Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican

Herbicide pollution poses a worldwide threat to plants and freshwater ecosystems. However, the understanding of how organisms develop tolerance to these chemicals and the associated trade-off expenses are largely unknown. This study aims to investigate the physiological and transcriptional mechanisms underlying the acclimation of the green microalgal model species Raphidocelis subcapitata (Selenastraceae) towards the herbicide diflufenican, and the fitness costs associated with tolerance development. Algae were exposed for 12 weeks (corresponding to 100 generations) to diflufenican at the two environmental concentrations 10 and 310 ng/L. The monitoring of growth, pigment composition, and photosynthetic performance throughout the experiment revealed an initial dose-dependent stress phase (week 1) with an EC₅₀ of 397 ng/L, followed by a time-dependent recovery phase during weeks 2 to 4. After week 4, R. subcapitata was acclimated to diflufenican exposure with a similar growth rate, content of carotenoids, and photosynthetic performance as the unexposed control algae. This acclimation state of the algae was explored in terms of tolerance acquisition, changes in the fatty acids composition, diflufenican removal rate, cell size, and changes in mRNA gene expression profile, revealing potential fitness costs associated with acclimation, such as up-regulation of genes related to cell division, structure, morphology, and reduction of cell size. Overall, this study demonstrates that R. subcapitata can quickly acclimate to environmental but toxic levels of diflufenican; however, the acclimation is associated with trade-off expenses that result in smaller cell size.

How, not if, is the question mycologists should be asking about DNA-based typification

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.

The curse of the uncultured fungus

The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.

Tolerance Patterns in Stream Biofilms Link Complex Chemical Pollution to Ecological Impacts

Preventing and remedying fresh waters from chemical pollution is a fundamental societal and scientific challenge. With other nonchemical stressors potentially co-occurring, assessing the ecological consequences of reducing chemical loads in the environment is arduous. In this case study, we comparatively assessed the community structure, functions, and tolerance of stream biofilms to micropollutant mixtures extracted from deployed passive samplers at wastewater treatment plant effluents. These biofilms were growing up- and downstream of one upgraded and two nonupgraded wastewater treatment plants before being sampled for analyses. Our results showed a substantial decrease in micropollutant concentrations by 85%, as the result of upgrading the wastewater treatment plant at one of the sampling sites with activated carbon filtration. This decrease was positively correlated with a loss of community tolerance to micropollutants and the recovery of the community structure downstream of the effluent. On the other hand, downstream biofilms at the nonupgraded sites displayed higher tolerance to the extracts than the upstream biofilms. The observed higher tolerance was positively linked to micropollutant levels both in stream water and in biofilm samples, and to shifts in the community structure. Although more investigations of upgraded sites are needed, our findings point toward the suitability of using community tolerance for the retrospective assessment of the risks posed by micropollutants, to assess community recovery, and to relate effects to causes in complex environmental conditions.

Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations

Copper (Cu) pollution in coastal areas is a worldwide threat for aquatic communities. This study aims to demonstrate the usefulness of the DNA metabarcoding analysis in order to describe the ecotoxicological effect of Cu at environmental concentrations on marine periphyton. Additionally, the study investigates if Cu-induced changes in community structure co-occurs with changes in community functioning (i.e., photosynthesis and community tolerance to Cu). Periphyton was exposed for 18 days to five Cu concentrations, between 0.01 and 10 μM, in a semi-static test. Diversity and community structure of prokaryotic and eukaryotic organisms were assessed by 16S and 18S amplicon sequencing, respectively. Community function was studied as impacts on algal biomass and photosynthetic activity. Additionally, we studied Pollution-Induced Community Tolerance (PICT) using photosynthesis as the endpoint. Sequencing results detected an average of 9,504 and 1,242 OTUs for 16S and 18S, respectively, reflecting the high biodiversity of marine periphytic biofilms. Eukaryotes represent the most Cu-sensitive kingdom, where effects were seen already at concentrations as low as 0.01 μM. The structure of the prokaryotic part of the community was impacted at slightly higher concentrations (0.06 μM), which is still in the range of the Cu concentrations observed in the area (0.08 μM). The current environmental quality standard for Cu of 0.07 μM therefore does not seem to be sufficiently protective for periphyton. Cu exposure resulted in a more Cu-tolerant community, which was accompanied by a reduced total algal biomass, increased relative abundance of diatoms and a reduction of photosynthetic activity. Cu exposure changed the network of associations between taxa in the communities. A total of 23 taxa, including taxa within Proteobacteria, Bacteroidetes, Stramenopiles, and Hacrobia, were identified as being particularly sensitive to Cu. DNA metabarcoding is presented as a sensitive tool for community-level ecotoxicological studies that allows to observe impacts simultaneously on a multitude of pro- and eukaryotic taxa, and therefore to identify particularly sensitive, non-cultivable taxa.

