The future of fish-based ecological assessment of European rivers: from traditional EU Water Framework Directive compliant methods to eDNA metabarcoding-based approaches.

Most of the present EU Water Framework Directive (WFD) compliant fish-based assessment methods of European rivers are multi-metric indices computed from traditional electrofishing (TEF) samples, but this method has known shortcomings, especially in large rivers. The probability of detecting rare species remains limited, which can alter the sensitivity of the indices. In recent years, environmental (e)DNA metabarcoding techniques have progressed sufficiently to allow applications in various ecological domains as well as eDNA-based ecological assessment methods. A review of the 25 current WFD-compliant methods for river fish shows that 81% of the metrics used in these methods are expressed in richness or relative abundance and thus compatible with eDNA samples. However, more than half of the member states' methods include at least one metric related to age or size structure and would have to adapt their current fish index if reliant solely on eDNA-derived information. Most trait-based metrics expressed in richness are higher when computed from eDNA than when computed from TEF samples. Comparable values are obtained only when the TEF sampling effort increases. Depending on the species trait considered, most trait-based metrics expressed in relative abundance are significantly higher for eDNA than for TEF samples or vice versa due to over-estimation of sub-surface species or under-estimation of benthic and rare species by TEF sampling, respectively. An existing predictive fish index, adapted to make it compatible with eDNA data, delivers an ecological assessment comparable with the current approved method for 22 of the 25 sites tested. Its associated uncertainty is lower than that of current fish indices. Recommendations for the development of future fish eDNA-based indices and the associated eDNA water sampling strategy are discussed.

Seasonal dynamics of riverine fish communities using eDNA.

As fish communities are a major concern in rivers ecosystems, we investigated if their environmental (e)DNA signals vary according to the sampling period or hydromorphological conditions. Three rivers were studied over a year using eDNA metabarcoding approach. The majority of the species (c. 80%) were detected all year round in two rivers having similar hydromorphological conditions, whereas in the river affected by an upstream lake waterflow, more species were detected sporadically (42%). For all the rivers, in more than 98% of the occasional detections, the reads abundance represented <0.4% of the total reads per site and per sampling session. Even if the majority of the fish communities remained similar over the year for each of the three rivers, specific seasonal patterns were observed. We studied if the waterflow or the reproduction period had an effect on the observed dynamics. Waterflow, which influences eDNA downstream transportation, had a global influence in taxonomic richness, while the fishes' reproductive period had only an influence on certain species. Our results may help selecting the best sampling strategy according to research objectives. To study fish communities at local scale, seasons of low waterflow periods are recommended. This particularly helps to restraint effects of external eDNA coming from connections with other aquatic environment (tributaries, lakes, wetlands, sewage effluents, etc.). To obtain a more integrative overview of the fish community living in a river basin, high waterflow or breeding seasons are preferable for enhancing species detection probability, especially for rare species.

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding.

Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR.

Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density/biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer the absolute abundance of fish species. We carried out a 2850-km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a nonlinear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65 × 106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results provide a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.

Spatio-temporal variability of eDNA signal and its implication for fish monitoring in lakes.

Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are still needed to better assess the spatial and temporal variability of the eDNA signal and to ultimately design an optimal sampling strategy for eDNA monitoring. In this context, we sampled three different lakes (a dam reservoir, a shallow eutrophic lake and a deep oligotrophic lake) every 6 weeks for 1 year. We performed four types of sampling for each lake (integrative sampling of sub-surface water along transects on the left shore, the right shore and above the deepest zone, and point sampling in deeper layers near the lake bottom) to explore the spatial variability of the eDNA signal at the lake scale over a period of 1 year. A metabarcoding approach was applied to analyse the 92 eDNA samples in order to obtain fish species inventories which were compared with traditional fish monitoring methods (standardized gillnet samplings). Several species known to be present in these lakes were only detected by eDNA, confirming the higher sensitivity of this technique in comparison with gillnetting. The eDNA signal varied spatially, with shoreline samples being richer in species than the other samples. Furthermore, deep-water samplings appeared to be non-relevant for regularly mixed lakes, where the eDNA signal was homogeneously distributed. These results also demonstrate a clear temporal variability of the eDNA signal that seems to be related to species phenology, with most of the species detected in spring during the spawning period on shores, but also a peak of detection in winter for salmonid and coregonid species during their reproduction period. These results contribute to our understanding of the spatio-temporal distribution of eDNA in lakes and allow us to provide methodological recommendations regarding where and when to sample eDNA for fish monitoring in lakes.

Cortisol awakening response among Latinx and Black students transitioning to college prior to and during the COVID-19 pandemic.

