Project title: Sub-BioMon – Developing and testing approaches to monitor subterranean biodiversity in karst

Project duration: 36 months

Funding organization: European Union – Biodiversa+, Horizon2020

Description (short description): The Sub-BioMon project will provide standardized methods and protocols for monitoring subterranean biodiversity in European karst areas. Consistent with Theme 1, a common approach to monitoring subterranean biodiversity in karst areas will be developed, incorporating a new paradigm which considers caves as either habitats or windows to subterranean habitats. Consistent with Theme 2, it addresses the major gap created by the lack of a standardized protocol for monitoring subterranean biodiversity in karst habitats. Although many conservation measures and management plans for subterranean biodiversity are being developed and implemented, there is no standardized methodology that would allow for an actual assessment of their positive impact. Consistent with Theme 3, the project will use data from large species distribution and existent DNA databases, as well as collect new data through monitoring protocols. Sub-BioMon provides a scientific basis for monitoring schemes that are relevant to a variety of stakeholders from authorities to the public, all of which will be involved from the beginning in the project. Subterranean habitats are, therefore, a key example where international collaboration is needed for effective management and conservation, based on scientifically tested and developed monitoring protocols. Subterranean habitats extend through more countries, as karst massifs may be extended in two countries and karst aquifers may be fed in one country while drinking water may be used in a neighboring country. Caves are listed as a habitat type (8310 “Caves not open to the public”) in the EU Habitats Directive and must be monitored using standardized methods on the national and international levels.

About the project

Description: The karst regions in Europe represent 21.8% of the territory and host a unique and highly endemic part of European biodiversity. However, due to their difficult accessibility and the complexity of exploration, which requires expertise and specialized equipment, they are one of the most difficult habitats for biodiversity monitoring. In addition, there is no standardized sampling method for monitoring rare species and quantifying and identifying trends in subterranean biodiversity. However, cave or species monitoring protocols have been established in some European countries. In addition, species identification is extremely problematic due to the general lack of taxonomists, but specifically for the subterranean realm. The Sub-BioMon project is defining and testing methods based on the novel paradigm for caves: distinction of caves as habitats or as windows into an extensive subterranean habitat, consisting of cavities and crevices inaccessible for humans.

Based on these two main concepts, it is clear that for some species there is a fairly well-developed monitoring protocol (e.g., bats, which are not addressed in this project), while for obligate subterranean organisms that occur in caves but also live in the system of crevices surrounding them, there is no unified and standardized
monitoring protocol. Thus, there are several interrelated challenges. The first issue to solve is selection of monitoring sites and microhabitat location, which will be representative to estimate and compare cave biodiversity and long-term trends in subterranean habitats. This challenge must be addressed at several spatial levels. Most subterranean species are endemic, and species turnover is high across broad geographic areas as well as between regions, individual karst massifs and/or hydrographic basins, or even sites. Second, there is the question of how to sample. The rarity of subterranean animals makes them difficult to detect; thus, repeated visits to selected monitoring sites with standardized sampling procedures are needed. Third, there is the challenge of identifying sampled individuals at the species level, which is necessary for sound conservation planning. This is particularly difficult in subterranean habitats where endemism is very high and cryptic species are common. This requires trained taxonomists, whose numbers are decreasing at amateur and professional levels. For this reason, DNA-based molecular
approaches can help to overcome the so-called “taxonomic barrier”. Barcoding, metabarcoding, and environmental DNA (eDNA), in conjunction with robust databases and DNA libraries, provide the ability to identify species and help estimate subterranean biodiversity.

In the past, caves were treated as uniform environments with low species richness, being “truncated ecosystems” without primary producers. In recent decades, cave
ecosystems have been shown to have rich biodiversity and harbor rare and endemic species not found in surface habitats. Even from a global perspective, subterranean biodiversity is particularly rich and diverse in Europe, where approximately 5,000 exclusively subterranean species have been discovered and where most subterranean biodiversity hotspots are located. EU countries are required to conserve favourable conservation status of habitat type “caves not open to the public (8310)” under the Habitats Directive and therefore monitor subterranean biodiversity within the habitat (in addition to e.g. environmental factors or human impacts). The subterranean environment is spatially heterogeneous, which affects the choice of efficient monitoring methods and makes comparisons between different sites, regions or countries difficult. At large (continental and regional) scales, as well as at local scales, there are differences in the extent of karst, the diversity of subterranean habitats, and their isolation and connectivity. At smaller scales (between and within caves), different microhabitats require different sampling methods and consideration of the variable ecology of taxa. Furthermore, even in EU countries there is no precise definition of what subterranean habitats are and how they should be monitored (e.g. based on caves or karst areas; a single or multiple times a year). The Sub-BioMon project will address this complexity by combining experience and knowledge from different geographic regions and small-scale local (i.e., caves, springs) monitoring of selected taxa (except bats). Sub-BioMon targets karst areas defined by a karst bedrock, typically full of crevices and cavities of varying sizes, accessed via caves or springs. Caves are anthropogenically defined voids in karstic rocks, i.e., they allow humans to enter and sample them directly. Springs are ecotones between surface and subterranean aquatic habitats, usually at the boundary between karstic and non-karstic rocks. The main challenge for monitoring methods is to take into account the high endemicity and rarity of
subterranean species and to develop low-impact methodologies that must not affect the subterranean population size. This is especially important when it comes to involving non-scientists in monitoring activities.