Applicability of a Functional Trait-Based Methodology in Stream Porous Matrices for Assessing Point-Source Pollution and Vertical Exchange Dynamics
Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
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Author to whom correspondence should be addressed.
Ecologies 2026, 7(3), 89; https://doi.org/10.3390/ecologies7030089
Submission received: 3 August 2026
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Revised: 22 August 2026
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Accepted: 26 August 2026
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Published: 1 September 2026
(This article belongs to the Special Issue Monitoring and Ecological Assessment of River Biodiversity)
Abstract
Stream ecosystems are threatened by chemical contamination and altered vertical connectivity between surface water and groundwater. Vertical hydrological exchanges occur through the porous matrix—comprising coarse surface sediments and the hyporheic zone—which acts as a critical interface for pollutant storage. The Functional Trait (FTR) method, based on oligochaete communities in these two compartments, allows for simultaneous assessment of toxic stress and vertical hydrological exchange dynamics. We applied this method upstream and downstream of four wastewater treatment plants as well as within an impacted tributary and around its confluence zone. Our results, supported by physicochemical analyses confirming effluent-driven pollution, demonstrate marked degradation of biological quality and ecosystem functioning downstream of all discharge points. While coarse surface sediments provided a reliable diagnostic of point-source pollution impacts, investigating the hyporheic zone refined the assessment by identifying site-specific hydrological trends. In one case, it revealed enhanced infiltration dynamics and pollutant accumulation in deep interstitial spaces, while in another, it highlighted groundwater exfiltration as a driver of ecosystem resilience. These findings highlight the FTR method as a robust and flexible tool for water managers. While integrating the hyporheic zone allows for a comprehensive analysis of vertical exchange dynamics and ecosystem vulnerability, focusing on coarse surface sediments alone provides a cost-effective strategy for routine impact assessment and the detection of major exfiltrations reaching the surface. Future research should integrate this biological approach with high-resolution physicochemical monitoring and direct physical measurements of vertical hydrological exchanges.
1. Introduction
The negative effects of human activities on aquatic ecosystems include both the contamination of water resources and the alteration of connectivity between surface water and groundwater [1,2]. Stream ecosystem functioning is driven by complex longitudinal, lateral, and vertical connectivity dynamics. Within these multi-dimensional exchanges, the surface–groundwater interface plays a critical role in regulating the input, storage, and transformation of nutrients and chemical pollutants [3,4,5,6].
Coarse surface sediments and the hyporheic environment, collectively referred to as the “porous matrix,” represent predominant stream habitats that sequester pollutants and act as filters for vertical hydrological exchanges. These exchanges can facilitate essential ecosystem services, such as stream self-purification [7]. Consequently, environmental monitoring programs should ideally assess both the biological quality of the porous matrix and vertical hydrological exchange dynamics [7,8,9].
While standard regulatory biomonitoring frameworks worldwide typically rely on general surface macroinvertebrate indices (such as the Swiss IBCH or the British BMWP) for broad riverbed assessments, these metrics can be significantly influenced by localized habitat heterogeneity [10]. To minimize habitat-driven variations and to specifically investigate the pollutant storage and hydrological exchange dynamics of the porous matrix, specialized tools targeting uniform interstitial compartments are required. In this regard, oligochaetes represent a key component of the interstitial fauna within these environments, comprising species with diverse resistance levels to chemical pollution as well as species characteristic of surface sediments or groundwater (specifically stygophilous and stygobiont taxa) [3,7,11]. Although traditional oligochaete-based indices are widely used to track pollution in fine and depositional sediments [12], they are unsuited for such coarse matrices. To address the specific realities of coarse and deep interstitial matrices and integrate vertical exchange dynamics into a single diagnostic framework, the Functional Trait (FTR) method was developed from an extensive dataset spanning a gradient from pristine to highly impaired sites [3,7].
The FTR method was previously applied in Switzerland to detect the specific effects of obsolete wastewater treatment plant (WWTP) effluents in anthropized contexts [13,14]. Those studies demonstrated more altered biological quality and stream functioning downstream of effluents in both the coarse surface sediments and the hyporheic zone. Furthermore, the method identified sites with high self-purification capacity via unpolluted groundwater exfiltration, as well as areas where groundwater was vulnerable to surface pollution. Following the upgrading of two WWTPs, subsequent applications of the FTR method revealed a substantial reduction in pollution-resistant taxa and improved stream functioning both in the coarse surface sediments and the hyporheic zone [14,15].
The objective of the present study was to obtain new data to further confirm the suitability of the FTR method for detecting point-source pollution impacts. While the method has been tested on several WWTPs, validating its sensitivity across a wider range of contexts and discharge types remains crucial. Here, the FTR method was applied upstream and downstream of four WWTP effluents, as well as within an anthropized tributary and both upstream and downstream of its confluence in the receiving stream. Two WWTPs were studied in detail (both compartments), while the remaining two plants and the tributary-confluence system were investigated, focusing solely on coarse surface sediments. This choice follows previous demonstrations [13,14,15] that coarse surface sediment analysis alone provides, in most cases, a sufficient ecological diagnosis of stream quality and functioning while substantially reducing costs.
2. Material and Methods
2.1. Description of Sites
The four studied WWTPs are located in Switzerland: Falkenstein (Canton of Solothurn), Bremblens and Vullierens (Canton of Vaud), and Villeret (Canton of Bern). Additionally, an impacted tributary (Marais River) and its receiving stream (Drize River) were investigated in the Canton of Geneva. Chemical monitoring by cantonal water protection services had previously identified all these effluents and the tributary as clear sources of pollution. Biological impacts were also evident: a marked decline in brown trout (Salmo trutta) and bullhead (Cottus gobio) populations has been recorded downstream of the Villeret WWTP since 2018 [16], and a similar decline (brown trout and minnow, Phoxinus phoxinus) occurred in the Marais River in October 2022 [17].