Globally, the COVID-19 (coronavirus disease 2019) pandemic has resulted in abrupt shifts in ecological and social environments, including school contexts, which became predominately virtual. This study (1) examines the role of the COVID-19 pandemic (transitioning to college prior to vs. during the COVID-19 pandemic) on cortisol awakening response (CAR) - a biological marker of chronic psychosocial stress - and university belonging among Latinx and Black first-year college students; and (2) explores whether university belonging serves as a mediator in the relationship between the COVID-19 pandemic and CAR. Latinx and Black students who were in their first semester at a four-year public university in Los Angeles County - one of the United States' hot spots for COVID-19, were recruited for this study. Across two separate cohorts (fall 2019, fall 2020), participants (N = 136) completed an online survey and provided salivary samples to assess for morning cortisol levels. Findings revealed that students who transitioned to college during the COVID-19 pandemic exhibited a flatter CAR and lower levels of belonging than students who transitioned to college prior to the COVID-19 pandemic. Implications for intervention, programs and policies aimed at fostering positive transitions to college during the COVID-19 pandemic and beyond are discussed.

Physician perceptions of recruitment and retention factors in an area with a regional medical campus.

BACKGROUND: The factors that influence physicians to establish and maintain their practice in a region are variable. The presence of a regional medical campus (RMC) could influence physicians' choice. The objective of this study was to explore the factors influencing physician recruitment and retention, and in particular the role of a RMC, in a region of Quebec. METHODS: A literature review of factors influencing physicians to stay in a rural area was conducted in order to create an interview guide. Questions were divided into sections: general information, family situation, medical training, career choice, current practice, intent to stay in the region, and impact of the RMC. Thirteen semi-structured individual interviews were conducted with practicing physicians. Data were analyzed using QDAMiner. RESULTS: Recruitment factors were divided into six major themes: type of practice, spousal interest, opportunity for teaching, training in a region, workforce planning, and quality of life. Participants identified positive and negative factors associated with retention. In both cases, family and quality of work environment were mentioned. The RMC was perceived as having important impacts on the quality of professional life, research, medical practice, and regional development. CONCLUSION: This study highlights the role of RMCs in physician recruitment and retention via multiple impacts on the quality of practice of physicians working in the same area.

CONTEXTE: Les facteurs influençant les médecins à s'établir et à rester dans une région sont variables. La présence d'un campus médical régional (CMR) pourrait influencer ce choix. L'objectif de cette étude était d'explorer les facteurs de recrutement et de rétention influençant les médecins ayant choisi de pratiquer dans la région du Saguenay-Lac-Saint-Jean au Québec, en particulier le rôle du CMR. MÉTHODES: Une synthèse de la littérature a permis d'identifier différents facteurs influençant les médecins dans leur choix de lieu de pratique. Un guide d'entrevue a été élaboré à partir de ces facteurs. Les questions étaient séparées selon les sections suivantes: informations générales, situation familiale, études médicales, choix de carrière, pratique actuelle, intention de rester dans la région, impact du CMR. Treize entrevues semi-dirigées individuelles ont été réalisées avec des médecins en pratique. Les données ont été analysées avec QDA Miner. RÉSULTATS: Les facteurs influençant le recrutement étaient séparés en six thèmes majeurs : type de pratique, intérêt du conjoint, opportunité d'enseigner, formation en région, planification gouvernementale des effectifs médicaux et qualité de vie. Les participants ont identifié des facteurs de rétention négatifs et positifs. Ceux-ci concernaient la famille et la qualité de l'environnement de travail. D'après les participants, le CMR avait un impact direct sur la qualité de la vie professionnelle, la recherche, la pratique médicale et le développement régional. CONCLUSION: Cette étude a permis de mettre en évidence le rôle des CMRs dans le recrutement et la rétention via de multiples impacts sur la qualité de pratique des médecins exerçant dans la même région.

Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation.

Despite the ecological and societal importance of large rivers, fish sampling remains costly and limited to specific habitats (e.g., river banks). Using an eDNA metabarcoding approach, we regularly sampled 500 km of a large river (Rhône River). Comparisons with long-term electrofishing surveys demonstrated the ability of eDNA metabarcoding to qualitatively and quantitatively reveal fish assemblage structures (relative species abundance) but eDNA integrated a larger space than the classical sampling location. Combination of a literature review and field data showed that eDNA behaves in the water column like fine particulate organic matter. Its detection distance varied from a few km in a small stream to more than 100 km in a large river. To our knowledge, our results are the first demonstration of the capacity of eDNA metabarcoding to describe longitudinal fish assemblage patterns in a large river, and metabarcoding appears to be a reliable, cost-effective method for future monitoring.

Microsatellite development and first population size estimates for the groundwater isopod Proasellus walteri.

Effective population size (N e) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of N e in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small N e. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proaselluswalteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for N e estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that N e in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small N e.