Development of a diatom-based multimetric index for acid mine drainage impacted depressional wetlands

Indigenous metal-tolerant mine water bacterial populations under varying metal stresses

The present study investigated the indigenous metal-tolerant bacterial populations in the mine-water microbiome. Our intention was to assess the effects of the metal concentrations in mine water on the bacterial community of mine waters. The bacterial communities in Vanadium and Gold mine-water samples were exposed to different heavy-metal Arsenic, Cadmium, Chromium, Nickel, Mercury and Vanadium at two different concentrations (5 and 25 mM). The 16S rRNA amplicon from mine waters were sequenced using the Illumina's NGS MiSeq platform. Data analysis revealed a high diversity in the bacterial populations associated with the different heavy metals at different concentrations. The taxonomic profiles obtained after the exposure were different in different salts, but mostly dominated by Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Firmicutes at variable relative abundance. Principal Component Analysis (PCoA) predicts the clear community shift after exposure with heavy metals salts and emergence of tolerant community depending upon the specific community present in the original mine water.

A new diatom-based multimetric index to assess lake ecological status

Eutrophication impairs lake ecosystems at a global scale. In this context, as benthic microalgae are well-established warnings for a large range of stressors, particularly nutrient enrichment, the Water Framework Directive required the development of diatom-based methods to monitor lake eutrophication. Here, we present the diatom-based index we developed for French lakes, named IBDL (Indice Biologique Diatomées en Lacs). Data were collected in 93 lakes from 2015 to 2020. A challenge arose from the discontinuous pressure gradient of our dataset, especially the low number of nutrient-impacted lakes. To analyze the data we opted for the so-called "Threshold Indicator Taxa ANalysis" method, which makes it possible to determine a list of "alert taxa." We obtained a multimetric index based on specific pressure gradients (Kjeldahl nitrogen, suspended matter, biological oxygen demand, and total phosphorous). Considering the European intercalibration process, the very good correlation between IBDL and the common metric (R2 from 0.52 to 0.87 according to the lake alkalinity type) makes us very confident in our ability to match future IBDL quality thresholds with European standards. The IBDL proved at last to be particularly relevant as it has a twofold interest: an excellent relationship with total phosphorus (R2 from 0.63 to 0.83 according to the lake alkalinity type) and a possible application to any lake metatype. Its complementarity with macrophyte-based indices moreover justifies the use of at least two primary producer components for lake ecological status classification.

Macroinvertebrate diversity in relation to limnochemistry in an Austral semi-arid transboundary aquifer region pan system

Pan-wetland systems are one of the world's essential and productive ecosystems and are considered important, unique and complex ecosystems. Anthropogenic activities around the temporary pans in the Khakhea Bray Transboundary Aquifer region are increasingly becoming a big issue of concern as this may affect pan biodiversity. The study specifically aimed to investigate spatial and temporal distributions of metal and nutrient concentrations within the pans in relation to land use, identify potential pollution sources in this water-scarce region, and assess macroinvertebrate diversity and distribution in relation to pan limnochemistry using a combination of multivariate analyses from 10 pans across three seasons. Environmental and anthropogenic variables influence water quality and the distribution of metals concentration in Khakhea-Bray pan systems. Anthropogenic activities such as animal grazing, infrastructure degradation, water withdrawal and littering have resulted in poor water quality within temporary pans, which may strongly influence macroinvertebrate diversity and distribution. Forty-one macroinvertebrate species from 5 insect orders (i.e., Coleoptera, Hemiptera, Odonata, Ephemeroptera, Diptera), Crustacea and Mollusca were identified. Significant differences were observed across the seasons for macroinvertebrate taxa, with high and low species richness being observed in autumn and winter, respectively. Water (i.e., temperature, dissolved oxygen, pH, salinity, conductivity), physical (i.e., stone composition) and sediment (i.e., sulphur, sodium) parameters were found to have a significant impact on the macroinvertebrate communities. Therefore, understanding the relationships between macroinvertebrates and their environment is crucial in understanding how the ecosystem taxa are structured and is vital for informing conservation managers on how to properly manage and protect these systems from further degradation.

