Taxonomy- or trait-based ecological assessment for tropical rivers? Case study on benthic diatoms in Mayotte island (France, Indian Ocean)

How do multidimensional traits of dominant diatom Aulacoseira respond to abiotic and biotic factors in a river delta system?

Trait-based approaches are being increasingly applied in ecology, and the influence of individual-level trait variation on communities and species has been demonstrated. However, the responses of individual trait variation to environmental changes remain to be explored. To examine the indicating functions of multidimensional traits, individual-level measurements of the dominant diatom genus Aulacoseira Thwaites in the Pearl River Delta were performed, and corresponding responses of three trait indices (trait richness, trait evenness, and trait dispersion) to abiotic and biotic factors were examined. Our results indicated that the three individual trait diversity indices were regulated by different factors. Trait richness was only significantly affected by abiotic factors (temperature), while trait evenness and trait dispersion were regulated by both abiotic and biotic factors. In addition, the direct influence of abiotic factors was more significant than that of biotic factors, implying that the multidimensional trait variation of Aulacoseira was more responsive to environmental changes than to interspecific interactions. Therefore, the multidimensional trait variation of Aulacoseira could be used as an effective indicator to track environmental changes. Our study elucidated the mechanisms relating individual-level trait variation to phytoplankton community dynamics; this could improve our ability to forecast changes in ecosystem properties across environmental gradients.

Genus-level, trait-based multimetric diatom indices for assessing the ecological condition of rivers and streams across the conterminous United States

Taxonomic inconsistency in species-level identifications has constrained use of diatoms as biological indicators in aquatic assessments. We addressed this problem by developing diatom multimetric indices (MMIs) of ecological condition using genus-level taxonomy and trait-based autecological information. The MMIs were designed to assess river and stream chemical, physical and biological condition across the conterminous United States. Trait-based approaches have the advantage of using both species-level and genus-level data, which require less effort and expense to acquire than traditional species-based approaches and eliminate the persistent taxonomic biases introduced over vast geographic extents. For large-extent assessment programs that require multiple taxonomic laboratories to process samples, such as the United States Environmental Protection Agency's (U.S. EPA's) National Rivers and Streams Assessment (NRSA), the trait approach can eliminate discrepancies in species-level identification or nomenclature that hinder diatom data interpretation. We developed trait-based MMIs using NRSA data for each of the three large ecoregions across the U.S. - the East, Plains, and West. All three MMIs performed well in discriminating least-disturbed from most-disturbed sites. The MMI for the East had the greatest discrimination ability, followed by MMIs for the Plains and West, respectively. The performance of the MMIs was comparable to that observed in existing NRSA fish and macroinvertebrate MMIs. Our research shows that trait-based diatom indices constructed on genus-level taxonomy can be effective for large-scale assessments, and may also allow programs such as NRSA to assess trends in freshwater condition retrospectively, by revisiting older diatom datasets. Moreover, our genus-based approach facilitates including of diatoms into other assessment programs that have limited monitoring resources.

Catchment scale deforestation increases the uniqueness of subtropical stream communities

Local communities and individual species jointly contribute to the overall beta diversity in metacommunities. However, it is mostly unknown whether the local contribution (LCBD) and the species contribution (SCBD) to beta diversity can be predicted by local and regional environmental characteristics and by species traits and taxonomic relatedness, respectively. We investigated the LCBD and SCBD of stream benthic diatoms and insects along a gradient of land use intensification, ranging from streams in pristine forests to agricultural catchments in southeast subtropical Brazil. We expected that the LCBD would be negatively related to forest cover and positively related to the most unique streams in terms of environmental characteristics and land use (hereafter environmental and land use uniqueness, respectively). We also expected that species with a high SCBD would occur at sites with reduced forest cover. We found that the LCBD of diatoms and insects was negatively related to forest cover. The LCBD of insects was also positively related to environmental and land use uniqueness. As forest cover was negatively related to uniqueness in land use, biologically unique streams were those that deviated from the typical regional land cover. We also found that diatom traits, insect traits, and taxonomic relatedness partly explained SCBD. Furthermore, the SCBD of diatoms was positively correlated with forest cover, but the inverse was found for insects. We showed that deforestation creates novel and unique communities in subtropical streams and that species that contribute the most to beta diversity can occur at opposite ends of a land use gradient.

