Understanding spatial patterns of biodiversity within the context of long-term climatic shifts is of high importance, particularly in the face of contemporary climate change. In comparison to aboveground taxa, subterranean organisms respond to changing climates with generally much lower dispersal and recolonization potential, yet possible persistence in refugial groundwater habitats under ice-shields. However, knowledge on general and geographically large-scale effects of glaciation on contemporary groundwater biodiversity patterns is still very limited. Here, we tested how Late Pleistocene glaciation influenced the diversity and distribution of 36 groundwater amphipod species in Alpine and peri-Alpine regions, characterized by extensive glaciation cycles, and how its legacy explains contemporary diversity patterns. We based our analysis on an unprecedented density of ~ 1000 systematic sampling sites across Switzerland. Using presence–absence data, we assessed biodiversity and species' ranges, and calculated for each site within-catchment distance to the Last Glacial Maximum (LGM) glacier extent. We then applied a sliding window approach along the obtained distance gradient from LGM ice-covered to ice-free sites to compute biodiversity indices reflecting local richness, regional richness, and differentiation, respectively. We found a strong signal of the LGM ice extent on the present-day distribution of groundwater amphipods. Our findings revealed pronounced species turnover and spatial envelopes of individual species' occurrences in formerly ice-covered, ice-free, or transitional zones, respectively. While local richness remained constant and low along the LGM distance gradient, groundwater communities in LGM ice-covered areas were more similar to each other and had lower gamma diversities and decreased occurrence probabilities per sliding window compared to communities in Pleistocene ice-free areas. These results highlight the significant impact of Pleistocene glaciation on shaping biodiversity patterns of subterranean communities and imprinting contemporary distribution of groundwater organisms.

Aim: groundwater ecosystems harbour a unique biodiversity, but remain poorly studied, mainly due to difficulties in accessibility and imperfect species detection. Consequently, knowledge on the state and change of groundwater biodiversity remains highly deficient. In the context of global warming and excessive groundwater extraction, understanding groundwater from an ecosystem-perspective, including organism diversity and distribution, is essential. This study presents the largest ever systematic assessment of groundwater amphipods, which are a key component of European groundwater biodiversity.
Location: Switzerland (41,285 km²), including data from 906 sampling sites.
Taxon: groundwater amphipods, genera Niphargus and Crangonyx (Crustacea, Amphipoda).
Methods: we applied a highly standardized citizen science approach to collect repeated groundwater fauna samples in collaboration with municipal drinking water providers. Using detection–nondetection data of the genetically identified groundwater amphipod species, we assessed the overall species diversity of both rare and common species. The distribution of commonly found species was predicted using multispecies occupancy modelling.
Results: we retrieved 3882 samples from 906 sites, yielding 2350 groundwater amphipod individuals. We identified a remarkable species diversity, comprising few commonly and many rarely found species. Considering commonly found species, we identified distinct distribution ranges, low local species richness and a predominance of negative co-occurrences. In contrast, a major portion of species were found rarely (generally at just one or two sites each), distributed uniformly throughout the study area and unrelated to common species' recognized hotspots. Many of these rarely found species are not yet formally described.
Main conclusions: Our results give robust emphasis on the rare occurrence and narrow distribution of many groundwater dwellers. Our systematic and standardized sampling data of groundwater amphipods suggest that rarity is particularly prominent and inherent to groundwater organisms. We emphasize the need of systematic data to integrate rare groundwater species in biodiversity assessments, especially in times of global change.

Implementing and optimizing biodiversity monitoring is crucial given the current, worldwide biodiversity decline. Compared to other ecosystems, monitoring of biodiversity is lagging behind in groundwater ecosystems, both because of sparse taxonomic knowledge and methodological constraints. We here assessed temporal variation in the occurrence and abundance of macroinvertebrates collected systematically from shallow groundwater aquifers of Switzerland to establish general principles on seasonality and repeatability of assessment outcomes. We found no seasonal abundance pattern for obligate groundwater amphipods and isopods, indicating temporal consistency. In contrast, other macroinvertebrates (predominantly stygophiles and stygoxenes) showed pronounced seasonality in their detection rate. However, we found variability in detection rates across groundwater amphipod species and especially across sampling sites. For groundwater communities, characterized by narrowly-distributed and rare species, our results highlight the need for tailored and extensive sampling strategies. When setting up monitoring programs on groundwater fauna, detection probability, temporal autocorrelation, and standardization of sampling effort should be carefully considered. Applying novel, systematic approaches, can offer promising methodologies for understanding and conserving groundwater ecosystems.