Rapid transcriptomic and physiological changes in the freshwater pennate diatom Mayamaea pseudoterrestris in response to copper exposure

Diatoms function as major primary producers, accumulating large amounts of biomass in most aquatic environments. Given their rapid responses to changes in environmental conditions, diatoms are used for the biological monitoring of water quality and for performing ecotoxicological tests in aquatic ecosystems. However, the molecular basis for their toxicity to chemical compounds remains largely unknown. Here, we sequenced the genome of a freshwater diatom, Mayamaea pseudoterrestris NIES-4280, which has been proposed as an alternative strain of Navicula pelliculosa UTEX 664 for performing the Organisation for Economic Co-operation and Development ecotoxicological test. This study shows that M. pseudoterrestris has a small genome and carries the lowest number of genes among freshwater diatoms. The gene content of M. pseudoterrestris is similar to that of the model marine diatom, Phaeodactylum tricornutum. Genes related to cell motility, polysaccharide metabolism, oxidative stress alleviation, intracellular calcium signalling, and reactive compound detoxification showed rapid changes in their expression patterns in response to copper exposure. Active gliding motility was observed in response to copper addition, and copper exposure decreased intracellular calcium concentration. These findings enhance our understanding of the environmental adaptation of diatoms, and elucidate the molecular basis of toxicity of chemical compounds in algae.

DNA metabarcoding and morphological methods show complementary patterns in the metacommunity organization of lentic epiphytic diatoms

Diatoms are important organisms in freshwater ecosystems due to their position as primary producers and therefore, analyzing their assemblages provides relevant information on ecosystem functioning. Diatoms have historically been identified based on morphological traits, which is time-consuming and requires well-trained specialists. Nevertheless, DNA barcoding offers an alternative approach to overcome some limitations of the morphological method. Here, we assess if both approaches are comparable methods to study patterns and mechanisms (including environmental filtering and dispersal limitation) of epiphytic diatom metacommunities using a comprehensive dataset from 22 Mediterranean ponds at different taxonomic resolutions. We used a fragment of rbcL barcode gene combined with High-Throughput Sequencing to infer diatom community composition. The overall degree of correspondence between both approaches was assessed by Procrustean rotation analysis and Procrustean randomization tests, whereas the role of local environmental variables and geographical distances was studied using a comprehensive combination of BIOENV, Mantel tests and distance-based redundancy analysis. Our results showed a relatively poor correspondence in the compositional variation of diatom metacommunity between both approaches. We speculate that the incompleteness of the reference database and the bioinformatics processing are the biases most likely affecting the molecular approach, whereas the limited counting effort and the presence of cryptic species are presumably the major biases related with the morphological method. On the other hand, variation in diatom community composition detected with both approaches was strongly related to the environmental template, which may be related with the narrow community-environment relationships in diatoms. Nevertheless, we found no significant relationship between compositional variation and geographical distances. Overall, our work shows the complementary nature of both approaches and highlights the importance of DNA metabarcoding to address empirical research questions of community ecology in freshwaters, especially once the reference databases include most genotypes of occurring taxa and bioinformatics biases are overcome.

Improving biological condition assessment accuracy by multimetric index approach with microalgae in streams and lakes

Multimetric index (MMI) approach is a broadly used in ecological assessment because it can integrate information of various kinds of ecologically related metrics of freshwater ecosystems and provide an easily understandable score for purpose of further evaluation and managements. Accounting for natural variation and disentangling covariation between natural environmental factors and human disturbance factors are imperative for an accurate assessment. Lots of progress has been made recently on the aforementioned two aspects. Three approaches, a priori classification of sites by regions or typologies, site-specific modeling of expected reference condition and varying metrics in site groups, have been tested in lakes and streams to improve assessment accuracy. All existed studies support that site-specific modeling can efficiently account for natural variation and generate a MMI with good performance. However, until now, no strong evidence has shown that diatom/blue-algae typologies are better than regionalization frameworks on accounting for natural variation either in lakes or in streams. To separate the natural variation explained by site specific modeling from that of varying metrics is necessary for a thorough and accurate evaluation on the valuableness of site-grouping by typologies. Different performance of varying metrics among site groups of streams and lakes was most probably caused by the lack of representativeness of diatom metrics on biological condition rather than the complex multi-stressor gradients in streams and rivers. A recent study showed that blue-green algae enhanced performance of diatom-based MMI on defining lake condition under high level of human disturbance. On the other hand, with more and more extensive and intensive use of statistics techniques in developing MMI, we also discussed some statistical challenges faced by scientists in field of ecological assessment, especially on setting significance level of a statistical test and multiple comparison issue in MMI performance comparison.