Sampling sites were strategically selected to capture longitudinal gradients (Table 1): Falkenstein & Bremblens: One site upstream (UPS) and two downstream (Dws1 and Dws2). In Falkenstein, Dws1 and Dws2 were ~175 m and ~1600 m from the outlet, respectively. In Bremblens, they were ~40 m and ~150 m from the outlet; Vullierens: One site upstream (UPS) and one downstream (Dws, ~60 m from the outlet); Villeret: Two upstream sites (S9, upstream of the city; S8, downstream of the city) and three downstream sites (S6, near the outlet; S4, ~600 m downstream; S2, ~1.7 km downstream); Canton of Geneva (Tributary-Confluence System): One site in the Marais River (M1) and two in the Drize River (receiving stream): one upstream (UPS, 2 km from the confluence) and one downstream (Dws, ~30 m from the confluence). At all locations, downstream sites were positioned to ensure complete mixing of the effluents or affluent water with the receiving stream across the entire channel width. The studied municipal installations operate under standardized regulatory configurations. The Falkenstein WWTP (serving approximately 10,000–15,000 population equivalents, PE) utilizes a conventional treatment train combining primary mechanical sedimentation, secondary biological activated sludge, and tertiary chemical phosphorus removal. The Villeret WWTP is a smaller facility (3000–5000 PE) featuring a standard primary and secondary biological configuration, which also processes specific organic loads from local dairy industries. The small regional installations of Vullierens and Bremblens (1000–4000 PE) operate using standard primary mechanical and secondary biological treatment layouts.
One sampling campaign was conducted at each location: 5 April 2023 in Villeret, 25 August 2023 in Falkenstein, 2 October 2023 in the Canton of Geneva, 7 February 2024 in Vullierens, and 15 March 2024 in Bremblens. Oligochaete communities were analyzed in the coarse surface sediments at all sites. In addition, the hyporheic zone was also investigated at Sites UPS and Dws in Vullierens, and at Sites UPS and Dws1 in Bremblens.
The watersheds upstream of the sampling sites are characterized by a mix of agricultural, industrial, and urban areas; consequently, some baseline chemical pollution was expected at all upstream sites. In the Marais River, pollution sources are particularly diverse, including stormwater overflows and agricultural runoff (pesticides, plant protection products, and organic matter). Regarding stream ecomorphology, conditions were natural or near-natural in Bremblens, Vullierens, and in the Canton of Geneva, while the streams in Villeret and Falkenstein were artificial or semi-natural, characterized by straightened channels with relatively natural banks.
2.2. Physicochemical Analysis and Compliance
To support the biological assessment, physicochemical data for each site were included as supplemental information. These data were provided by the respective cantonal water protection services (Vaud, Solothurn, Bern, and Geneva) or derived from WWTP self-monitoring data.
- Nutrients and carbon: Concentrations of nitrate, ammonium, nitrite, phosphate, total phosphorus, dissolved organic carbon (DOC), total organic carbon (TOC), and total nitrogen were provided for the treated effluents (Vullierens, Bremblens, Falkenstein) and specific stream sites (sites S8 and S4 in Villeret, UPS, Dws and M1 in the Canton of Geneva). Sampling periods ranged from 2023 to early 2024 (see Supplemental Materials for exact dates and composite sample details). The specific parameters analyzed for nutrients and carbon varied slightly between locations depending on the available cantonal monitoring data. However, for each site, these analyses consistently included key indicators of organic and mineral enrichment, such as nitrogen, phosphorus, and organic carbon compounds.
- Micropollutants and metals:
- o
- Falkenstein: Micropollutants were measured in August 2023 at Sites UPS, and Dws1, and within the treated effluent.
- o
- Villeret: Screening for semi-polar and polar organic micropollutants (target and non-target) was performed at Sites S8 and S4 using high-resolution liquid chromatography-mass spectrometry (LC-HRMS) on 8-h composite samples collected between 20 March and 3 April 2023 [16].
- o
- Canton of Geneva: Metal concentrations (November 2023) and micropollutant levels (October–December 2023) were analyzed at Sites UPS, Dws, and M1.
Compliance assessment: Nutrient and metal concentrations were compared against Swiss water quality standards as defined by Liechti [18] and the Swiss Federal Council [19], respectively. Micropollutants and metals were monitored only at specific locations based on data availability. All physicochemical parameters were used solely to verify the presence of chemical pressure from the targeted discharge points rather than to establish a direct pairwise correlation with the biological indices.
2.3. Analysis of Oligochaete Communities
2.3.1. Sampling and Laboratory Procedures
The methodology follows the protocol detailed in Vivien & Ferrari [14]. At each site, four subsamples spaced 5–10 m apart were collected and pooled into a single composite sample for each compartment. Coarse surface sediments were collected using a shovel, while hyporheic material was extracted from a depth of 20–30 cm using a Bou-Rouch pump connected to a driven probe (Uwitec, Mondsee, Austria). All samples were fixed in situ with neutral buffered formalin (Epredia, Kalamazoo, MI, USA). In the laboratory, the material was sieved (0.2 mm mesh size), and oligochaetes were sorted under a binocular microscope (Olympus, model SZ51, Basel, Switzerland). Specimens were then mounted on slides using a mounting medium (lactic acid, glycerol, and polyvinyl alcohol) and identified to the lowest practical taxonomic level (mostly species) using a compound microscope (Olympus, model BX43, Basel, Switzerland), consistent with the species nomenclature and definitions provided in Timm (2009) [20].
