Are cave-sediment bacteria reacting to climate change?

cave-sediment bacteria

Karst subterranean cave sediments are vulnerable ecosystems, hosting microbial communities that provide crucial services, such as nutrient cycling and pollutant degradation.

So far, these systems have not been studied adequately at the microbial functional level, yet, they currently contribute around 25% of the world’s drinking water. Rather than passive deposits, cave sediments are dynamic microbial habitats that influence fundamental biogeochemical processes through nitrogen, sulfur, and carbon cycling.

A new study on cave microbiology addresses this gap, co-authored by LifeWatch Slovenia member Janez Mulec (Karst Research Institute – ZRC SAZU), together with Lejla Pašić (Sarajevo Medical School) and Andreea Oarga-Mulec (Materials Research Laboratory).

The paper, recently published in Frontiers in Microbiology, highlights how cave-sediment bacteria in the the Slovenian eLTER Postojna-Planina Cave System site respond to environmental change, examining key environmental factors such as sediment age and short-term environmental variability.

Slovenian researchers are trying to understand whether these factors have any influence on substrate degradation, taxonomic composition, and on the metabolic potential of bacterial communities. In the midst of hydroclimatic extremes such as floods, droughts, and rising cave temperatures, it is fundamental to understand if these communities are capable of adapting to climate change.

The paper examines two types of sediments that host these microbial habitats: alluvial sediments recently deposited (surface), subject to hydrological and geochemical variability, and ancient palaeo-river deposit (subsurface), the latter still under-investigated in comparison to the first type, despite its potential to tell us a lot more about microbial ecological functions.

The authors have shown that older sediments can actually function as a geochemical filter: the palaeo-deposit exhibited low taxonomic and functional diversity alongside elevated heavy metal concentrations, consistent with constraints on microbial functioning under long-term geochemical stress. Adaptive traits have been revealed in key taxa, such as Polaromonas, Methylibium, and Beggiatoa.

The study integrates functional and taxonomic approaches, using metagenomic analysis, community-level physiological profiling (CLPP), and sediment geochemistry to assess the roles of sediment age, oxygen availability and temperature, as well as the potential of the microbial communities for applied environmental use.

Read the full article: (DOI: 10.3389/fmicb.2025.1724116).

New paper analyses patterns and drivers of subterranean biodiversity hotspots

Subterranean biodiversity

LifeWatch Slovenia members Magdalena Nǎpǎruş-Aljančič and Tanja Pipan (Karst Research Institute – ZRC SAZU) co-authored a new, open-access article in BioScience, titled “Patterns and Drivers of Subterranean Biodiversity Hotspots across the Globe”.

The study maps global subterranean biodiversity hotspots, highlighting the exceptional richness of the Dinaric Karst. In fact, the extreme environment of caves hosts a surprising number of aquatic and terrestrial species that are highly specialised for these habitats: no eyes and pigments, elongated appendages, elaborate extraoptic sensory structures make these species unique in the world, and extremely rare.

Starting from recently published lists of such invertebrate and vertebrate cave-limited species, the researchers mapped hotspots of cave biodiversity – globally – to understand if any patterns emerge, and if these patterns may have any specific drivers.

These may include historical climate change, cave systems density, and resource availability, highlighting conservation challenges associated with protecting these ecosystems with unique characteristics.

The publication of this study was made possible by Prof. Emeritus David C. Culver, mentor of the paper, and a pioneer of speleobiology, whose work has shaped many studies and conservation actions of the subterranean life.

Read the full article here: https://doi.org/10.1093/biosci/biaf159

The BioScience journal, founded in 1964, collects timely and authoritative overviews of current research in biology, as well as essays and discussion sections on education, public policy, history, and the conceptual underpinnings of the biological sciences.

The cave-dwelling olm: a sentinel for environmental change – LifeWatch Slovenia on Nautilus Magazine

ProteusWatch_Gregor_Aljancic

ProteusWatch vLab’s Research, part of the LifeWatch Slovenia Consortium, has been featured on Nautilus Magazine.

Deep beneath Europe’s karst landscapes lives the olm (Proteus anguinus), a pale, blind amphibian once thought to be the offspring of dragons. Elusive and long-lived, it is exquisitely sensitive to changes in groundwater quality and temperature, making it a living gauge of ecosystem health in subterranean aquifers that supply drinking water to millions.