Fluvial biofilms exposed to desiccation and pharmaceutical pollution: New insights using metabolomics

In many arid and semi-arid systems, biological communities in river ecosystems are submitted to flow interruption and desiccation, as well as to the impact of urban wastewaters. In this work, we studied (using a LC-LTQ-Orbitrap) the metabolomic response of biofilm communities exposed to both hydrological and chemical stressors. Fluvial biofilms were exposed to a mixture of 9 pharmaceuticals at a total concentration of 5000ng/L (mimicking concentrations and compounds found in polluted aquatic environments) and/or to seven days of desiccation, under laboratory conditions. The biosynthesis of fatty acids was the main metabolic pathway disrupted in biofilms. Endogenous biofilm's metabolites (metabolome) altered due to these stressors were identified. The metabolites that significantly changed only due to one of the stressors could be proposed as potential specific biomarkers. A biomarker of pharmaceutical exposure was the lysophosphatidic acid, which decreased a 160%, while for desiccation stearidonic acid (increased 160%), 16-Oxohexadecanoic acid (increased 340%) and palmitoleic acid (decreased 290%) were the biomarkers proposed. Besides, other metabolites showed different responses depending on the treatment, such as palmitic acid, linolenic acid, behenic acid, lignoceric acid and azelaic acid. The Carbon:Phosphorus (C:P) molar ratio increased due to all stress factors, whereas the algal community composition changed mainly due to desiccation. A possible relationship between those changes observed in structural parameters and the metabolome of biofilms was explored. Overall, our findings support the use of metabolomics to unravel at molecular level the effects from chemical and physical stressors on complex microbial communities, such as biofilms, and pinpoint biomarkers of exposure.

Cumulative Stressors Trigger Increased Vulnerability of Diatom Communities to Additional Disturbances

Chronic, non-lethal stressors occurring gradually (in space or time) can result in cumulative impacts that are more dramatic than higher intensities or occasional critical levels of any single one of these stressors. The negative effects of the chronic stressors trigger lasting impacts that may grow in intensity and become problematic over time and/or to higher trophic levels. In rivers, aquatic organisms experience this type of cumulative stress along the up- to downstream gradient in natural and anthropogenic contaminants generally observed in inhabited watersheds. Diatoms are a major component of the periphyton in rivers; their richness and diversity in natural communities are directly related to their varied ecological preferences and sensitivity to disturbance. In this study, we monitored from 2003 to 2008 the changes in the diversity of taxonomic and non-taxonomic features along a small river (Riou-Mort, South West France), at three sites: one site upstream considered as a reference for this watershed, one intermediate site with high nutrient load, and one downstream site exposed to both nutrient and metal pollution. The cumulative impacts of nutrients plus metals led to a gradual decrease in species richness and diversity, and in a potential capacity to cope with additional stresses, e.g., climate change-related ones. This is reflected by a decrease in species richness downstream, more dramatic in the hot summer of 2003 than in cooler summers. With the increasingly protective environmental regulations (e.g., Water Framework Directive in Europe), accumulation of stresses on aquatic resources are recommended to receive increasing attention, in particular considering the expected changes in climate.