2.3.2. Functional Traits and Ecological Potential
The FTR methodology follows the framework described by Vivien & Ferrari [14]. Oligochaete taxa are classified into five functional trait groups (FTRs) based on their ecological requirements and sensitivity [3,8]:
- FTR1: Taxa indicating groundwater exfiltration.
- FTR2: Taxa sensitive to chemical pollution.
- FTRi: Taxa moderately resistant to chemical pollution.
- FTR3: Taxa resistant to chemical pollution.
- FTR4: Taxa highly resistant to chemical pollution, indicating the presence of polluted sludge within the interstitial spaces.
The relative abundance (percentage) of these five groups is used to assess both the degree of chemical stress and the dynamics of vertical hydrological exchanges. Note that because some sensitive or tolerant taxa can be assigned to more than one FTR group, the total sum of percentages for a given sample may not strictly equal 100% [14].
To quantify the functional state of each compartment, the Ecological Potential (EP) was calculated according to Lafont et al. [3]:
EP = Log2 [(%FTR1 + %FTR2 + 1)/(%FTR3 + %FTR4 + 1)]
The EP values define five classes of ecosystem functioning: EP ≥ 7: preserved functioning; 4–6.9: slightly altered; 2–3.9: moderately altered; 0.1–1.9: altered; ≤0: very altered.
3. Results
3.1. Oligochaete Diversity
A total of 43 taxa were identified across the 16 samples. The community was dominated by the family Naididae, represented by 29 taxa (11 Tubificinae, 13 Naidinae, 4 Pristininae, and 1 Rhyacodrilinae). Other families included Enchytraeidae (7 taxa), Lumbriculidae (5 taxa), and Lumbricidae (2 taxa). Detailed taxonomic inventories for each site are provided in the Supplementary Materials (Tables S1–S5).
3.2. Chemical Data
Chemical analyses confirmed clear point-source contamination across the study sites (Tables S6–S9). In Falkenstein, Bremblens, and Vullierens, the concentrations of at least four nutrient parameters in the treated effluents clearly exceeded Swiss water quality criteria (Table S6). In Falkenstein specifically, micropollutant levels were markedly higher in the treated water and at Site Dws1 compared to the upstream reference (Table S9).
In Villeret, although nutrient concentrations at Sites S8 and S4 remained within Swiss quality criteria and target organic micropollutants were within the expected range, non-target screening revealed a critical anomaly. A very high concentration of an unknown substance—potentially a byproduct of biological treatment from dairy and cheese industry waste—was detected [16]; its toxicity remains currently uncharacterized.
In the Canton of Geneva, chemical degradation was evident at both the confluence (Dws) and within the tributary (M1). While only one nutrient parameter slightly exceeded criteria at the upstream site (UPS), two parameters clearly exceeded these thresholds downstream (Sites Dws and M1). Furthermore, Cu and Zn concentrations significantly surpassed Swiss quality criteria at Sites Dws and M1 (Table S7), where overall micropollutant levels were also higher than at Site UPS (Table S8).
3.3. Ecological Diagnoses
3.3.1. Falkenstein WWTP
Compared to Site UPS, Site Dws1 exhibited a marked decrease in the percentage of sensitive (FTR2) and moderately resistant (FTRi) taxa, alongside a sharp increase in highly resistant taxa (FTR4) (Table 2). At Site Dws2, the percentages of FTR2 and FTRi remained low, whereas the proportion of FTR4 was substantially lower than at Site Dws1. Consequently, stream functioning was markedly more altered at Site Dws1 than at Site UPS. At Site Dws2, the level of alteration was lower than at Site Dws1 but remained higher than at the upstream reference.
3.3.2. Bremblens WWTP
In the coarse surface sediments, clear differences were observed between the upstream and downstream sites (Table 3). Compared to Site UPS, both Sites Dws1 and Dws2 showed a marked decrease in the percentages of taxa indicating groundwater exfiltration (FTR1) and sensitive taxa (FTR2), while resistant taxa (FTR3) increased. Consequently, stream functioning in this compartment was markedly more altered at both downstream sites than at Site UPS. In the hyporheic zone, the percentage of sensitive taxa (FTR2) was clearly lower at Site Dws1 compared to Site UPS. However, both sites maintained very high percentages of FTR1 (>90%), indicating strong groundwater exfiltration in this compartment. As a result, stream functioning in the hyporheic zone was only slightly more altered at Site Dws1 than at the upstream reference.
3.3.3. Vullierens WWTP
In the coarse surface sediments, the percentage of FTR1 taxa (groundwater exfiltration indicators) at Site Dws was half that observed at Site UPS, while the proportion of resistant taxa (FTR3) doubled (Table 4). In the hyporheic zone, the percentage of FTR1 was clearly reduced at Site Dws compared to Site UPS, suggesting enhanced infiltration dynamics. Furthermore, a shift in dominant taxa was observed: while FTR3 dominated the community at Site UPS (65.4%), FTR4 (highly resistant taxa) became dominant at Site Dws (70.8%). Consequently, the Ecological Potential (EP) values indicated that stream functioning was more altered at Site Dws than at Site UPS in both investigated compartments.
