicate that diatoms can prove useful environmental indicators even in harsh environments like swamps and can be a potential tool for assessing ecological and climatic change.

Response of Benthic Diatom Assemblages to Contamination by Metals in a Marine Environment

Studies on marine benthic diatoms in environments contaminated by metals are scarce. The typical structure of benthic diatom assemblages (species richness, diversity, dominance, dominant taxa) from undisturbed environments may be used as reference for contrasting with contaminated environments in order to observe how said assemblages respond to such disturbance. Thus, the Ho that the structure of benthic diatom associations and morphology of their frustules under contamination by metals would be normal, as in unpolluted environments was tested. To do this, concentrations of 24 metals were surveyed in a coastal zone impacted by mining residues, and the structure of benthic local diatom assemblages was described. Metal concentrations measurements for 15 metals surpassed the normal values of the upper earth cortex, seven were under the low range effect, and three (Cd, Cu, Zn) surpassed the medium range effect values. At a control site no element concentration was above the reference values for low range effect (LRE) or medium range effect (MRE) standards. There, diatom species richness (S) was high, particularly on seaweeds; where, 397 diatom taxa were recorded. In contrast, at the contaminated area 217 diatom taxa were recorded, but diversity (H’) ranged from 2.4 to 4.3. Relative high frequencies of deformed diatom valves mainly of Achnanthes spp. were recorded in contaminated sediments. In general, diatom taxocenoses presented a typical structure for non-contaminated environments. However, scarceness of specimens, lower S, and frequency of deformed valves suggest responses to metal contamination. For marine environments, the latter values corresponding to A. longipes may be considered a reliable reference to the response of benthic diatoms to metal contamination.

Applicability of diatom metabarcoding in the ecological status assessment of Hungarian lotic and soda pan habitats

Diatoms, eukaryotic algae with silica cell wall have been proved to be reliable bioindicators and are applied in ecological status assessment of aquatic ecosystems using indices calculated from pollution sensitivity and indicator values of species. Traditional method of identification of diatom species is based on morphological features of frustule that requires in-depth taxonomical knowledge and expertise. Metabarcoding that combines barcodes and high-throughput sequencing offers a promising alternative. In this pilot study we tested the applicability of metabarcoding of benthic diatom assemblages for ecological status assessment of water bodies in Hungary comparing its performance to that of morphology-based identification of species. Samples from 78 rivers and streams arranged along a trophic gradient and 14 soda pans representing unique types of habitats were investigated. Sequences of the barcode region of rbcL gene suggested by Vasselon et al. (2017) were acquired revealing 1135 diatom amplicon sequence variants (ASVs) of which 54% could be assigned at species level using Diat.barcode (Rimet et al. 2019) as reference database. Morphological investigation detected more species and intraspecific taxa in the lotic and lentic samples (413 and 78, respectively) than metabarcoding (190 and 75). Correspondence between taxa detected based on morphology and DNA sequences was relatively low (on average 24% in lotic and 26% in lentic samples) but considerably increased (on average 66% and 56%, respectively) when taking into account only the taxa reaching higher than 5% relative abundance in microscopy counting. The differences mainly derived from that a considerable portion (59% and 32%, respectively) of the morphologically identified taxa were not recorded in the reference database. Community structure of samples from both running and standing waters based on microscopy and DNA sequence analysis showed significant correlation as revealed using Mantel test. For rivers and streams diatom index IPS (Specific Pollution Sensitivity Index, (Coste in Cemagref, 1982) for soda pans indices H (Ziemann et al., 2001) and IBD (Indice Biologique Diatomées, Lenoir and Coste, 1996) were calculated from the results of the two aspects. Strong correlation was found between morphology- and sequence-based indices and in about half of the samples, the ecological status class obtained with the two methods coincided. Our results suggest that metabarcoding inheres a great opportunity and could be successfully applied in benthic diatom-based ecological status assessment of Hungarian waters after the reference database is supplemented with taxa frequently occurring in these habitats. References Cemagref, 1982. Etude des méthodes biologiques quantitativesd’appréciation de la qualité des eaux, Rapport Division Qualité des Eaux Lyon. Agence financière de Bassin Rhône-Méditerranée-Corse, Pierre-Bénite, France. Lenoir, A., Coste, M., 1996. Development of a practical diatom index of overall water quality applicable to the French National Water Board Network. Presented at the International symposium, Volksbildungsheim Grilhof Vill, AUT, 17-19 September 1995, Universität Innsbruck, pp. 29–43. Rimet, F., Gusev, E., Kahlert, M., Kelly, M.G., Kulikovskiy, M., Maltsev, Y., Mann, D.G., Pfannkuchen, M., Trobajo, R., Vasselon, V., Zimmermann, J., Bouchez, A., 2019. Diat.barcode, an open-access curated barcode library for diatoms. Sci. Rep. 9, 15116. Vasselon, V., Rimet, F., Tapolczai, K., Bouchez, A., 2017. Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France). Ecol. Indic. 82, 1–12. Ziemann, H., Kies, L., Schulz, C.-J., 2001. Desalinization of running waters: III. Changes in the structure of diatom assemblages caused by a decreasing salt load and changing ion spectra in the river Wipper (Thuringia, Germany). Limnologica 31, 257–280.