Epiphytic Diatom-Based Biomonitoring in Mediterranean Ponds: Traditional Microscopy versus Metabarcoding Approaches

Benthic diatoms have traditionally been used as bioindicators of aquatic ecosystems. Because diatom-based monitoring of water quality is required by European legislation, molecular-based methods had emerged as useful alternatives to classical methods based on morphological identification using light microscopy. The aim of this study was to test the reliability of DNA metabarcoding combined with High-Throughput Sequencing (HTS) techniques in the bioassessment of the trophic status of 22 Mediterranean shallow ponds in NW Spain. For each pond, the Trophic Diatom Index (TDI) was calculated from inventories obtained by identification using light microscopy (LM) followed by high-throughput sequencing (HTS) at the molecular level. Ponds were subsequently classified into five water quality classes. The results showed a good correspondence between both methods, especially after applying a correction factor that depended on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, which mainly included those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Thus, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to using traditional methods in Mediterranean shallow ponds.

Understanding divergences between ecological status classification systems based on diatoms

A large number of diatom-based classification systems have been developed worldwide in recent years. These new systems, together with the oldest, emerged on the need to assess the water quality of rivers, but knowledge on possible divergences resulting from their simultaneous application within a territory is limited. This study aimed to compare the ecological status classification provided by conceptually different methodological approaches, of use or potential use within the same region. 402 monitoring samples were collected from Atlantic siliceous streams (NW-Iberian Peninsula) and temporary Mediterranean streams (Balearic Islands, Spain). Two multimetric indices specifically developed for these areas (MDIAT and DIATMIB, respectively) were calculated, as well as the Specific Polluosensitivity Index (IPS). Multimetric indices were more sensitive methods at diagnosing degradation than IPS since they took directly account of abundance (i.e. chlorophyll a in DIATMIB) or indirectly by its proved inverse relationship with Chl a (MDIAT), together with their use of the regional reference diatom community. Alteration gradients were identified in both studied regions based on the distribution of diatoms, with the first axis of distance-based redundancy analyses (dbRDA) being related to nutrient enrichment and organic loads. Threshold Indicator Taxa ANalysis (TITAN) performed on diatoms sampled along environmental (dbRDA axis 1 and phosphate) and biological gradients (as Ecological Quality Ratio scores of classifications), pointed to lower than current Good/Moderate boundaries for phosphate maximum values (e.g. 22.5 and 71.6 μg L^-1 for Galicia and the Balearic Islands, respectively) as well as for higher Good/Moderate boundaries for the MDIAT and IPS classifications. A 'transition group' of species was classified as sensitive or as tolerant depending on the regional nutrients range. Findings of the present study highlight the need to perform auto-ecological studies to increase the knowledge on regional diatoms and their optimal survival ranges across regions prior to adopt other non-regional diatom indices.

The Impact of Metal-Rich Sediments Derived from Mining on Freshwater Stream Life

Metal-rich sediments have the potential to impair life in freshwater streams and rivers and, thereby, to inhibit recovery of ecological conditions after any remediation of mine water discharges. Sediments remain metal-rich over long time periods and have long-term potential ecotoxicological interactions with local biota, unless the sediments themselves are physically removed or replaced by less metal-rich sediment. Laboratory-derived environmental quality standards are difficult to apply to the field situation, as many complicating factors exist in the real world. Therefore, there is a strong case to consider other, field-relevant, measures of toxic effects as alternatives to laboratory-derived standards and to seek better biological tools to detect, diagnose and ideally predict community-level ecotoxicological impairment. Hence, this review concentrated on field measures of toxic effects of metal-rich sediment in freshwater streams, with less emphasis on laboratory-based toxicity testing approaches. To this end, this review provides an overview of the impact of metal-rich sediments on freshwater stream life, focusing on biological impacts linked to metal contamination.