Since 1960, the Tular Cave Laboratory in Kranj, Slovenia, has advanced olm research and conservation from a unique underground facility. Building on innovations that ranged from early CCTV systems to digital infrared video, the team has  revealed the behaviour and ecology of olm, from its unique cave-related sensoric capabilities to reproduction. Yet caves are dangerous and difficult to access, and lab studies can only go so far.

To bridge this gap, the research team from the Tular Cave Laboratory together with their colleagues from Karst Research Institute ZRC SAZU (both partners in LifeWatch Slovenia Consortium), and in partnership with LifeWatch ERIC Virtual Lab Innovation Center (the Netherlands), have mapped out plans for the ProteusWatch Virtual Lab: a virtual cave laboratory that brings long-term, in-situ monitoring to the karst underworld. Combining low-impact video analysis, machine learning, advanced sensors, imaging sonar and underwater drones, ProteusWatch aims to observe the olm’s behaviour – movement, foraging, interactions and breeding – in real time, without disturbing its fragile habitat. A second virtual lab, the Karst Groundwater Virtual Lab, will track groundwater dynamics to assess ecosystem stability and pressures of pollution.

“The main reason for building the cave laboratory 65 years ago was to circumvent the inaccessibility of Proteus’ natural habitat and allow long-term observations under more controlled conditions,” said Gregor and Magdalena Aljančič. “With advanced technologies, the idea of studying olms in the wild is becoming more and more realistic. The new approach would not only be more efficient but could also save lives.”

Christos Arvanitidis, CEO of LifeWatch ERIC, is backing the team’s efforts as a new leading example of accessible, multidisciplinary science. “You can show your data to other communities in [a] way they can take advantage of, prove to them that this type of research can be done, and they can perhaps use their own data, for the same kind of analysis,” he says. “That’s amazing, because it leads progressively to a kind of knowledge which is produced by as many data, from as many domains, as possible.”

Read the full article on Nautilus Magazine.

Photo credit: Gregor Aljančič.

Join LifeWatch ERIC’s Thematic Services Working Groups

Thematic Services Working Groups

LifeWatch ERIC launches the minisites of the six Thematic Services Working Groups: hubs for knowledge and resources sharing, networking, and collaboration.

Co-developed by the LifeWatch ERIC Common Facilities in collaboration with the National Distributed Centres, they reflect the main priority areas of e-Service construction, and therefore are central to the 2022-2026 Infrastructure Strategic Working Plan.

The Thematic Services Working Groups are coordinated by the LifeWatch ERIC Service Centre and pursue three main objectives:

  • Strengthen collaboration between and within the Common Facilities and the Distributed Centres;
  • Review and update the mapping of the National scientific communities’ research needs in relation to the Thematic Services, and identify priority areas for development;
  • Promote and coordinate the participation of Distributed Centre research institutions in Horizon Europe and other European and international projects, on behalf of and in collaboration with LifeWatch ERIC, to co-design and co-construct the priority services with other key actors in the biodiversity and ecosystem research landscape.

The initiative officially took off in 2024, marked by a series of Thematic Service Workshops hosted by the National Distributed Centres, engaging local communities from the start.

Today, we are glad to present the Working Groups on the website: six dedicated entry points, each focused on a specific topic and open for participation!
Each page offers a brief overview of the scope and objectives, as well as a timeline of activities, including some future actions already planned.

The activities in each group are led by a coordinator from one of our National Distributed Centres, who will oversee the follow-up of its activities.

Moreover, the abstract submission topics for this year’s ‘BEeS’, LifeWatch ERIC’s Biodiversity & Ecosystem eScience Conference, have been selected in alignment with those of the Working Groups, given that they had been previously identified as key priority areas by the National Distributed Centres.

What are you waiting for? Find out more about the Working Groups, join forces with fellow experts and contribute to biodiversity and ecosystem research!

LifeWatch Slovenia hosted the 5th Thematic Service Workshop on Biodiversity Observatory Automation

On April 11, LifeWatch Slovenia recently hosted the 5th Thematic Service Workshop on Biodiversity Observatory Automation at the National Institute of Biology in Ljubljana. The workshop focused on reviewing and updating the requirements for effective biodiversity assessment in light of current environmental changes and biodiversity loss. The event had 33 participants who attended the workshop in person, while 30 others joined online.

The workshop brought together experts to present the key achievements and obstacles in monitoring and observation approaches and discuss various stakeholders’ drawbacks and needs through an extensive programme of twelve presentations.

