The study of hypogean fauna is critical for preserving subterranean biodiversity and ecosystem functions despite climate change. However, underground habitats, often hosting unique and endemic species, present significant challenges for traditional biodiversity assessments owing to their inaccessibility and the specialised nature of their inhabitants, resulting in a paucity of academic studies. Furthermore, even when these studies exist, data are often held in personal notes and databases that are not interoperable according to current standards, making them less usable for research purposes. Reawakening this dormant data, standardising, and sharing it according to modern criteria offers enormous opportunities to expand existing knowledge and provide support for future studies.

In the Apulian region of Southern Italy, a biodiversity hotspot for subterranean life, the paucity of recent systematic surveys and reliance on expert knowledge poses both opportunities and challenges for ecological research. By integrating data from various sources, this study provides an overview of the subterranean faunal assemblages documented in this region. Overall, the dataset is comprehensive, comprising 109 species (29 of which are considered endemic to Apulia) and 224 sites, totalling 622 presence-only records. As our records have expanded over 93 years, this dataset represents a unique resource for elucidating the characteristics of Apulian subterranean ecosystems and potentially their changes over time. Integrating observations already published in previous studies with unpublished records, this is the first complete data collection on Apulian subterranean fauna organised according to modern standards of data sharing.

Apulia, biodiversity hotspot, historical data, presence-only, subterranean fauna

Groundwater ecosystems remain understudied due to the inherent challenges posed by subterranean habitats. The inaccessibility of these environments, combined with the specialised and often cryptic nature of their inhabitants, makes traditional biodiversity assessment methods difficult to implement and, in many cases, insufficient (Mammola et al. 2020). Even when studies on hypogean fauna are conducted, the resulting data are frequently stored in personal notes, project-specific datasets, or non-standardised formats that are not interoperable with modern data management practices. Such limitations hinder the ability to build a comprehensive understanding of subterranean biodiversity, its drivers, and its vulnerabilities (Neimanis 2023). By applying modern data management frameworks, these fragmented datasets can be transformed into cohesive resources, enabling the integration of existing knowledge with new findings. Moreover, standardised and shared data can inform conservation strategies, guide sustainable groundwater management, and support compliance with international biodiversity directives (Di Lorenzo et al. 2024).

Geology and hydrogeology

The karst landscape of Apulia, covering approximately 8,600 km², includes over 2,300 natural caves, several of which are show caves or touristic sites, and holds historical significance with rock settlements, various hypogea, and numerous important Palaeolithic and Neolithic sites. The Alta Murgia Regional Park, which includes a large part of the corresponding aquifer, was designated as the 12^th Italian UNESCO Geopark on 9 September 2024. However, as one of the southernmost major aquifers in Europe, southern Apulia’s groundwater temperatures are relatively high and potentially subjected to the effects of global warming (Casarano et al. 2019). Moreover, due to the extensive connection with marine waters, increasing aridity, impacting land use (agricultural, industrial), and consistent and often uncontrolled human groundwater extraction, Apulian groundwaters are particularly exposed to chemical stress, including salinisation (ISPRA 2014).

Apulia is divided into six main hydrogeological units: Gargano, Tavoliere, Murge Plateau, Brindisi Plain, Ionian Arch of Taranto, and Salento (Bitetto et al. 2008, Fig. 1). The groundwater in the extreme northwestern part of the region (Daunia) is continuous with the Central-Southern Apennine aquifer. The Tavoliere consists of a shallow, porous aquifer less than a few dozen meters deep, with a clayey impermeable bottom (Cotecchia and Polemio 1998). The Brindisi Plain is a structural depression of the Mesozoic carbonate basement filled by sediments from the Fossa Bradanica and terraced marine deposits. The Ionian Arch of Taranto, corresponding to the area where the limestone hills of the Murge slope steeply towards the sea, whose deep aquifer is fed by the Murge Plateau, is characterised by numerous important coastal and submarine springs. The remaining three units, Gargano, Murge, and Salento, are characterised by a high proportion of soluble Cretaceous limestone. The action of weakly acidic waters on carbonate rocks in these latter units has led to the development of extensive karst phenomena, resulting in a variety of surface and subsurface karst landforms, whereas surface water is limited because it rapidly infiltrates through fractures or sinkholes into the subsoil, leading to most freshwater movement occurring underground (Parise et al. 2015). Aquifers in the Gargano and Murge regions are under artesian pressure, except along narrow coastal strips, while in Salento, water flows predominantly under phreatic conditions (Cotecchia and Polemio 1998). The Salento hydrogeological unit is unique in that it is bordered by the sea on both sides.