Multiple Estuarine Gradients Influencing Tidal Flat Benthic Algal Biomass and Community Structure in the Yaquina Estuary, OR, USA

Tidal flat is often the dominant habitat type in US Pacific Northwest (PNW) estuaries. This research examined environmental factors that explain the spatial patterns of microphytobenthos (MPB) biomass and community structure in a PNW estuary with complex nutrient dynamics. MPB biomass, individual species abundances, diatom community metrics, and diatom community structure were strongly correlated with distance from the estuary mouth, salinity, substrate composition, and pore water-soluble reactive phosphorus (SRP). The microphytobenthos was dominated by diatoms and diatom diversity and species richness were negatively associated with salinity, substrate sand content, and pore water SRP. Diatom community structure varied with estuary position, with the epipsammic taxa Catenula adhaerens, Opephora spp. 1, and Planothidium delicatulum dominating the assemblage at sites near the estuary mouth and epipelic taxa, such as Nitzschia frustulum and Nitzschia palea, being more abundant at sites in the middle and upper estuary. Distance from the estuary mouth and salinity were the most important predictors of diatom assemblage structure, based on CCA analysis. MPB biomass was highest at sites in the lower estuary, characterized by higher salinities, SRP, and substrate sand composition. Pore water nitrogen and surrounding land use were not important predictors of MPB biomass or community structure. We attribute our findings to the nutrient dynamics of Yaquina estuary, which is high in nutrients due to both coastal upwelling and watershed-derived nitrate and exhibits an increasing gradient of phosphorus towards the estuary mouth.

DNA metabarcoding effectively quantifies diatom responses to nutrients in streams

Nutrient pollution from human activities remains a common problem facing stream ecosystems. Identifying ecological responses to phosphorus and nitrogen can inform decisions affecting the protection and management of streams and their watersheds. Diatoms are particularly useful because they are a highly diverse group of unicellular algae found in nearly all aquatic environments and are sensitive responders to increased nutrient concentrations. Here, we used DNA metabarcoding of stream diatoms as an approach to quantifying effects of total phosphorus (TP) and total nitrogen (TN). Threshold indicator taxa analysis (TITAN) identified operational taxonomic units (OTUs) that increased or decreased along TP and TN gradients along with nutrient concentrations at which assemblages had substantial changes in the occurrences and relative abundances of OTUs. Boosted regression trees showed that relative abundances of gene sequence reads for OTUs identified by TITAN as low P, high P, low N, or high N diatoms had strong relationships with nutrient concentrations, which provided support for potentially using these groups of diatoms as metrics in monitoring programs. Gradient forest analysis provided complementary information by characterizing multi‐taxa assemblage change using multiple predictors and results from random forest models for each OTU. Collectively, these analyses showed that notable changes in diatom assemblage structure and OTUs began around 20 µg TP/L, low P diatoms decreased substantially and community change points occurred from 75 to 150 µg/L, and high P diatoms became increasingly dominant from 150 to 300 µg/L. Diatoms also responded to TN with large decreases in low N diatoms occurring from 280 to 525 µg TN/L and a transition to dominance by high N diatoms from 525–850 µg/L. These diatom responses to TP and TN could be used to inform protection efforts (i.e., anti‐degradation) and management goals (i.e., nutrient reduction) in streams and watersheds. Our results add to the growing support for using diatom metabarcoding in monitoring programs.