Effects of flow intermittency and pharmaceutical exposure on the structure and metabolism of stream biofilms

Increasing concentrations of pharmaceutical compounds occur in many rivers, but their environmental risk remains poorly studied in stream biofilms. Flow intermittency shapes the structure and functions of ecosystems, and may enhance their sensitivity to toxicants. This study evaluates the effects of a long-term exposure of biofilm communities to a mixture of pharmaceutical compounds at environmental concentrations on biofilm bioaccumulation capacity, the structure and metabolic processes of algae and bacteria communities, and how their potential effects were enhanced or not by the occurrence of flow intermittency. To assess the interaction between those two stressors, an experiment with artificial streams was performed. Stream biofilms were exposed to a mixture of pharmaceuticals, as well as to a short period of flow intermittency. Results indicate that biofilms were negatively affected by pharmaceuticals. The algal biomass and taxa richness decreased and unicellular green algae relatively increased. The structure of the bacterial (based on denaturing gradient gel electrophoresis of amplified 16S rRNA genes) changed and showed a reduction of the operational taxonomic units (OTUs) richness. Exposed biofilms showed higher rates of metabolic processes, such as primary production and community respiration, attributed to pharmaceuticals stimulated an increase of green algae and heterotrophs, respectively. Flow intermittency modulated the effects of chemicals on natural communities. The algal community became more sensitive to short-term exposure of pharmaceuticals (lower EC50 value) when exposed to water intermittency, indicating cumulative effects between the two assessed stressors. In contrast to algae, the bacterial community became less sensitive to short-term exposure of pharmaceuticals (higher EC50) when exposed to water intermittency, indicating co-tolerance phenomena. According to the observed effects, the environmental risk of pharmaceuticals in nature is high, but different depending on the flow regime, as well as the target organisms (autotrophs vs heterotrophs).

Pollution-induced community tolerance to non-steroidal anti-inflammatory drugs (NSAIDs) in fluvial biofilm communities affected by WWTP effluents

We assessed the tolerance acquired by stream biofilms to two non-steroidal anti-inflammatory-drugs (NSAIDs), ibuprofen and diclofenac. Biofilms came from a stream system receiving the effluent of a wastewater treatment plant (WWTP). The response of biofilms from a non-polluted site (upstream the WWTP) was compared to that of others downstream with relevant and decreasing levels of NSAIDs. Experiments performed in the laboratory following the pollution-induced community tolerance (PICT) approach determined that both algae and microbial communities from biofilms of the sites exposed at the highest concentrations of ibuprofen and diclofenac acquired tolerance to the mixture of these NSAIDs occurring at the sites. It was also observed that the chronic pollution by the WWTP effluent affected the microbial metabolic profile, as well as the structure of the algal community. The low (at ng L(-1) level) but chronic inputs of pharmaceuticals to the river ecosystem result in tolerant communities of lower diversity and altered microbial metabolism.

Experimental evaluation of the contribution of acidic pH and Fe concentration to the structure, function and tolerance to metals (Cu and Zn) exposure in fluvial biofilms

An indoor channel system was colonised with fluvial biofilms to study the chronic effects of high Fe and SO4(2-) concentrations and acidic pH, the water chemistry in the surrounding streams of Aljustrel mining area (Alentejo, Portugal), and their contribution to community (in)tolerance to metal toxicity by short-term experiments with Cu and Zn. Biofilms were subjected to four different treatments during 8 weeks: high Fe and SO4(2-) concentrations (1 mg Fe l(-1)+ 700 mg SO4(2-) l(-1)) and acidic pH, high Fe and SO4(2-) at alkaline pH; lower Fe and SO4(2-) at acidic pH: and lower Fe and SO4(2-) concentrations at alkaline pH as negative control. During chronic exposure, acidic pH affected growth negatively, based on low values of algal biomass and the autotrophic index, high values of the antioxidant enzyme activities and low diversity diatom communities, dominated by acidophilic species (Pinnularia aljustrelica) in acidic treatments, being the effects more marked with high Fe and SO4(2-). Co-tolerance to metals (Cu and Zn) was also shown in biofilms from the acidic treatments, contrasting with the higher sensitivity observed in the alkaline treatments. We can conclude that the Aljustrel mining area acidic environment limits algal growth and exerts a strong selection pressure on the community composition which is in turn, more tolerant to metal exposure.