Figure 1. 

Apulian hydrogeological units (from project Tiziano, Bitetto et al. 2008). The different units are reported in colour.

The bibliographic dataset was compiled based on the authors’ personal knowledge of the limited literature existing on Apulian stygofauna, supplemented by: a) a systematic bibliographic search conducted using Google Scholar, SCOPUS, and ISI Web with the keywords “Apulia” ˄ (“Stygofauna” | “Groundwater fauna”) in both English and Italian; b) a substantial collection of unpublished records primarily contributed by Salvatore Inguscio and other amateur biospeleologists; c) the consultation of updated sources such as The New Checklist of Italian Fauna (Bologna et al. 2023). Owing to the incomplete and fragmentary nature of the available knowledge, our dataset does not claim to comprehensively cover the entire body of information on Apulian subterranean fauna, particularly regarding insects. However, the dataset will undergo continuous updates as part of the STIGE-CLIMAQUIFERI project. These updates incorporate both new observations and previously documented information that is currently not included.

Observations reported in the literature were collected using various methods, primarily visual surveys, baited traps, and plankton nets. Novel or repeated observations dated between 2020 and 2024 were collected mainly from the authors of this study using two different sampling techniques. The first method involved the use of a hand-operated net with a mesh size of 0.5 mm; three replicates of 10 shots each were taken at each sampling point. The second method consisted of the deployment of plastic cylindrical traps (length 30 cm and diameter 6 cm) baited with fish or meat fragments. The collected material was fixed in 85% ethanol and preserved in 75% ethanol. In the laboratory, the collected material was sorted, and the specimens were identified at the species level using a stereomicroscope (Olympus SZX-16) and an optical microscope (Leica DM2000LED).

Specimens have been identified morphologically mostly to the species level, with occasional classifications at the genus or subspecies level, and categorised based on taxonomy, lifestyle (aquatic or terrestrial), degree of adaptation to subterranean environments (stygo- and troglobites, stygo- and trogloxenes, and stygo- and troglophiles), and endemic status of the species within Apulian aquifers (TRUE or FALSE). These classifications were primarily based on Ruffo (1955), Pesce (1983), and Karaman (1993), supplemented by a review of more recent sources such as The New Checklist of Italian Fauna (Bologna et al. 2023). The sites are categorised into five typologies (Caves, Wells, Sinkholes, Springs, and Draining Galleries) and six hydrogeological units: Tavoliere, Gargano, Murge Plateau, Brindisi Plain, Ionian Arch of Taranto, and Salento. The latter classification follows the framework established by the “Progetto Tiziano”, a comprehensive five-year governmental initiative (2006–2011) aimed at monitoring Apulian aquifers (Bitetto et al. 2008, Fig. 1). Seven sites distributed along the Cervaro River and located in the Sub-Apennine Daunia aquifer were included, as they were reported in the same study investigating sites in the Tavoliere aquifer along the river’s course (Cianfanelli et al. 2019). The sites were georeferenced using WGS84 coordinates reported in the original publications, except when these were erroneous or missing. For unpublished observations, the coordinates were provided by the observers. For extended caves, the coordinates indicate the location of the main entrance to the cave system. The cited bibliographic sources correspond to the first known record of a given species sampled at a specific site. When the collection period was not explicitly indicated in the article, the year of publication was used as a proxy. In addition, the dataset specifies whether the observation was repeated in recent years (2020–2024).

Currently, the dataset is available as Suppl. materials of this article accompanied by a summary of the bibliographic sources, recorded species, sampling sites, and metadata. Metadata are also available in the Metadata Catalogue of LifeWatch EIRC (Boulamail et al. 2024, https://doi.org/10.48372/8AM6-VJ47). Data are structured using the Darwin Core standard (Wieczorek et al. 2012) and other controlled vocabularies available in different semantic artefact catalogues (for example, EcoPortal, AgroPortal, and BioPortal). Metadata follows the LifeWatch ERIC Metadata Profile (https://www.lifewatch.eu/download/lifewatch-eric-application-profiles/) of the Ecological Metadata Language (EML 2.2.0). Additionally, the dataset is freely available in the Zenodo (Boulamail 2025a, https://doi.org/10.5281/zenodo.14793315) repositories. In the near future, the STIGE-CLIMAQUIFERI project will archive and publicly share its dataset through the LifeWatch Italy Data Portal, ensuring permanent and interoperable access to the data in accordance with FAIR principles (Findable, Accessible, Interoperable, and Reusable; Wilkinson et al. 2016). The dataset includes detailed information on the chemical and physical parameters recorded at various collection sites (where available from original publications) or current conditions. Observations of further species from ongoing research will be integrated as they become available.