3.3.4. Villeret WWTP
In the coarse surface sediments, marked community shifts were observed downstream of the WWTP (Table 5). At Site S6 (immediately downstream of the effluent), there was a marked decrease in sensitive taxa (FTR2) and a sharp increase in moderately resistant taxa (FTRi) compared to the upstream sites (S9 and S8). This FTRi group was largely dominated by the species Nais communis, which accounted for 72% of the total abundance at Site S6, while it was absent at Site S9 and scarce (≤10%) at all other sites (Table S4). Further downstream (Sites S4 and S2), the community structure shifted again: the percentage of FTR2 increased while FTRi (and specifically N. communis) decreased compared to Site S6. Consequently, the Ecological Potential (EP) was at its lowest at Site S6, indicating a more altered state of functioning than at the far-upstream sites (S9 and S8). The EP values then increased at the further downstream sites (S4 and S2), returning to levels comparable to the upstream references.
3.3.5. Marais and Drize Rivers (Tributary-Confluence System)
In the coarse surface sediments, community composition reflected the impact of both the tributary and the confluence (Table 6). Compared to the upstream reference (Site UPS), both the Marais River (M1) and the downstream site in the Drize (Site Dws) exhibited a lower percentage of sensitive taxa (FTR2) and a higher proportion of resistant taxa (FTR3). Despite these shifts in community sensitivity, the percentage of FTR1 taxa remained high across all three sites, indicating the persistent presence of marked groundwater exfiltration throughout the study area. Regarding ecosystem health, the Ecological Potential (EP) values confirmed that stream functioning was clearly more altered in the Marais River and at Site Dws than at the upstream site (UPS).
4. Discussion
The FTR method proved suitable for assessing the effects of point sources of pollution, even in catchment areas already impacted by human activities. Beyond biological quality, it provided critical insights into the streams’ self-purification capacity and the vulnerability of associated groundwater.
4.1. Chemical Stress and Biological Response
Physicochemical results confirmed that the four WWTP effluents and the Marais River were clear sources of contamination. In Villeret, although nutrient concentrations met legal requirements, the presence of numerous organic pollutants and the high concentration of the unknown substance (see Section 3.2)—potentially from the dairy industry—likely impacted stream health. This unknown substance may have triggered the proliferation of Nais communis at Site S6, suggesting this species is either highly tolerant of or benefits from this specific organic load. In Falkenstein, Vullierens, in the Canton of Geneva, and in Bremblens (coarse surface sediments only), point-source impacts were clearly detected through a marked reduction in EP values and an increase in resistant taxa (FTR3 or FTR4). In Falkenstein, the partial recovery observed at Site Dws2 is likely due to the distance from the outlet (~1600 m), allowing for longitudinal attenuation of the pollution. In the Canton of Geneva, the degradation in the Drize River is largely attributable to the influx from the Marais River; however, the high exfiltration rates observed likely prevented a more severe biological decline.
4.2. Vertical Exchanges: Vulnerability vs. Resilience
The dual analysis of the porous matrix revealed contrasting hydrological scenarios. In Vullierens, lower EP values downstream appeared to be linked to a decrease in FTR1 taxa, suggesting that the added flow from the effluent enhanced infiltration dynamics. This indicates a high vulnerability of groundwater to surface pollution at this site. Furthermore, a high percentage of FTR4 was observed in the hyporheic zone at Site Dws, unlike at Site UPS, indicating a marked accumulation of polluted sludge within the deep interstitial spaces of the porous matrix. Conversely, in Bremblens, the hyporheic zone showed signs of resilience. The effects of the effluent were nonetheless detectable in this compartment through a decrease in the percentage of sensitive taxa (FTR2). However, the hyporheic zone remained largely protected by strong exfiltration (FTR1 > 90%), which prevented the proliferation of resistant taxa and maintained a relatively preserved functional state compared to the surface. The higher alteration observed in the coarse surface sediments at this site can be attributed to both direct exposure to pollutants and physical clogging.
4.3. Methodological Robustness and Optimization of Monitoring Strategies
Our results are generally concordant with previous studies in Switzerland [13,14]. In all 20 samples analyzed to date (Table 7), the percentages of indicators of preserved functioning (combined FTR1 + FTR2) and EP values were consistently lower downstream than upstream. The diversity of oligochaete responses—varying from increases in FTRi, FTR3, or FTR4—supports the method’s sensitivity to different types and intensities of stress.
From a management perspective, a clear distinction can be made between the two sampling scales based on the operational objectives and available monitoring budgets. Integrating the hyporheic zone allows for a comprehensive and high-definition analysis of vertical exchange dynamics. It is valuable for characterizing the vulnerability of the surface–groundwater interface, whether by indicating deep pollutant and sludge infiltration or by detecting localized, deep exfiltrations. Conversely, focusing exclusively on coarse surface sediments represents an optimized, cost-effective strategy for routine spatial screening. While this simplified approach substantially reduces analytical costs and cannot directly demonstrate deep interstitial storage dynamics, sub-surface exfiltration, or localized ecosystem resilience, it remains well-suited for a sufficient diagnostic overview. It successfully signals direct point-source chemical stress as well as major, cross-sedimentary groundwater exfiltrations that reach the stream surface, thereby integrating the influence of such resurgences on benthic community health.