Diatom assemblages are controlled by light attenuation in oligotrophic and mesotrophic lakes in northern Ontario (Canada)

Diatom communities are composed of three distinct water-depth-associated assemblages: a nearshore benthic assemblage, a deep-water benthic assemblage, and a primarily planktonic assemblage. Light attenuation with depth has been hypothesized to be the factor that controls benthic-to-planktonic (B:P) assemblage transitions. Previous studies, however, could not distinguish between the individual effects of light and temperature on diatom assemblage transition because the depth of the B:P transition occurred at or near the depth of the thermocline. This has caused confusion regarding which factor is the more influential variable on benthic-planktonic diatom assemblage transition in surface sediments along water-depth transects in lakes. Two boreal lakes in northeast Ontario were selected to examine this problem. The study lakes are sufficiently deep and clear (Secchi disk depths ~ 9–10 m; dissolved organic carbon ~ 3 mg/L), making it possible to distinguish between the depth of 1% light penetration and the depth of the thermocline. Surface sediment samples were collected along water-depth transects from these lakes to examine intra-lake diatom assemblage structure. In both lakes, the water depth of the diatom assemblage B:P transition was closely associated with the depth of the ~ 1% photosynthetically active radiation value, and was well below the depth of the thermocline, suggesting that light penetration has more influence on this transition than does the thermocline. Because temporal fluxes in nutrients and DOC concentrations can attenuate light, understanding how the light regime influences benthic diatoms in lakes can help inform interpretations of diatom assemblage changes in paleolimnological studies.

Depth-distribution of lake benthic diatom assemblages in relation to light availability and substrate: implications for paleolimnological studies

We analyzed the depth distributions of benthic diatoms in two adjacent, but hydrologically distinct subalpine lakes (Lakes Soiernseen, S-Germany). Lake Unterer Soiernsee is affected by marked water-level fluctuations and is light-penetrated to the bottom most of the year, while Lake Oberer Soiernsee provides more stable conditions and an extended aphotic zone. Mixed samples of epiphytic, epilithic, epipsammic and epipelic periphyton were taken in one-meter depth steps by scuba divers. Most of the common benthic diatoms occurred in distinct depth-areas. RDA analyses showed that depth was strongly correlated with species distribution in both lakes. Depth-constrained cluster analyses indicated three distinct diatom community zones in each lake. A shallow littoral zone hosting mainly epiphytic and epilithic species and a deeper littoral zone with mainly epipsammic and epipelic taxa existed in both lakes. Additionally, a highly disturbed near-shore littoral zone with diatoms adapted to unstable conditions (aerophilic taxa, pioneer species) was found in Lake Unterer Soiernsee, and a deep-water pelagic zone with mainly planktonic taxa in Lake Oberer Soiernsee. Light availability, substrate, physical stressors and nutrient concentrations were linked closely with water depth. While light availability affected the ratio of benthic and planktonic diatoms, substrate type influenced benthic diatom assemblage structures. Diatoms occurring in surficial sediments of the aphotic zone represent an ideal cross-section of the recent diatom assemblage of the lake, including benthic and planktonic species. However, sediment samples taken in light-flooded depths are inappropriate for studies based on shifts between benthic and planktonic taxa, because in situ benthic species dominate the surface-sediment assemblages, while settled tychoplanktonic and planktonic species occur less frequently. A diatom-inferred depth model was created for each lake to prove the usability for down-core studies using weighted-averaging approaches. For both lakes these models are highly appropriate to reconstruct past fluctuations in water-transparency or lake-level. With regard to the development of diatom-based TP-transfer-functions for Bavarian mountain lakes, we found it is highly important to consider lake depth and transparency. Based on the findings of this study we recommend the creation of two different training-sets, one for deep or low-transparency lakes with an aphotic zone including both benthic and planktonic diatoms, and another one for shallow, clear water lakes solely using benthic diatoms.

Environmental filtering and limiting similarity as main forces driving diatom community structure in Mediterranean and continental temporary and perennial streams

Climatic extreme events such as droughts (unpredictable), dry periods (predictable) or even flush floods, threaten freshwater ecosystems worldwide. The filtering mechanisms of these events and their strength on communities, however, can be different among regions. While time-for-adaptation theory defines whether or not water scarcity can be considered as disturbance, the stress-dominance theory predicts an increase in importance of environmental filtering and a decrease in the role of biotic interactions in communities with increasing environmental stress. Here, we tested whether environmental filtering (leading to trait convergence) or limiting similarity (leading to trait divergence) is the main assembly rule shaping the structure and trait composition of benthic diatom assemblages in Mediterranean (Portuguese) and continental (Hungarian) temporary and perennial streams. We assumed that the trait composition of diatom assemblages in the two stream types would be less different in the Mediterranean than in the continental region (addressed to time-for-adaptation theory). We also hypothesized that trait composition would be shaped by environmental filtering in the Hungarian streams while by biotic interactions in Portuguese streams (addressed to stress-dominance theory). Our results supported our first hypothesis since traits, which associated primarily to temporary streams were found only in the continental region. Our findings, however, only partially proved the stress-dominance hypothesis. In the continental region, where drying up of streams were induced by unpredictable droughts, biotic interactions were the main assembly rules shaping community structure. In contrast, environmental filtering was nearly as important as limiting similarity in structuring trait composition in the Mediterranean region during the predictable dry phase with no superficial flow. These analyses also highlighted that drought events (both predictable and unpredictable ones) have a complex and strong influence on benthic diatom assemblages resulting even in irreversible changes in trait composition and thereby in ecosystem functioning.