The dataset was organised and analysed within the R free software environment (R Core Team 2024), mostly using the packages sf (Pebesma and Bivand 2023) and OpenStreetMap (Fellows and Stots 2023).

Currently, the dataset includes 622 records collected from over 224 sites. It is representative of 109 species, 72 genera, 49 families, and 26 orders of organisms observed in Apulian subterranean environments. Most of the observations were collected from caves (46 sites) and wells (149 sites). Stygobionts represent 30% of the 82 reported aquatic species, while troglobionts represent 60% of the 27 reported terrestrial species. Overall, 29 species were considered endemic to Apulia (Fig. 2).

Figure 2. 

Number of records (top panel) and number of species (bottom panel) according to the level of adaptation to the underground environment (High = stygo/troglobites, Medium = stygo/trogloxenes, and Low = stygo/troglophiles) and the endemic status of the species within Apulia.

In terms of contributions to the dataset, the most influential studies are those of Pesce et al. 1978 (206 records) and Karanovic and Pesce 2001 (134 records). A significant contribution (63 records) came from unpublished personal observations collected and validated by Salvatore Inguscio and other amatorial biospeleologists. Additional unpublished and recently collected observations were provided by the ongoing PRIN 2022 project STIGE-CLIMAQUIFERI (27 novel records and multiple recent confirmations of historical records). The reported observations span the entire Apulian region, although they are particularly concentrated in the Salento hydrogeological unit (481 records) due to greater research activity in this area, followed by the Murge Plateau (66 records), Gargano (41 records), Tavoliere (24 records), and Daunia (13 records) units. There are no observations available for Brindisi Plain and Ionian Arch of Taranto (Fig. 3). Most of the records were collected during the seventies and the nineties of the past century and presence data were confirmed by recent investigations (2020–2024) only in a few cases (12% of records).

Figure 3. 

Number of records (top panel) and number of species (bottom panel) according to the Apulian hydrogeological units in which they were observed/collected and the endemic status of the species within Apulia.

The vast majority of the records pertain to Arthropoda, though there are also 41 records of Mollusca, 6 records of Platyhelminthes, 1 record of Annelida, and 1 notable record of Porifera, specifically the stygobitic sponge Higginsia ciccaresi Pansini & Pesce, 1998, found in the Zinzulusa caves. The recorded classes of Arthropoda included Copepoda (50 species), Malacostraca (19 species), and Ostracoda (6 species) for aquatic organisms and Arachnida (11 species) for terrestrial organisms (Fig. 4). The most represented families in terms of species richness were Cyclopidae (27 species), Halicyclopidae (6 species), and Ameiridae (6 species). The most common aquatic species were Spelaeomysis bottazzii Caroli, 1924 (57 records), Proasellus banyulensis (Racovitza, 1919) (57 records), and Eucyclops (Eucyclops) serrulatus (Fischer, 1851) (52 records), while the most common terrestrial species were Italodytes stammeri (30 records) and Hadoblothrus gigas (13 records). Among the largest European groundwater organisms, the aquatic Decapoda Typhlocaris salentina Caroli, 1924 was also relatively common (17 records) (Fig. 5).

Figure 4. 

Number of records (top panel) and number of species (bottom panel) for each taxonomic class and the endemic status of the species within Apulia.

Figure 5. 

Number of records of the 12 most represented species and endemic status of the species within Apulia.

The highest number of species (87) was reported in the Salento unit, which exhibited both higher intrinsic biodiversity and more intense investigations. A lower number of species was reported for the Murge Plateau (27), Gargano (23), and Tavoliere (12) units (Fig. 3). The sites of caves Zinzulusa (27 species) and L’Abisso (22 species), along with the drainage tunnel named Fonti di Carlomagno (18 species), all located in Salento, were the sites characterised by the highest number of species (Fig. 6). Castro, where both the caves Zinzulusa and L’Abisso are located, emerges as one of the richest European municipalities in terms of stygofauna biodiversity with a total of 40 reported species occurrences (Fig. 6).

Figure 6. 