Raman spectroscopy applied to diatoms (microalgae, Bacillariophyta): Prospective use in the environmental diagnosis of freshwater ecosystems

Diatom species are good pollution bioindicators due to their large distribution, fast response to changes in environmental parameters and different tolerance ranges. These organisms are used in ecological water assessment all over the world using autoecological indices. Such assessments commonly rely on the taxonomic identification of diatom species-specific shape and frustule ornaments, from which cell counts, species richness and diversity indices can be estimated. Taxonomic identification is, however, time-consuming and requires years of expertise. Additionally, though the diatom autoecological indices are region-specific, they are often applied indiscriminately across regions. Raman spectroscopy is a simpler, fast and label-free technique that can be applied to environmental diagnosis with diatoms. However, this approach has been poorly explored. This work reviews Raman spectroscopy studies involving the structure, location and conformation of diatom cell components and their variation under different conditions. A critical appreciation of the pros and cons of its application to environmental diagnosis is also given. This knowledge provides a strong foundation for the development of environmental protocols using Raman spectroscopy in diatoms. Our work aims at stimulating further research on the application of Raman spectroscopy as a tool to assess physiological changes and water quality under a changing climate.

Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers

Aquatic biofilms are heterogeneous assemblages of microorganisms surrounded by a matrix of extracellular polymeric substances (EPS). Recent studies suggest that aquatic biofilms can physically act as sorptive sponges of DNA. We took the opportunity from already available samples of stone biofilms and macroinvertebrates specimens collected in parallel at the same sites to test the capacity of biofilms to act as DNA samplers of macroinvertebrate communities in streams. Macroinvertebrate communities are usually studied with metabarcoding using the DNA extracted from their bodies bulk samples, which remains a time-consuming approach and involves the destruction of all individual specimens from the samples. The ability of biofilms to capture DNA was explored on 19 rivers sites of a tropical island (Mayotte Island, France). First, macroinvertebrate specimens were identified based on their morphological characteristics. Second, DNA was extracted from biofilms, and macroinvertebrate communities were targeted using a standard COI barcode. The resulting morphological and molecular inventories were compared. They provided comparable structures and diversities for macroinvertebrate communities when one is working with the unassigned OTU data. After taxonomic assignment of the OTU data, diversity and richness were no longer correlated. The ecological assessment derived from morphological bulk samples was conserved by the biofilms samples. We also showed that the biofilm method allows to detect a higher diversity for some organisms (Cnidaria), that is hardly accessible with the morphological method. The results of this study exploring the DNA signal captured by natural biofilms are encouraging. However, a more detailed study integrating more replicates and comparing the biodiversity signal based on both morphological and molecular bulk macroinvertebrate samples to the one captured by biofilms will be necessary. Better understanding how the DNA signal captured by natural biofilms represents the biodiversity of a given sampling site is necessary before considering its use for bioassessment applications.

Benthic Diatoms in River Biomonitoring—Present and Future Perspectives within the Water Framework Directive

The European Water Framework Directive 2000/60/EC (WFD) has been implemented over the past 20 years, using physicochemical, biological and hydromorphological elements to assess the ecological status of surface waters. Benthic diatoms (i.e., phytobenthos) are one of the most common biological quality elements (BQEs) used in surface water monitoring and are particularly successful in detecting eutrophication, organic pollution and acidification. Herein, we reviewed their implementation in river biomonitoring for the purposes of the WFD, highlighting their advantages and disadvantages over other BQEs, and we discuss recent advances that could be applied in future biomonitoring. Until now, phytobenthos have been intercalibrated by the vast majority (26 out of 28) of EU Member States (MS) in 54% of the total water bodies assessed and was the most commonly used BQE after benthic invertebrates (85% of water bodies), followed by fish (53%), macrophytes (27%) and phytoplankton (4%). To meet the WFD demands, numerous taxonomy-based quality indices have been developed among MS, presenting, however, uncertainties possibly related to species biogeography. Recent development of different types of quality indices (trait-based, DNA sequencing and predictive modeling) could provide more accurate results in biomonitoring, but should be validated and intercalibrated among MS before their wide application in water quality assessments.