Terrestrial and aquatic ecosystems are tightly linked, with direct implications for applied resource management and conservation. It is well known that human land use change and intensification of terrestrial systems can have large impacts on surface freshwater ecosystems. Contrastingly, the study and understanding of such land use impacts on groundwater communities is lagging behind. Both the impact strength of land use on groundwater communities and the spatial extents at which such interlinkages are operating are largely unknown, despite our reliance on groundwater for drinking water extraction as a key ecosystem service. Here, we analyzed groundwater amphipod occurrence from several hundred shallow groundwater aquifers used for drinking water extraction across a region of varying agricultural intensity and human population density in Switzerland. Despite drinking water extraction sites being generally built at locations with expected minimal aboveground impacts on water quality, we found a direct correlation between land use type and intensity within the surrounding catchment area and the locally measured nitrate concentrations, which is a direct proxy for drinking water quality. Furthermore, groundwater amphipods were more likely to be found at sites with higher forest coverage than at sites with higher crop and intensive pasture coverages, clearly indicating a tight connection between aboveground land use and groundwater biodiversity. Our results indicate that land use type effects on groundwater communities are most relevant and pronounced to spatial scales of about 400–1000 m around the groundwater sampling site. Importantly, the here identified spatial scale is 1.2- to 3-fold exceeding the average extent of currently defined groundwater protection zones. We postulate that incorporating an ecosystem perspective into groundwater management strategies is needed for effective protection of groundwater quality and biodiversity.

Die noch wenig bekannte Grundwasserfauna ist ein bedeutender Bestandteil der Biodiversität und trägt zum Funktionieren der Grundwasserökosysteme bei. Mittels Proben aus der ganzen Schweiz wurde erstmals ein Überblick über die Vielfalt und Biomasse von Makroinvertebraten in Grundwasserökosystemen der Schweiz erarbeitet. Eine hohe Diversität an ober- und unterirdischen Makroinvertebraten im Grundwasser weist auf die Wechselwirkungen zwischen Oberfläche und Grundwasser hin.

The genus Niphargus is the most diverse subterranean amphipod genus in the western Palearctic region but, owing to the presence of cryptic species and homoplasy, its taxonomy and biogeographic scenarios are complex, making molecular methods essential to understand its evolution. We conducted a study combining dna-based taxonomy with traditional morphotaxonomy to investigate Niphargus bihorensis Schellenberg, 1940, known from the Western Alps and Carpathians. We redescribed the type material of N. bihorensis from Bihor County, Romania, and revealed the presence of a cryptic species, N. absconditus n. sp., in the same karstic area (Pădurea Craiului Mountains). Additionally, the Alpine populations previously attributed to N. bihorensis turned out to belong to a new, not so closely related species, N. tizianoi n. sp. Phylogenetic analyses based on a concatenated dataset of one mitochondrial and two nuclear markers suggest that the N. bihorensis species complex belongs to a strongly supported clade, together with several species distributed from Switzerland to Iran.

Groundwater is the physically largest freshwater ecosystem, yet one of the least explored habitats on earth, both because of accessing difficulties and the scarcity of the organisms inhabiting it. Here, we demonstrate how a two-fold approach provides complementary information on the occurrence and diversity of groundwater amphipods. Firstly, we used a citizen science approach in collaboration with municipal water providers who sampled groundwater organisms in their spring catchment boxes over multiple weeks, followed by DNA barcoding. Secondly, we collected four 10 L water samples at each site, in one sampling event, for environmental DNA (eDNA) metabarcoding. We found that citizen science was very effective in describing the distribution and abundance of groundwater amphipods. Although the single time-point of eDNA sampling did not detect as many amphipods, it allowed the assessment of the entire groundwater community, including microorganisms. By combining both methods, we found different amphipod species co-occurring with distinct sequences from the eDNA-metabarcoding dataset, representing mainly micro-eukaryotic species. We also found a distinct correlation between the diversity of amphipods and the overall biodiversity of groundwater organisms detected by eDNA at each site. We thus suggest that these approaches can be used to get a better understanding of subterranean biodiversity.