Index of biotic integrity based on phytoplankton and water quality index: Do they have a similar pattern on water quality assessment? A study of rivers in Lake Taihu Basin, China

Our study illustrated the ecological conditions in the rivers of Lake Taihu Basin (LTB) using an index of biotic integrity based on phytoplankton (P-IBI), and its performance was compared with the previously developed water quality index (WQI). Samples were collected seasonally at 96 sites covering the major rivers from September 2014 to January 2016. Three critical ecological indices, i.e., phytoplankton density, chlorophyll a (chl a), and Menhinick, were selected from a pool of 22 candidate indices mainly according to the correlations among indices and environmental parameters. The results indicated that the ecological status of LTB based on P-IBI was significantly different at spatial (especially between Tiaoxi and the other 5 river systems) and seasonal scales. Furthermore, the proposed P-IBI effectively identified the major environmental parameters (total nitrogen, ammonium, total phosphorus, and permanganate index) associated with each level (bad, low, and moderate). Moreover, the P-IBI was closely and positively correlated with the WQI at the spatial scale regardless of season. However, the ecological conditions were significantly worse according to the P-IBI at both the spatial (P < 0.001) and seasonal scales (P values of 0.018 in winter and < 0.001 in other seasons, respectively), and the seasonal distribution pattern differed between the two methods. Our study suggests that the P-IBI provides an essential supplement for the assessment of ecological conditions of rivers and that the selected critical indices (phytoplankton density, chl a, and Menhinick) are suitable for river ecosystems. Additionally, compared with WQI, the water quality condition was generally worse when using P-IBI, and this phenomenon requires further attention during water quality assessments, as well as different seasonal distribution patterns.

A freshwater diatom challenged by Zn: Biochemical, physiological and metabolomic responses of Tabellaria flocculosa(Roth) Kützing

Freshwater ecosystems are under threatening anthropogenic pressures worldwide, namely by metals. Diatoms are used as water quality indicators, but the influence of micronutrients such as Zn and its impacts are poorly understood. Thus, our study aimed to elucidate the tolerance level, the cellular targets and the responses to counteract Zn toxicity of freshwater diatoms by exposing Tabellaria flocculosa, isolated from a Zn contaminated stream. Biochemical, physiological and metabolomic approaches were used. It was demonstrated that Zn is toxic to T. flocculosa at concentrations occurring in contaminated environments. At low stress (30 μg Zn/L) few alterations in the metabolome were observed, but the enzymatic (SOD, CAT) and molecular (GSH, GSSG) antioxidant systems were induced, protecting cells from oxidative stress. At moderate stress (500 μg Zn/L) the main changes occurred in the metabolome (increases in fatty acids, amino acids, terpenoids, glycerol and phosphate, decreases in sucrose and lumichrome) with a moderate increase in cell damage (LPO and PC). The concerted action of all these mechanisms resulted in a non-significant decrease of growth, explaining the survival of this T. flocculosa strain in an environment with this Zn concentration. At the highest stress level (1000 μg Zn/L) the metabolome was identical to 500 μg Zn/L, and the induction of antioxidant systems and extracellular ion chelation (exopolysaccharides, frustulins) were the main responses to the increase of Zn toxicity. However, these mechanisms were unable to effectively abrogate cellular damage and growth reduction was observed. Moreover, the decrease in sucrose and especially in lumichrome should be tested as new specific markers of Zn toxicity. The information obtained in this study can assist in environmental risk assessment policies, support the prediction of diatom behaviour in highly impacted Zn environments, such as mining scenarios, and may help develop new indices, which include alterations induced by metals.