Antioxidant enzyme activities in biofilms as biomarker of Zn pollution in a natural system: an active bio-monitoring study

This study aimed to explore the use of antioxidant enzyme activities (AEA) and biofilm metal accumulation capacity in natural communities as effect-based indicator of metal exposure in fluvial systems. To achieve these objectives, an active biomonitoring using fluvial biofilm communities was performed during 5 weeks. Biofilm was colonized over artificial substrata in a non-polluted site. After 5 weeks, biofilms were translocated to four different sites with different metal pollution in the same stream. The evolution of environmental parameters as well as biofilm responses was analysed over time. Physicochemical parameters were different between sampling times as well as between the most polluted site and the less polluted ones, mainly due to Zn pollution. In contrast, AEA and metal accumulation in biofilms allowed us to discriminate the high and moderate metal pollution sites from the rest. Zn, the metal with the highest contribution to potential toxicity, presented a fast and high accumulation capacity in biofilms. According to the multivariate analysis, AEA showed different responses. While catalase (CAT) and ascorbate peroxidase (APX) variability was mainly attributed to environmental stress (pH, temperature and phosphate concentration), glutathione-S-transferase (GST) changes were related to metal pollution. Glutathione reductase (GR) and superoxide dismutase (SOD) responses were related to both stress factors. AEA and metal accumulation are proposed as sensitive effect-based field methods, to evaluate biofilm responses after acute metal exposure (e.g. an accidental spill) due to their capacity to respond after few hours, but also in routinely monitoring due to their persistent changes after few weeks of exposure. These tools could improve the Common Implementation Strategy (CIS) of the Water Framework Directive (WFD) as expert group request.

Seasonal changes in antioxidant enzyme activities of freshwater biofilms in a metal polluted Mediterranean stream

While seasonal variations in fluvial communities have been extensively investigated, effects of seasonality on community responses to environmental and/or chemical stress are poorly documented. The aim of this study was to describe antioxidant enzyme activity (AEA) variability in fluvial biofilms over an annual cycle, under multi-stress scenarios due to environmental variability (e.g., light intensity, water flow, and temperature) and metal pollution (Zn, Mn and Fe). The annual monitoring study was performed at three sites according to their water and biofilm metal concentrations. Metal concentration was affected by water flow due to dilution. Low flow led to higher dissolved Zn concentrations, and thus to higher Zn accumulation in the biofilm. Water temperature, light intensity and phosphate concentration were the environmental factors which determined the seasonality of biofilm responses, whereas dissolved Zn and Zn accumulation in biofilms were the parameters linked to sites and periods of highest metal pollution. Community algal succession, from diatoms in cold conditions to green algae in warm conditions, was clearer in the non metal-polluted site than in those metal-polluted, presumably due to the selection pressure exerted by metals. Most AEA were related with seasonal environmental variability at the sites with low or no-metal pollution, except glutathione-S-transferase (GST) which was related with Zn (dissolved and accumulated in biofilm) pollution occurring at the most polluted site. We can conclude that seasonal variations of community composition and function are masked by metal pollution. From this study we suggest the use of a multi-biomarker approach, including AEA and a set of biological and physicochemical parameters as an effect-based field tool to assess metal pollution.

Light History Influences the Response of Fluvial Biofilms to Zn Exposure

Fluvial biofilms are subject to multistress situations in natural ecosystems, such as the co-occurrence of light intensity changes and metal toxicity. However, studies simultaneously addressing both factors are rare. This study evaluated in microcosm conditions the relationship between short-term light intensity changes and Zn toxicity on fluvial biofilms with long-term photoacclimation to different light conditions. Biofilms that had long-term photoacclimation to 25 μmol photons · m(-2)  · s(-1) (low light [LL] biofilms), 100 μmol photons · m(-2)  · s(-1) (medium light [ML] biofilms), and 500 μmol photons · m(-2)  · s(-1) (high light [HL] biofilms) were characterized by different structural (Chlorophyll-a [Chl-a], total biomass-AFDW, EPS, algal groups, and diatom taxonomy) and physiological attributes (ETR-I curves and photosynthetic pigments). HL biofilms showed higher light saturation intensity and a higher production of xanthophylls than LL biofilms. In contrast, LL biofilms had many structural differences; a higher proportion of diatoms and lower AFDW and EPS contents than ML and HL biofilms. A clear effect of light intensity changes on Zn toxicity was also demonstrated. Zn toxicity was enhanced when a sudden increase in light intensity also occurred, mainly with LL biofilms, causing higher inhibition of both the Φ'PSII and the ΦPSII . A decoupling of NPQ from de-epoxidation reaction (DR) processes was also observed, indicating substantial damage to photoprotective mechanisms functioning in biofilms (i.e., xanthophyll cycle of diatoms) due to Zn toxicity. This study highlights the need to take into account environmental stress (e.g., light intensity changes) to better assess the environmental risks of chemicals (e.g., metals).