4.4. Scope and Critical Evaluation of the Study Design
While this study demonstrates the practical applicability of the FTR method, several specific constraints intrinsic to the operational study design must be explicitly analyzed:
- Absence of independent spatial replication: Biological samples at each site were pooled into a single composite sample (n = 1) to adhere to routine biomonitoring protocols. Consequently, fine-scale intra-site sampling variability could not be evaluated. However, sorting and analyzing separate replicates per station represents a fundamental research track focused on micro-distribution patchiness rather than a requirement for applied bioassessment. In practice, separating replicates for both the coarse surface sediments and the hyporheic zone would exponentially increase field and laboratory processing times and costs, making the method completely unfeasible for routine monitoring. Furthermore, in low-density matrix environments like the hyporheic zone, total oligochaete abundance per site is frequently low (often below 50 specimens), which would translate to only 6–12 specimens per individual replicate. At such extremely low thresholds, calculating functional trait percentages becomes mathematically unstable and highly susceptible to sampling artifacts, making separate replicate testing statistically invalid. Therefore, this pooling procedure represents a standard operational design in regulatory bioassessment, directly mirroring official national indices (such as the Swiss macroinvertebrate index IBCH), where field subsamples are composite-pooled to deliver a single, integrated site diagnostic. To assess diagnostic reproducibility, evaluating intra-site variability through the comparison of two independent pooled composite samples (each comprising 4 combined replicates) represents a far more adequate and ecologically relevant methodology. The spatial robustness of this composite protocol within a single reach is empirically supported by a dedicated intra-site spatial representativeness test performed at a site in Muri (UPS2, coarse surface sediments) in May 2025 [15]. Two independent pooled composite samples were collected simultaneously from non-overlapping locations spaced a few meters apart (approximately 5–10 m) within the same site boundaries. The results yielded highly consistent total proportions of resistant taxa (combined FTR3 + FTR4 of 16.8% vs. 18.9%). Even if these non-overlapping sampling positions captured localized variations in specific sensitive or moderately resistant taxa (higher proportions of Nais alpina (FTR2) and Cernosvitoviella sp. (FTR1/FTR2) alongside a decrease in Nais bretscheri (FTRi) in the upstream sample), both independent spatial samples delivered the exact same environmental diagnostic, falling strictly within the identical ecological potential class (EP scores of 0.79 and 1.51, both classifying the functional state as “altered”). These shifts in community structure can be explained by the spatial positioning of the sampling points. The replicate sample was collected further upstream, closer to the WWTP overflow point, where the discharged water was possibly not yet fully mixed across the entire riverbed. Under this hypothesis, this specific spot was less exposed to the overflow pollution plume, as reflected by a higher proportion of sensitive taxa (Nais alpina and Cernosvitoviella sp.) that closely mirrored the baseline communities observed at the upstream reference sites (UPS1 and UPS0a). Despite this fine-scale hydrodynamic gradient, the multi-subsample pooling successfully integrated the overarching environmental signal, supporting the operational suitability of the protocol for routine bioassessment. Full taxonomic inventories are provided in Supplementary Table S10. Furthermore, although the hyporheic zone carries its own distinct ecohydrological information, the strong diagnostic concordance routinely observed between the surface and deep compartments [13,14,15] provides an additional layer of cross-validation, and the hyporheic zone thus serves as a structural “safety sample” that confirms the overall site diagnostic. To fully standardize this approach for routine surface-only screening, future large-scale validation frameworks should focus on demonstrating across multiple upstream-downstream gradients that intra-site spatial variability remains systematically lower than the overarching biological changes driven by point-source discharges. Confirming that the anthropogenic signal consistently overrides local spatial noise will definitively benchmark the reliability of a single four-replicate composite sample for routine management.
- Single-campaign temporal snapshots: Due to the prioritization of broad spatial screening (multiplying case studies across five distinct hydrographic systems), each site in this specific study was sampled during a single campaign. This single-time sampling prevents the continuous characterization of seasonal fluctuations. Specifically, one may argue that shifting seasons—accompanied by variations in community composition (e.g., higher proportions of Naidinae) or changing vertical water exchange dynamics—could potentially mask or alter the diagnostic signal. However, the fact that the FTR method successfully detected point-source impacts across 10 different upstream-downstream contexts spanning highly contrasting seasons (winter, spring, and summer) and varied hydrological exchange regimes strongly suggests its consistency and operational robustness against such seasonal noise. The validity of this temporal resilience is further supported by our multi-campaign study on the upgrade of the Oberglatt WWTP [14]. In that case, the biological recovery and reduction in downstream impacts remained clearly detectable over time despite seasonal shifts in both vertical connectivity and oligochaete community composition: during the first post-upgrade campaign in spring (May), groundwater exfiltration dominated and the abundance of Naidinae was low-moderate, whereas during the subsequent campaign in autumn (November), surface water infiltration dominated and Naidinae abundance was high. This temporal coherence shows that the integrated biological diagnostic may effectively transcend seasonal variations in both community structures and hydrological fluctuations. However, multiplying temporal monitoring campaigns remains a valuable asset to confirm discharge impacts, substantiate the necessity of restoration measures, and track their long-term effectiveness.
- Biological inferences vs. direct hydrological measurements: The assessment of groundwater infiltration and exfiltration dynamics in this study relies exclusively on biological proxies (FTR groupings). No direct physical or hydraulic measurements (e.g., piezometric heads or hydraulic gradients) were conducted simultaneously. While the ecohydrological links between oligochaete traits and vertical fluxes are well-established in the literature (e.g., Ref. [11]), our conclusions must be interpreted as biological indications of short- to medium-term dynamics rather than direct physical proof of instantaneous hydraulic direction.
Despite these operational constraints, this simplified and context-driven design offers a highly valuable, cost-effective screening tool. It provides environmental managers with a practical, financially advantageous alternative to alleviate the need for complex, continuous chemical or physical monitoring networks, while still delivering a consistent, integrative diagnostic overview of point-source anthropogenic pressures and ecosystem functional state.