Assessing Alternative Microscopy-Based Approaches to Species Abundance Description of Intertidal Diatom Communities

Diatoms usually dominate microphytobenthic biofilms in coastal and estuarine intertidal environments. Yet, functional studies on biofilms often skip species analysis because benthic diatoms are notoriously difficult to extract from sediments and challenging to identify at that taxonomic level. Valid, less time consuming, alternatives would surely be welcomed and increase the inclusion of community structure information in microphytobenthos ecophysiological studies. Starting with an original 181-species abundances matrix (OSM), obtained during a two-year spatial-temporal survey in a Tagus Estuary intertidal flat with contrasting sediment textures, the current study assessed the effectiveness of several approaches to species abundances analysis. The effect of excluding abundance data or rare species, the influence of taxonomic resolution or the use of size-based metrics on biotic multivariate patterns was tested and examined by an objective comparison that replicated these different approaches on three different levels: (1) inter-matrix correlations; (2) performance in several non-parametric multivariate analyses (ANOSIM, MDS); (3) correlations with the environmental dataset. When compared with the OSM, all matrices had strong or very strong positive correlations. All discriminated successfully spatial patterns, separating well assemblages from sandy and muddy sediments and all had significant correlations with the environmental dataset. Apart from the relative biovolume species matrix (BSM), only the species matrices were able to discriminate significantly temporal patterns. The exclusion of 48% of the rarest species had a negligible effect, with the common and original species abundances matrices having a ρ > 0.99 correlation. Of the alternative approaches to species abundances, species presence/absence and the genera abundances matrices yielded the best results overall. Genera presence/absence and the size-class matrices had intermediate performances, with the former performing comparatively poorly with regard to seasonal patterns. BSM had the lowest correlation environmental variable dataset (ρ = 0.598) and the worst overall performance in the other multivariate routines. This means that either a high-taxonomic resolution qualitative analysis (i.e. species presence/absence) or, in alternative, a genus level analysis retaining abundance data may be sufficient to describe basic spatial differences in estuarine intertidal flats. However, if seasonal variations in mudflat diatom assemblage structure are to be detected, species-level abundance data is still necessary.

Diatoms as indicators of the effects of river impoundment at multiple spatial scales.

River impoundment constitutes one of the most important anthropogenic impacts on the World's rivers. An increasing number of studies have tried to quantify the effects of river impoundment on riverine ecosystems over the past two decades, often focusing on the effects of individual large reservoirs. This study is one of the first to use a large-scale, multi-year diatom dataset from a routine biomonitoring network to analyse sample sites downstream of a large number of water supply reservoirs (n=77) and to compare them with paired unregulated control sites. We analysed benthic diatom assemblage structure and a set of derived indices, including ecological guilds, in tandem with multiple spatio-temporal variables to disclose patterns of ecological responses to reservoirs beyond the site-specific scale. Diatom assemblage structure at sites downstream of water supply reservoirs was significantly different to control sites, with the effect being most evident at the regional scale. We found that regional influences were important drivers of differences in assemblage structure at the national scale, although this effect was weaker at downstream sites, indicating the homogenising effect of river impoundment on diatom assemblages. Sites downstream of reservoirs typically exhibited a higher taxonomic richness, with the strongest increases found within the motile guild. In addition, Trophic Diatom Index (TDI) values were typically higher at downstream sites. Water quality gradients appeared to be an important driver of diatom assemblages, but the influence of other abiotic factors could not be ruled out and should be investigated further. Our results demonstrate the value of diatom assemblage data from national-scale biomonitoring networks to detect the effects of water supply reservoirs on instream communities at large spatial scales. This information may assist water resource managers with the future implementation of mitigation measures such as setting environmental flow targets.