Antioxidant enzyme activities as biomarkers of Zn pollution in fluvial biofilms

The potential of the antioxidant enzyme catalase (CAT) and ascorbate peroxidase (APX) as molecular biomarkers of Zn toxicity in freshwater biofilms has been explored in this study jointly with other classical functional and structural endpoints (photosynthetic parameters, algal group composition and bioaccumulation). Biofilms were colonized in an indoor microcosm system for 5 weeks and then exposed to Zn for 5 weeks. To evaluate Zn effects, biofilms were sampled 5 and 3 days before exposure, just before exposure (time 0), and after 6h, 1, 3, 7, 21 and 35 days of metal exposure. Most endpoints measured were affected by Zn exposure (320 μg Zn L(-1)) during both periods of exposure. APX was the only functional parameter responding after a few hours of Zn exposure, highlighting its use as an early toxicity biomarker. Structural changes began after 3 days of exposure, starting with a decrease in algal biomass and an increase in the OD 430:665 ratio. Structural changes in biofilm communities were observed after 1 week, leading to a shift from diatoms to cyanobacteria and green algae-dominated communities. CAT activity was thereafter enhanced (after three weeks of exposure) and attributed not only to a direct effect of Zn bioaccumulation but also to an indirect effect of the community composition changes driven by chronic metal exposure. It can be concluded that biofilm antioxidant enzyme activities may provide evidence of early stress caused by metal exposure and also provide information about the mechanism of community adaptation. This information can be of great interest to improve current tools used for risk assessment.

Catalase in fluvial biofilms: a comparison between different extraction methods and example of application in a metal-polluted river

Antioxidant enzymes are involved in important processes of cell detoxification during oxidative stress and have, therefore, been used as biomarkers in algae. Nevertheless, their limited use in fluvial biofilms may be due to the complexity of such communities. Here, a comparison between different extraction methods was performed to obtain a reliable method for catalase extraction from fluvial biofilms. Homogenization followed by glass bead disruption appeared to be the best compromise for catalase extraction. This method was then applied to a field study in a metal-polluted stream (Riou Mort, France). The most polluted sites were characterized by a catalase activity 4-6 times lower than in the low-polluted site. Results of the comparison process and its application are promising for the use of catalase activity as an early warning biomarker of toxicity using biofilms in the laboratory and in the field.

Copper accumulation and toxicity in fluvial periphyton: the influence of exposure history

Periphyton communities have a good bioaccumulation capacity and can be used to monitor metal pollution in fluvial ecosystems. Depending on the dose and exposure time, metals may produce changes in the structure and function of these communities, thus it is expected that the kinetics of metal accumulation and metal sensitivity will also be influenced by the exposure history. In this study, the effects of pulsed and continuous Cu exposures during the colonization of the communities were investigated under controlled conditions. This investigation includes the study of metal accumulation kinetics and the evaluation of community tolerance. Pulsed copper exposure did not affect the community structure but influenced the accumulation kinetics (decreasing intracellular copper uptake). On the other hand, continuous copper exposure caused a huge increase in metal content (both total and intracellular) and modified the structure of the community (increasing the percentage of cyanobacteria and diatom diversity). Both pulsed and continuous periphyton metal exposure may have negative repercussions for the fluvial ecosystem. While Cu pulsed exposure may be toxic to periphyton communities, continuous exposures may lead to community adaptation, which is often related to changes in species composition and higher metal contents being transferred to higher trophic levels of the stream food chain.