The event included a panel discussion among Prof Rudolf Meier from the Museum of Natural History Berlin, Dr Klaas Deneudt from VLIZ, and Dr Gentile Francesco Ficetola from the University of Milan, moderated by Dr Cene Fišer from the Biotechnical Faculty of the University of Ljubljana. The panel discussed various modern biodiversity monitoring and detection approaches, including aerial observations and eDNA. They explored the possibilities of data collection design, data curation, data exploration, and the use of AI. Additionally, they discussed FARIfication of data and digital twins.

Although biodiversity assessment has various challenges, including time-consuming fieldwork and the complicated data processing and storage involved after fieldwork, scientists are making progress in automating data collection. Furthermore, the advancement of computing power and artificial intelligence have opened up new possibilities to aid them in their work. 

The workshop about Biodiversity Observatory Automation was organised by LifeWatch Slovenia—LifeWatch ERIC National Node—and its members, by Dr Andreja Ramšak from the National Institute of Biology and the national coordinator, Dr Tanja Pipan, from the Karst Research Institute ZRC SAZU.

To learn more about our Thematic Service Workshop Series, please visit our minisite: https://www.lifewatch.eu/thematic-services-workshops/.

LifeWatch ERIC launches the 2024 Thematic Service Workshop Series

lifewatch eric thematic workshop

Last update: 1 February 2024

The LifeWatch ERIC Thematic Services, co-developed by the LifeWatch ERIC Common Facilities and National Distributed Centres, are a key component of the 2022-2026 Infrastructure Strategic Working Plan (SWP). They represent the key priority areas of eService construction in LifeWatch ERIC proposed by the National Distributed Centres.

Activities, developments and physical outcomes of the LifeWatch ERIC Thematic Services, as eServices, Virtual Labs (vLabs) and more complex and complete Virtual Research Environments (VREs), are planned to be coordinated by Thematic Service Working Groups participated by scientists from both the National Distributed Centres and the Common Facilities, with an overall coordination of the LifeWatch ERIC Service Centre.

The following main objectives are envisaged for the Working Groups:

  • Enhance collaboration both between and within the Common Facilities and Distributed Centres;
  • Review and update the mapping of the research needs of the National scientific communities regarding the Thematic Services and highlight the construction priorities;
  • Promote and coordinate the participation of Distributed Centre research Institutions to Horizon Europe and other European/international projects, on behalf of and in collaboration with LifeWatch ERIC, in order to co-design and co-construct the priority services with other key actors in the biodiversity and ecosystem research landscape, including the relevant communities.

For the launch of Working Group constitution and the promotion of the activities and developments currently running on each LifeWatch ERIC Thematic Service, a series of LifeWatch ERIC Thematic Service Workshops have been co-organised by the LifeWatch ERIC National Distributed Centres and Common Facilities. Each Workshop is then locally organised by a LifeWatch ERIC National Distributed Centre, engaging the relevant national community, with the support of the Service Centre.

Workshops programme by Thematic Service

Click the Thematic Service for more information. The agenda will be updated with new workshops soon.

LifeWatch Slovenia: new website launched

The picture shows a snapshot of the new LifeWatch Slovenia website

The new LifeWatch Slovenia website is online since 31 May 2023. It provides biodiversity and ecosystem researchers with facilities, data resources, web services and Virtual Research Environments. LifeWatch Slovenia remains fully integrated with LifeWatch ERIC in facilitating open data sharing, aggregation and modelling. Besides that, it offers immediate access to national priority projects, as in the case of karst groundwater habitat research and conservation of that national symbol, Proteus anguinus, the only exclusively cave-dwelling aquatic salamander in Europe.

In 2022, the Government of the Republic of Slovenia adopted the Research Infrastructure Roadmap 2030 (NRRI 2030) in which LifeWatch was listed as a priority area in the field of Sustainable Energy and Environmental Technologies. LifeWatch-SI is also part of the Slovenian Strategy for Smart Specialisation (S4) and Horizon 2020, focusing on the development of technological solutions in the field of biodiversity and socio-ecological research.

Since 2015, the Slovenian Consortium has been promoting the importance of integrating and networking information and data to:

  • Coordinate biodiversity research in marine, freshwater and terrestrial ecosystems;
  • Plan common access to a vast array of data from various sources and observatories;
  • Predict computing capabilities with analytical and modelling tools in virtual laboratories; and
  • Support training and educational programs that will enable a proper understanding of biodiversity.