Nitrogen as the main driver of benthic diatom composition and diversity in oligotrophic coastal systems

Phytoplankton is the main indicator group for eutrophication in coastal ecosystems, however its high dispersal potential does not enable the assessment of localized effects of coastal nutrient enrichment. Benthic diatoms are sessile microalgae associated with sandy substrates and have the potential to reflect more localized pollution impacts. Although benthic diatoms are widely used bioindicators in freshwater systems, they have rarely been used for assessing the eutrophication status of oligotrophic environments such as the eastern Mediterranean Sea. In the present study, we assess the efficiency of benthic diatoms as bioindicators of nutrient enrichment in oligotrophic coastal systems, by investigating the effect of different physicochemical conditions and nutrient concentrations on the assemblage composition, diversity and individual species populations. To do this, we sampled along a eutrophication gradient formed by anthropogenic nutrient inputs from a metropolitan area. The main driver of assemblage composition, diversity and biomass of diatoms was nitrogen concentration and its temporal and spatial changes. Nitrogen loadings were positively correlated with increased biomass of Cocconeis spp. and negatively correlated with Mastogloia spp. Our findings suggest that in coastal ecosystems of oligotrophic marine ecoregions, benthic diatom assemblage structure and specific taxonomic groups can be reliable predictors of coastal eutrophication offering higher spatial resolution compared to phytoplankton.

Assessment of Diatom Assemblages in Close Proximity to Mining Activities in Nunavik, Northern Quebec (Canada)

Nunavik (Northern Quebec, Canada) is experiencing a mining boom. While several studies have been conducted in the region in relation to climate change, the effects of mining have received much less attention. In this study, we explored the use of biofilms in natural streams as an indicator of potential stress on living organisms caused by metal contamination from nickel mining activities. More specifically, we assessed diatom assemblages and the presence of teratologies (morphologic abnormalities) as a response to metals in streams located in close proximity to mining sites. Metal concentrations (as well as other cations), anions and pH values varied markedly among stations. Different diatom assemblage structures (four biotypes, i.e., groups of samples with similar diatom species composition) were observed depending on the level and the type of contamination. The frequency of diatom teratologies was higher in metal contaminated sites. The present study lays the foundation for bioassessment of metal contamination in low Arctic streams using diatom-based approaches, and will serve as a point in time reference for future evaluation of ecosystems degradation or recovery in Nunavik.

Environmental and spatial factors drive diatom species distribution in Alpine streams: Implications for biomonitoring

Abstract Given their documented capacity to track changes in environmental conditions and human alterations, benthic diatom communities are at present widely used in biomonitoring programs to evaluate stream water quality. However, it is becoming more and more evident that species ecological preferences are not the only drivers of diatom community composition, since dispersal-related processes also play a role. This is particularly compelling in Alpine streams, where orographic conformation and human-related impacts limit dispersal of organisms. In addition, several environmental variables may influence diatom community in pristine or impacted sites. We here investigate the differential role of environmental and spatial factors in driving the community assemblages of diatoms in streams of the Eastern Italian Alps, focusing on both taxonomic and functional composition. We analysed data from 110 samples collected on two different geological substrates, i.e. calcareous and siliceous, during the last eight years of biomonitoring programs, among which 64 collected in reference sites and 46 in impacted sites. We first evaluated whether diatom communities in reference and impacted sites are differentially shaped by environmental and spatial factors, highlighting the major role of spatial constraints in both of them. In particular, anthropogenic disruption of longitudinal connectivity in streams likely shaped impacted communities, as demonstrated by the increasing abundance of motile taxa, which are associated with physical disturbance. Conversely, reference communities were mostly affected by spatially structured environmental variables, especially those related to streambed lithology. We then compared the taxonomic and functional composition of diatom communities between the two geological substrates in both reference and impacted sites to better highlight the differential role of this factor. Our results demonstrate that lithology strongly drives diatom community composition in reference but not in impacted sites, confirming our previous observations. The analysis of functional traits, however, highlighted how differences were due not only to the geological substrates, but also to other environmental variables, like flow velocity. Overall, the effect of the spatial component on the structure of diatom assemblages can represent a background noise in the framework of the river quality assessment, and this should be taken into account especially in those countries, like Italy, covering a broad range of mountain areas.