Trait-based diatom functional diversity as an appropriate tool for understanding the effects of environmental changes in soda pans

Saline lakes, among the most seriously endangered ecosystems, are threatened due to climate change and human activities. One valuable feature of these environments is that they constitute areas of high biodiversity. Ecologists are, therefore, under great pressure to improve their understanding of the effects of natural and anthropogenic disturbances on the biodiversity of saline lakes. In this study, a total of 257 samples from 32 soda pans in Central Europe between 2006 and 2015 were examined. The effects of environmental variables and of geographical and limnoecological factors on functional diversity were analyzed. Furthermore, the explanatory power of the trait-based approach was assessed, and the applicability of the indices for biomonitoring purposes was determined. It was found that low habitat heterogeneity and harsh environments lead to the selection of a small number of suitable traits, and consequently, to a naturally low level of functional diversity. Anthropogenic activities enhance diversity at functional level due to the shift toward freshwater characteristics. On the regional scale, the effects of the region and status (natural, degraded, reconstructed) on diatom functional diversity were significant and more pronounced than that of the environmental and other limnoecological factors. The degree of variance found in functional diversity ascribed to environmental variables is five times greater in the case of the application of a trait-based approach, than when a taxonomic one is employed in the literature. Each of the tested functional diversity indices was sensitive to the most important environmental variables. Furthermore, these were type-specific and proved to be more complex indicators than taxonomic metrics. It is possible to suggest four functional diversity indices (FGR, FRic, FDis, and FDiv) which emphasize their independence from substrate and seasonal variations for ecological status assessment and conservation planning.

Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks

Ecological status assessment of watercourses is based on the calculation of quality indices using pollution sensitivity of targeted biological groups, including diatoms. The determination and quantification of diatom species is generally based on microscopic morphological identification, which requires expertise and is time-consuming and costly. In Europe, this morphological approach is legally imposed by standards and regulatory decrees by the Water Framework Directive (WFD). Over the past decade, a DNA-based molecular biology approach has newly been developed to identify species based on genetic criteria rather than morphological ones (i.e. DNA metabarcoding). In combination with high throughput sequencing technologies, metabarcoding makes it possible both to identify all species present in an environmental sample and to process several hundred samples in parallel. This article presents the results of two recent studies carried out on the WFD networks of rivers of Mayotte (2013–2018) and metropolitan France (2016–2018). These studies aimed at testing the potential application of metabarcoding for biomonitoring in the context of the WFD. We discuss the various methodological developments and optimisations that have been made to make the taxonomic inventories of diatoms produced by metabarcoding more reliable, particularly in terms of species quantification. We present the results of the application of this DNA approach on more than 500 river sites, comparing them with those obtained using the standardised morphological method. Finally, we discuss the potential of metabarcoding for routine application, its limits of application and propose some recommendations for future implementation in WFD.

Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding

Freshwater ecosystems are continuously affected by anthropogenic pressure. One of the main sources of contamination comes from wastewater treatment plant (WWTP) effluents that contain wide range of micro- and macropollutants. Chemical composition, toxicity levels and impact of treated effluents (TEs) on the recipient aquatic ecosystems may strongly differ depending on the wastewater origin. Compared to urban TEs, hospital ones may contain more active pharmaceutical substances. Benthic diatoms are relevant ecological indicators because of their high species and ecological diversity and rapid response to human pressure. They are routinely used for water quality monitoring. However, there is a knowledge gap on diatom communities’ development and behavior in treated wastewater in relation to prevailing micro- and macropollutants. In this study, we aim to (1) investigate the response of diatom communities to urban and hospital TEs, and (2) evaluate TEs effect on communities in the recipient river. Environmental biofilms were colonized in TEs and the recipient river up- and downstream from the WWTP output to study benthic diatoms using DNA metabarcoding combined with high-throughput sequencing (HTS). In parallel, concentrations of nutrients, pharmaceuticals and seasonal conditions were recorded. Diatom metabarcoding showed that benthic communities differed strongly in their diversity and structure depending on the habitat. TE sites were generally dominated by few genera with polysaprobic preferences belonging to the motile guild, while river sites favored diverse communities from oligotrophic and oligosaprobic groups. Seasonal changes were visible to lower extent. To categorize parameters important for diatom changes we performed redundancy analysis which suggested that communities within TE sites were associated to higher concentrations of beta-blockers and non-steroidal anti-inflammatory drugs in urban effluents vs. antibiotics and orthophosphate in hospital effluents. Furthermore, indicator species analysis showed that 27% of OTUs detected in river downstream communities were indicator for urban or hospital TE sites and were absent in the river upstream. Finally, biological diatom index (BDI) calculated to evaluate the ecological status of the recipient river suggested water quality decrease linked to the release of TEs. Thus, in-depth assessment of diatom community composition using DNA metabarcoding is proposed as a promising technique to highlight the disturbing effect of pollutants in Alpine rivers.

The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high-throughput sequencing (HTS) and meta-barcoding methods now used for bioassessment traditionally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into operational taxonomic units, which is considered descriptive of species-level resolution. In this study, we analyzed the effect of the SST on the resulting diatom-based ecological quality index, which is based on OTU abundance distribution along a defined environmental gradient, ideally avoiding taxonomic assignments that could result in high rates of unclassified OTUs and biased final values. A total of 90 biofilm samples were collected in 2014 and 2015 from 51 stream sites on Mayotte Island in parallel with measures of relevant physical and chemical parameters. HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom-specific primers. Hierarchical clustering was used to group sequences into OTUs using 20 experimental SST levels (80%-99%). An OTU-based quality index (IdxOTU) was developed based on a weighted average equation using the abundance profiles of the OTUs. The developed IdxOTU revealed significant correlations between the IdxOTU values and the reference pressure gradient, which reached maximal performance using an SST of 90% (well above species level delimitation). We observed an interesting and important trade-off with the power to discriminate between sampling sites and index stability that will greatly inform future applications of the index. Taken together, the results from this study detail a thoroughly optimized and validated approach to generating robust, reproducible, and complete indexes that will greatly facilitate effective and efficient environmental monitoring.

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior

Sea turtles are distributed in tropical and subtropical seas worldwide. They play several ecological roles and are considered important indicators of the health of marine ecosystems. Studying epibiotic diatoms living on turtle shells suggestively has great potential in the study of turtle behavior because diatoms are always there. However, diatom identification at the species level is time consuming, requires well-trained specialists, and there is a high probability of finding new taxa growing on turtle shells, which makes identification tricky. An alternative approach based on DNA barcoding and high throughput sequencing (HTS), metabarcoding, has been developed in recent years to identify species at the community level by using a DNA reference library. The suitabilities of morphological and molecular approaches were compared. Diatom assemblages were sampled from seven juvenile green turtles (Chelonia mydas) from Mayotte Island, France. The structures of the epibiotic diatom assemblages differed between both approaches. This resulted in different clustering of the turtles based on their diatom communities. Metabarcoding allowed better discrimination between turtles based on their epibiotic diatom assemblages and put into evidence the presence of a cryptic diatom diversity. Microscopy, for its part, provided more ecological information of sea turtles based on historical bibliographical data and the abundances of ecological guilds of the diatom species present in the samples. This study shows the complementary nature of these two methods for studying turtle behavior.