5. Conclusions
This study highlights the FTR method’s applicability in diagnosing point-source impacts on stream biological quality and functioning, even in anthropized contexts. The integration of vertical hydrological exchange proxies provides a holistic view of ecosystem health, distinguishing between sites where groundwater exfiltration influences ecosystem quality and those where polluted water infiltrates, leading to pollutant or polluted sludge storage in deep interstices and potentially threatening groundwater health. Ultimately, this work offers water managers a scalable framework: a simplified, cost-effective screening tool restricted to coarse surface sediments, or a comprehensive assessment integrating both compartments to provide an indicator map of interface dynamics. While the current single-campaign format is fully sufficient for initial screening and routine impact detection, adding one campaign during another season represents a valuable management perspective to monitor ecosystem quality over time under varying hydrological regimes and shifting natural community structures. In parallel, as a short- to medium-term research task to further validate the routine surface-only screening approach, future studies could evaluate intra-site spatial variability by comparing two independent composite samples (i.e., two separate pools of four replicates) collected simultaneously across multiple upstream and downstream sites, ensuring that local spatial noise remains lower than the upstream-downstream differences.
From a long-term and more ambitious research perspective, future initiatives would benefit from combining the FTR method with high-resolution physicochemical monitoring (passive sensors, continuous sampling) and direct physical measurements of vertical hydrological exchanges. Such large-scale research projects should also focus on refining the assignment of functional traits to specific oligochaete species, as more precise trait attributions will enhance the diagnostic resolution for both hydrological exchange dynamics and physicochemical pressures. Furthermore, as part of our ongoing efforts [14,15], FTR tools are being developed to make them accessible to non-experts in aquatic oligochaete systematics. While the required expertise in microscopic identification could currently limit the widespread adoption of the FTR framework in routine biomonitoring, genetic tools offer promising future perspectives. However, standard bulk DNA metabarcoding remains unsuited for the FTR method, as it cannot deliver the precise and correct species-level proportions [21,22] required to calculate functional trait percentages. To overcome this limitation, current developments focus on a high-throughput, specimen-by-specimen sequencing approach of genetically tagged individuals, a method originally optimized for fine/sandy sediments [22] that could be transferred to the FTR matrix. Alternatively, a simplified morphological FTR key is being designed to allow operators to assign specimens directly to their respective functional groups by identifying only families, subfamilies, and a restricted number of easily recognizable species, bypassing the need for advanced taxonomic expertise [15].
Supplementary Materials
The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ecologies7030089/s1, Table S1: Oligochaete communities per sample in Falkenstein. The values correspond to the numbers of specimens per taxon. The functional trait(s) FTR(s) of each taxon is(are) indicated in brackets. Table S2: Oligochaete communities per sample in Bremblens. The values correspond to the numbers of specimens per taxon. The functional trait(s) FTR(s) of each taxon is(are) indicated in brackets. Table S3: Oligochaete communities per sample in Vullierens. The values correspond to the numbers of specimens per taxon. The functional trait(s) FTR(s) of each taxon is(are) indicated in brackets. Table S4: Oligochaete communities per sample in Villeret. The values correspond to the numbers of specimens per taxon. The functional trait(s) FTR(s) of each taxon is(are) indicated in brackets. Table S5: Oligochaete communities per sample in the Canton of Geneva. The values correspond to the numbers of specimens per taxon. The functional trait(s) FTR(s) of each taxon is(are) indicated in brackets. Table S6: Concentrations of nutrients obtained in Falkenstein, in Bremblens, in Vullierens (treated water), in the Canton of Geneva and in Villeret (stream water). Classification according to Liechti [19]: in blue: very good quality; in green: good quality; in yellow: medium quality; in orange: poor quality; in red: bad quality. Table S7: Concentrations of metals in µg/L obtained in the Canton of Geneva (stream water). In bold: concentrations higher than the Swiss quality criteria [20]. Table S8: Concentrations of micropollutants in ng/L obtained in the Canton of Geneva (stream water). Table S9: Concentrations of micropollutants in ng/L obtained in Falkenstein (treated water and stream water) measured in August 2023. Table S10: Taxonomic inventory and FTR/Ecological potential (EP) metrics for the intra-site spatial representativeness test in Muri (UPS2, coarse surface sediments) in May 2025.
Author Contributions
Conceptualization, R.V. and B.J.D.F.; sampling, R.V.; methodology, R.V. and B.J.D.F.; formal analysis, R.V. and B.J.D.F.; writing—original draft preparation, R.V.; writing—review and editing, R.V. and B.J.D.F. All authors have read and agreed to the published version of the manuscript.
Funding
The research was supported by Eawag Discretionary Funds and by the Ecotox Centre.
Data Availability Statement
Data are contained within the article and Supplementary Materials.
Acknowledgments
The authors would like to thank the water protection services of the Cantons of Bern, Solothurn, Vaud, and Geneva, as well as the Falkenstein WWTP, for providing the physicochemical data and for their logistical support. We also thank Emmanuelle Rohrbach and Pascal Mulattieri for their field assistance. The authors acknowledge the use of AI-assisted technologies to improve the language and readability of the manuscript. The final content was thoroughly reviewed and edited by the authors, who take full responsibility for its scientific integrity.
Conflicts of Interest
The authors declare no conflicts of interest.
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Table 1.
Characteristics of the sampling sites, including location, stream names, geographical coordinates (WGS84), and the investigated porous matrix compartments.
Table 1.