Critical approach to diatom-based bioassessment of the regulated sections of urban flowing water ecosystems

• Diatom indices faultily evaluated the ecological status of degraded urban streams. • We explained the inaccuracies between the bioassessment and the actual state. • The greatest influence on diatom communities had hydromorphological transformations. • The stream transformations caused tremendous changes of habitat conditions. • We showed that some dominant species disturb the bioassessment of ecological state. Hydromorphological transformations of small urban streams results in changes in habitat conditions, i.e. increase in water speed current and/or oxygen concentration, and finally changes in aquatic organism structure. The ecological status of two regulated urban streams was determined by diatom-based biomonitoring in their upper and lower sections using selected diatom indices (IO, IPS, IBD, GDI, TDI). Qualitative and quantitative analyses were performed to analyse the structure of diatom assemblages and to reveal the spatial relationships between stream sites. The bioassessment was supported with a chemical analysis of the water. The upper sections were found to be characterised by poor/bad ecological status, and the lower sections below highly-transformed and impacted streambeds by good/moderate status. Since the bioassessment revealed unexpected results, an analysis was performed of the dominant species, with special attention paid to the autecology of diatoms. A new model of bioassessment was implemented where the most frequent and dominant species, Achnanthidium minutissimum , was excluded from the analysis. The results obtained by the new analysis were similar to those of the chemical analysis. Such a critical approach is needed to reveal the true ecological status of flowing water ecosystems, particularly in the case of regulated streams where transformation has resulted in a change in more ‘pseudo-mountain’ habitat conditions.

Late spring bloom development of pelagic diatoms in Baffin Bay

The Arctic Ocean is particularly affected by climate change, with changes in sea ice cover expected to impact phytoplankton primary production. During the Green Edge expedition, the development of the late spring–early summer diatom bloom was studied in relation with the sea ice retreat by multiple transects across the marginal ice zone. Biogenic silica concentrations and uptake rates were measured. In addition, diatom assemblage structures and their associated carbon biomass were determined, along with taxon-specific contributions to total biogenic silica production using the fluorescent dye PDMPO. Results indicate that a diatom bloom developed in open waters close to the ice edge, following the alleviation of light limitation, and extended 20–30 km underneath the ice pack. This actively growing diatom bloom (up to 0.19 μmol Si L–1 d–1) was associated with high biogenic silica concentrations (up to 2.15 μmol L–1), and was dominated by colonial fast-growing centric (Chaetoceros spp. and Thalassiosira spp.) and ribbon-forming pennate species (Fragilariopsis spp./Fossula arctica). The bloom remained concentrated over the shallow Greenland shelf and slope, in Atlantic-influenced waters, and weakened as it moved westwards toward ice-free Pacific-influenced waters. The development resulted in a near depletion of all nutrients eastwards of the bay, which probably induced the formation of resting spores of Melosira arctica. In contrast, under the ice pack, nutrients had not yet been consumed. Biogenic silica and uptake rates were still low (respectively <0.5 μmol L–1 and <0.05 μmol L–1 d–1), although elevated specific Si uptake rates (up to 0.23 d–1) probably reflected early stages of the bloom. These diatoms were dominated by pennate species (Pseudo-nitzschia spp., Ceratoneis closterium, and Fragilariopsis spp./Fossula arctica). This study can contribute to predictions of the future response of Arctic diatoms in the context of climate change.

Diatom Assemblage Changes in Agricultural Alluvial Plain Streams and Application for Nutrient Management.

In large, alluvial floodplains dominated by agriculture, small streams have the potential to experience nutrient enrichment affecting algal assemblage structure and metabolism. Nutrient enrichment is largely driven by application of nutrients and altered hydrologic regimes. To inform stressor-response-based nutrient reduction goals for agricultural alluvial plain streams, diatom assemblages were sampled from 25 streams located within the Mississippi Alluvial Plain (MAP) with various land management practices and associated P and N inputs. From August through September 2015, epidendric diatom assemblage samples were collected from instream woody debris. Field nutrient gradients were skewed toward higher concentrations, and ranges of previously reported diatom assemblage response thresholds indicative of oligotrophic conditions were not well represented. Ordination analysis identified a gradient in species composition associated with increasing P and decreasing dissolved oxygen. A significant shift in diatom assemblage structure occurred when total P concentrations in the MAP streams exceeded 0.12 mg L-. Phosphorus-enriched systems were represented by a distinct set of indicator species, lower abundances of ubiquitous species, greater abundances of highly tolerant species, and greater abundances of high-P indicator species. No relationships were observed among diatom assemblage measures or traits with increasing N. Current results do not address potential criteria for identifying high-quality, oligotrophic streams. However, measures of diatom assemblage structure have potential for helping set benchmarks to reduce nutrient impacts and monitor effects of agricultural best management practices on MAP streams.