Subterranean fauna is an important contributor to the global fauna, but it is still understudied and a large part of its taxonomy is not yet resolved. One species complex with unresolved taxonomy is the groundwater amphipod Niphargus ruffoi, endemic to the Alpine chain. Here, we used new samples from across the Alpine arc to review the taxonomic status of the entire clade, including the species N. ruffoi and Niphargus arolaensis. We sequenced four genetic markers from the collected specimens, assessed the phylogenetic position of N. ruffoi within the genus, and studied the structure of this species complex using four molecular species delimitation methods. We tested for recombination using the alignments of the concatenated nuclear rDNA genes. The phylogenetic analyses revealed high support for the monophyly of the studied species complex, defining two lineages (i.e., N. arolaensis and N. ruffoi) within the clade. Molecular species delimitation methods suggested that N. arolaensis is a single species, while N. ruffoi should be considered as a species complex of three (using ITS) to eight (using COI) putative species. Moreover, we found a discrepancy between the different nuclear ribosomal DNA markers, indicating a possible recombination with fragments of 28S DNA of N. ruffoi s. lat. present in the genome of N. arolaensis. For the above-mentioned reasons, the internal phylogenetic structure of N. ruffoi s. lat. could not be fully resolved. Moreover, no clear morphological evidence supported the molecular species delimitation. Consequently, no taxonomic changes were proposed. We postulate that this complex scenario was influenced by Pleistocene climate oscillations with subsequent fragmentation events and secondary contacts, making this an interesting study system to investigate the evolution and biogeography of Alpine clades.

Haplotaxis Hoffmeister, 1843 is a poorly known genus: it is rarely collected because it usually inhabits groundwater, and many species are only known from immature specimens. Even the type species, Haplotaxis gordioides (Hartmann in Oken, 1819) remains poorly defined because of the absence of reference types. Most of the Haplotaxis species have been placed in synonymy with H. gordioides since the end of the 19^th century, a situation that has remained essentially unchanged until now. As a result, the species is supposedly present on all continents, except Antarctica. This observation is all the more questionable as the aquatic subterranean environment is nowadays well known to harbour many species with restricted distribution, due to the strong hydrogeographic isolation and the low dispersal abilities of its inhabitants.
In this study we assessed the hypothesis of H. gordioides as a single species with wide distribution versus a complex of cryptic species with narrow distribution. We used a DNA-barcoding approach based on the COI mitochondrial marker of 46 Haplotaxis specimens collected in Switzerland, mostly as part of a countrywide sampling campaign to study groundwater macroinvertebrates.
Preliminary results suggested that H. gordioides is a complex of at least 6 cryptic species in Switzerland, which has important implications both for the knowledge of the exact identity of the type species and for the synonymy of most of the species described in the 19^th century. However, as it is based on a single-locus approach, this study should be seen as the first step in an integrative taxonomic process that should include additional biological material, the study of complementary markers (especially nuclear), and the morphological study of specimens.

Groundwater is a vast ecosystem harboring a high diversity of specialized taxa. Despite its diversity, groundwater is a still relatively unexplored and threatened ecosystem. Especially the linkage of groundwater with other ecosystems remains largely unknown from the perspective of groundwater fauna. Here, we used citizen science data to get a first baseline knowledge of the occurrence, diversity, and biomass of major macroinvertebrate groups found in shallow groundwater systems of Switzerland. We investigated all organisms collected from the groundwater in 346 spring catchment boxes of municipal drinking water providers. We morphologically identified the organisms on a broad taxonomic level and estimated their biomass and pigmentation using automated image processing. Crustaceans, particularly Niphargus and groundwater isopods, were the most common taxa of obligate groundwater organisms. We also found a surprisingly high number of macroinvertebrates associated with surface and subsurface ecosystems. These taxa might be accidentally entering the groundwater or use it as temporary habitat. In both cases they possibly contribute essential allochthonous energy imports from the surface. We found a positive relationship between the estimated biomass of macroinvertebrates in the samples and the occurrence and abundance of Niphargus. Owing to the widespread occurrences of surface and subsurface macroinvertebrates in our groundwater samples, our study provides evidence for common interactions between groundwater, soil, and surface ecosystems.

Erstmals wurde die Verbreitung und Artenvielfalt der Grundwasserflohkrebse im Einzugsgebiet der Töss, unter Einbezug von Bürgerwissenschaft, räumlich hoch aufgelöst untersucht. Bei der durch die Eawag und die Universität Zürich durchgeführten Studie wurden vier in dieser Region bisher noch nicht nachgewiesene Arten gefunden. Auch konnte gezeigt werden, dass die Daten zur Fundwahrscheinlichkeit, die von Wasserversorgungen erhoben wurden, mit denen von Forschenden vergleichbar sind.