Characteristics of the sampling sites, including location, stream names, geographical coordinates (WGS84), and the investigated porous matrix compartments.
| Location | Stream | Site | Coordinates | Studied Compartment(s) |
|---|---|---|---|---|
| Falkenstein | Duennern | UPS | 47.29122° N, 7.74023° E | Coarse surface sediments |
| Falkenstein | Duennern | Dws1 | 47.29288° N, 7.74500° E | Coarse surface sediments |
| Falkenstein | Duennern | Dws2 | 47.29880° N, 7.76112° E | Coarse surface sediments |
| Bremblens | Venoge | UPS | 46.560543° N, 6.528744° E | Coarse surface sediments and hyporheic zone |
| Bremblens | Venoge | Dws1 | 46.559577° N, 6.527077° E | Coarse surface sediments and hyporheic zone |
| Bremblens | Venoge | Dws2 | 46.557898° N, 6.528337° E | Coarse surface sediments |
| Vullierens | Senoge | UPS | 46.569901° N, 6.493218° E | Coarse surface sediments and hyporheic zone |
| Vullierens | Senoge | Dws | 46.570401° N, 6.493284° E | Coarse surface sediments and hyporheic zone |
| Villeret | Suze | S9 | 47.15280° N, 7.01525° E | Coarse surface sediments |
| Villeret | Suze | S8 | 47.15949° N, 7.02223° E | Coarse surface sediments |
| Villeret | Suze | S6 | 47.16063° N, 7.02515° E | Coarse surface sediments |
| Villeret | Suze | S4 | 47.16235° N, 7.03164° E | Coarse surface sediments |
| Villeret | Suze | S2 | 47.16707° N, 7.04405° E | Coarse surface sediments |
| Canton of Geneva | Marais | M1 | 46.16863° N, 6.14422° E | Coarse surface sediments |
| Canton of Geneva | Drize | UPS | 46.15293° N, 6.14884° E | Coarse surface sediments |
| Canton of Geneva | Drize | Dws | 46.16844° N, 6.14165° E | Coarse surface sediments |
Table 2.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in Falkenstein (coarse surface sediments). For EP values, red color = very altered functioning; orange color = altered functioning; yellow color = medium quality.
Table 2.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in Falkenstein (coarse surface sediments). For EP values, red color = very altered functioning; orange color = altered functioning; yellow color = medium quality.
| UPS | Dws1 | Dws2 | |
|---|---|---|---|
| FTR1 | 43.4 | 38 | 69.7 |
| FTR2 | 22.2 | 1 | 4.6 |
| FTR3 | 3.03 | 0 | 4.6 |
| FTR4 | 4 | 61 | 22 |
| FTRi | 37.4 | 1 | 5.5 |
| EP | 3.05 | −0.63 | 1.45 |
Table 3.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in Bremblens in the coarse surface sediments and the hyporheic zone. For EP values, red color = very altered functioning; orange color = altered functioning; yellow color = moderately altered functioning; green color = slightly altered functioning.
Table 3.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in Bremblens in the coarse surface sediments and the hyporheic zone. For EP values, red color = very altered functioning; orange color = altered functioning; yellow color = moderately altered functioning; green color = slightly altered functioning.
| UPS | Dws1 | Dws2 | UPS | Dws1 | |
|---|---|---|---|---|---|
| Coarse Surface Sediments | Coarse Surface Sediments | Coarse Surface Sediments | Hyporheic Zone | Hyporheic Zone | |
| FTR1 | 73.2 | 30 | 40.6 | 91.2 | 93.3 |
| FTR2 | 32 | 3 | 3.8 | 67.6 | 18.3 |
| FTR3 | 9.3 | 25 | 44.3 | 0 | 3.3 |
| FTR4 | 3.1 | 1 | 4.7 | 7.4 | 3.3 |
| FTRi | 14.4 | 43 | 12.3 | 1.5 | 0 |
| EP | 2.99 | 0.33 | −0.14 | 4.25 | 3.89 |
Table 4.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in Vullierens in the coarse surface sediments and the hyporheic zone. For EP values, red color = very altered functioning; orange color = altered functioning.
Table 4.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in Vullierens in the coarse surface sediments and the hyporheic zone. For EP values, red color = very altered functioning; orange color = altered functioning.
| UPS | Dws | UPS | Dws | |
|---|---|---|---|---|
| Coarse Surface Sediments | Coarse Surface Sediments | Hyporheic Zone | Hyporheic Zone | |
| FTR1 | 60.7 | 27.3 | 84.6 | 10.4 |
| FTR2 | 11.2 | 12.5 | 7.7 | 0 |
| FTR3 | 25.2 | 59.1 | 65.4 | 18.8 |
| FTR4 | 28 | 21.6 | 15.4 | 70.8 |
| FTRi | 6.5 | 2.3 | 0 | 2.1 |
| EP | 0.43 | −1.00 | 0.19 | −2.99 |
Table 5.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in Villeret (coarse surface sediments). For EP values, red color = very altered functioning; orange color = altered functioning; yellow color = moderately altered functioning.
Table 5.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in Villeret (coarse surface sediments). For EP values, red color = very altered functioning; orange color = altered functioning; yellow color = moderately altered functioning.
| S9 | S8 | S6 | S4 | S2 | |
|---|---|---|---|---|---|
| FTR1 | 31.7 | 21.6 | 21.2 | 48 | 46.5 |
| FTR2 | 21.2 | 13.5 | 1 | 12 | 7.1 |
| FTR3 | 8.7 | 20.7 | 22.2 | 35 | 6.1 |
| FTR4 | 3.8 | 2.7 | 0 | 0 | 10.1 |
| FTRi | 52.9 | 48.6 | 75.8 | 29 | 37.4 |
| EP | 2.00 | 0.57 | 0.00 | 0.76 | 1.67 |
Table 6.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in the Drize River (UPS, Dws) and Marais River (M1) (coarse surface sediments). For EP values, orange color = altered functioning; yellow color = moderately altered functioning; green color = slightly altered functioning.