Species richness of the different sites included in the dataset, for the overall dataset and divided by the three most represented classes (Malacostraca, Copepoda and Gastropoda). “Others” include Arachnida, Clitellata, Collembola, Diplopoda, Diplura, Insecta, Ostracoda, Porifera, and Turbellaria.

By compiling observations from both published research and expert field records, this study fills a significant gap in our knowledge of subterranean biodiversity in Southern Italy. This comprehensive dataset offers a resource for understanding the rich and diverse stygofauna of the Apulian region, particularly its endemic species. However, it also highlights spatial and temporal gaps in knowledge, with some local areas (Tavoliere, Brindisi Plain, Ionian Arch of Taranto) unexplored or strongly underrepresented compared to others (mostly Salento, Gargano, and Murge Plateau). Although the data are not sufficient/appropriate to properly fit a Species Accumulation Curve, the high ratio between sampling effort and the number of observed species suggests that the biodiversity of the less sampled areas could be comparable to that of the more investigated ones. Moreover, many of the observations reported in our dataset were collected decades ago, and only a few of them have been recently repeated. Recent observations have confirmed the presence of notable species, such as S. bottazzii and T. salentina, at various historical sites. They also highlight the remarkable species richness of the L’Abisso site, although only a portion of the species recorded in the past was collected during recent surveys. However, the limited sampling efforts undertaken do not provide enough data to assess whether there has been a decline in the richness of subterranean species owing to recent environmental changes. While the relative abundance of past observations provides a crucial comparative baseline for interpreting the effects of recent changes, it might not represent the current-day biodiversity condition. Thus, there is a strong need to update these observations through a comprehensive sampling campaign covering the entire territory. Finally, it must be considered that the specimens documented in the literature have not been subjected to reanalysis; therefore, we adhered to the taxonomic classifications provided in the original publications or most recent checklists. Both recent and historical observation have relied on taxonomic identification based on morphological characteristics. Consequently, the presence of cryptic species cannot be ruled out. A reanalysis of these specimens using modern genetic tools could provide deeper insights into the true diversity of the taxa and reveal hidden evolutionary lineages, further enriching our understanding of subterranean biodiversity. The integration of modern data management principles and sharing through platforms such as LifeWatch ITA (https://dataportal.lifewatchitaly.eu/data) ensures that this dataset is accessible,and reusable for future research and conservation plans. As ongoing projects continue to provide new findings, we believe that this updatable database will form the basis for the study and conservation of Apulian stygofauna in the future.

We thank Dr. Alberto Potenza, Il Gruppo Speleologico Leccese ‘Ndronico, Il Gruppo Speleologico Tricase (GST) and TheMonumentsPeople for their irreplaceable logistical support and sharing of knowledge. We also thank Alessandro Silvestrini, Michele Bonfrate, Marcello Caramuscio, FORMICA S.R.L., and I.S.T.E. SUD for courtesy and assistance provided during the sampling operations. We extend our gratitude to Dr. Isabella Serena Liso for supporting the spatial analysis, Dr. Simone Cianfanelli for the malacological contribution, Dr. Tiziana Di Lorenzo and Dr. Fabio Stoch for their extremely valuable editorial comments and to Dr. Mattia De Cicco, as well as an anonymous reviewer, for their constructive feedback. Research funded by the project PRIN 2022 STIGE-CLIMAQUIFERI DTA.PN010.014 2022MM8P88_LS8_PRIN2022 - CUP:B53D23012170006 with the support of the project PRIN project “ANCHIALOS” (2022LLNF3N), funded by the Ministry of Universities and Research (Italy) Biodiversa+ (Project DarCo), the European Biodiversity Partnership under the 2021–2022 BiodivProtect joint call for research proposals, co-funded by the European Commission (GA N°101052342) and with the funding organisations Ministry of Universities and Research (Italy), Agencia Estatal de Investigación – Fundación Biodiversidad (Spain), Fundo Regional para a Ciência e Tecnologia (Azores, Portugal), Suomen Akatemia – Ministry of the Environment (Finland), Belgian Science Policy Office (Belgium), Agence Nationale de la Recherche (France), Deutsche Forschungsgemeinschaft e.V. (Germany), Schweizerischer Nationalfonds (Grant N° 31BD30_209583, Switzerland), Fonds zur Förderung der Wissenschaftlichen Forschung (Austria), Ministry of Higher Education, Science and Innovation (Slovenia), and the Executive Agency for Higher Education, Research, Development and Innovation Funding (Romania).