Table 6.
Percentages of the functional traits (FTR1–4; FTRi) and ecological potential (EP) values obtained in the Drize River (UPS, Dws) and Marais River (M1) (coarse surface sediments). For EP values, orange color = altered functioning; yellow color = moderately altered functioning; green color = slightly altered functioning.
| UPS | M1 | Dws | |
|---|---|---|---|
| FTR1 | 91.2 | 83.5 | 76.5 |
| FTR2 | 63.7 | 43.7 | 31.4 |
| FTR3 | 5.9 | 20.4 | 23.5 |
| FTR4 | 1 | 6.8 | 3.9 |
| FTRi | 5.9 | 9.7 | 9.8 |
| EP | 4.30 | 2.18 | 1.94 |
Table 7.
Summary of point-source pollution impacts on oligochaete communities across multiple studies. FTR1-2: indicators of preserved functioning; EP: Ecological Potential; FTRi, FTR3, FTR4: taxa with increasing resistance to chemical pollution; * Vivien et al. [13], ** Vivien & Ferrari [14] *** present study; dws = downstream; the downward arrows (↓) indicate a decrease downstream of the discharge points.
Table 7.
Summary of point-source pollution impacts on oligochaete communities across multiple studies. FTR1-2: indicators of preserved functioning; EP: Ecological Potential; FTRi, FTR3, FTR4: taxa with increasing resistance to chemical pollution; * Vivien et al. [13], ** Vivien & Ferrari [14] *** present study; dws = downstream; the downward arrows (↓) indicate a decrease downstream of the discharge points.
| Site and Study | Sampling Date | Compartment | %FTR1+%FTR2 (dws) | EP Value (dws) | Main Increase in Resistant Taxa (% FTRi, %FTR3 or %FTR4) (dsw) |
|---|---|---|---|---|---|
| Hochdorf * | March 2016 | Surface | ↓ | ↓ | Increase in %FTR3 |
| Hochdorf * | March 2016 | Hyporheic | ↓ | ↓ | Increase in %FTRi |
| Hochdorf * | September 2016 | Surface | ↓ | ↓ | Increase in %FTR3 and %FTR4 |
| Hochdorf * | September 2016 | Hyporheic | ↓ | ↓ | Increase in %FTR3 and %FTR4 |
| Buttisholz * | March 2016 | Surface | ↓ | ↓ | Increase in %FTR4 |
| Buttisholz * | March 2016 | Hyporheic | ↓ | ↓ | Increase in %FTR3 |
| Buttisholz * | September 2016 | Surface | ↓ | ↓ | Increase in %FTR3 and %FTR4 |
| Buttisholz * | September 2016 | Hyporheic | ↓ | ↓ | Increase in %FTR4 |
| Oberglatt ** | October 2020 | Surface | ↓ | ↓ | Increase in %FTRi and %FTR4 |
| Oberglatt ** | October 2020 | Hyporheic | ↓ | ↓ | Increase in %FTR4 |
| Muri ** | May 2021 | Surface | ↓ | ↓ | Increase in %FTR3 and %FTR4 |
| Muri ** | May 2021 | Hyporheic | ↓ | ↓ | Increase in %FTR3 and %FTR4 |
| Vallorbe ** | March 2022 | Surface | ↓ | ↓ | Increase in %FTR4 |
| Falkenstein *** | September 2023 | Surface | ↓ | ↓ | Increase in %FTR4 |
| Bremblens *** | February 2024 | Surface | ↓ | ↓ | Increase in %FTRi and %FTR3 |
| Bremblens *** | February 2024 | Hyporheic | ↓ | ↓ | No increase in %FTRi, %FTR3 or %FTR4 |
| Vullierens *** | March 2024 | Surface | ↓ | ↓ | Increase in %FTR3 |
| Vullierens *** | March 2024 | Hyporheic | ↓ | ↓ | Increase in %FTR4 |
| Villeret *** | April 2023 | Surface | ↓ | ↓ | Increase in %FTRi |
| Canton of Geneva *** | October 2023 | Surface | ↓ | ↓ | Increase in %FTR3 |
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Vivien, R.; Ferrari, B.J.D. Applicability of a Functional Trait-Based Methodology in Stream Porous Matrices for Assessing Point-Source Pollution and Vertical Exchange Dynamics. Ecologies 2026, 7, 89. https://doi.org/10.3390/ecologies7030089
AMA Style
Vivien R, Ferrari BJD. Applicability of a Functional Trait-Based Methodology in Stream Porous Matrices for Assessing Point-Source Pollution and Vertical Exchange Dynamics. Ecologies. 2026; 7(3):89. https://doi.org/10.3390/ecologies7030089
Chicago/Turabian StyleVivien, Régis, and Benoît J. D. Ferrari. 2026. "Applicability of a Functional Trait-Based Methodology in Stream Porous Matrices for Assessing Point-Source Pollution and Vertical Exchange Dynamics" Ecologies 7, no. 3: 89. https://doi.org/10.3390/ecologies7030089
APA StyleVivien, R., & Ferrari, B. J. D. (2026). Applicability of a Functional Trait-Based Methodology in Stream Porous Matrices for Assessing Point-Source Pollution and Vertical Exchange Dynamics. Ecologies, 7(3), 89. https://doi.org/10.3390/ecologies7030089