The LifeWatch Slovenia Consortium consists of the ZRC SAZU Karst Research Institute, the National Institute of Biology, the Slovenian Forestry Institute, the Slovenian Natural History Museum, the Škocjan Caves Park, the Tular Cave Laboratory, the University of Ljubljana, the University of Maribor, the University of Nova Gorica, and the University of Primorska. Of these, ZRC SAZU serves as the national coordinator and headquarters of LifeWatch-SI.

For more information, please explore the lifewatch.si website.

The LifeWatch Community Platform is here!

LifeWatch Community

Roll up, roll up! LifeWatch followers and collaborators are cordially invited to the grand unveiling of the LifeWatch Community platform, now openly available to everyone! Who should become a member? Well, if you’re interested in biodiversity and ecosystem research, then you should!

The content of the Community platform will be widely shaped by its members, allowing them to create and contribute to forums, add opportunities, jobs and events of interest to the community, and hold meetings and collaborative brainstorming together with other members. These features are particularly well-suited to the needs of partners involved in European projects focused on biodiversity, who can benefit from the working groups as the perfect collaborative space.

Once a member of the Community, you can select your skills from a preset list, in order to facilitate linkages among the community. In need of a collaborator with a specific specialisation? Whether the keywords are data sciences, environmental sciences or biotechnology, simply carry out a search for the skills you are looking for to identify potential matches.

The platform is also a great space to learn about upcoming events. Of immediate relevance to the community is the upcoming LifeWatch ERIC Biodiversity and Ecosystem eScience Conference in Seville, for which interested persons can already submit their abstract on the Community platform.

While many aspects of the platform can be browsed without registering, we recommend opening an account in order to benefit from the full range of resources available. Sign up now to enhance the community experience for everyone, put your range of abilities and knowledge at everyone’s disposal, in a mutual and sincere effort to foster open science.

If you require any assistance with any of the registration process or functionalities of the Community, please do not hesitate to get in touch with communications[@]lifewatch.eu.

Head over to the LifeWatch Community!

Voices of Women at LifeWatch ERIC for International Women’s Day

Voices of Women

In preparation for this year’s International Women’s Day, LifeWatch ERIC International Gender Officer, Africa Zanella, had a clear request: amplify women’s voices. As explored in the “Gender, Equity and Research” campaign for last year’s International Day of Women and Girls in Science, statistically, we know that while more women than ever are getting involved in STEM, there are significant obstacles still to overcome for women in research. 

In light of International Women’s Day 2023, we have therefore created a podcast miniseries specifically dedicated to learning more about authentic experiences of women working in LifeWatch ERIC fields of interest. We asked scientists from our eight member states to talk candidly about their work and experience. The guests were invited to speak in pairs, which produced spontaneous and insightful conversations on these topics, facilitated by LifeWatch ERIC podcast host, Julian Kenny. Being of all ages and hailing from a diversity of backgrounds, the end result produced is an enriching range of experiences and contemporary points of view of women working in research today. Listening to their voices, our eyes are opened to their contribution to society, to science, and the potential offered by the European Union’s Gender Equality Strategy, which LifeWatch ERIC actively supports and incorporates into its everyday work life.

The guests featured in “Voices of Women” are:

The episodes will be released over the course of the week beginning 6 March and will be consolidated with an overview and considerations from LifeWatch ERIC International Gender Officer, Africa Zanella, interviewed by Chief Communication Officer, Sara Montinaro, to be released on 8 March (International Women’s Day). This podcast will examine the progress of the infrastructure as a whole in terms of achieving gender sustainability and equity, a year on from the appointment of LifeWatch ERIC’s International Gender Officer, and explore future plans to continue the commendable and tangible work that she has already set in motion.

The podcasts are available here below. They can also be found on Spotify, Google, Apple, and Amazon.







LifeWatch Slovenia Publishes New Research Paper

LifeWatch Slovenia Research

Researchers affiliated with LifeWatch Slovenia have published the research paper: “Karst Groundwater Dependent Ecosystems—Typology, Vulnerability and Protection” (Nataša Ravbar, Tanja Pipan). You can read the abstract below and click on the link to access it in full.

Karst Groundwater Dependent Ecosystems—Typology, Vulnerability and Protection

Nataša Ravbar, Tanja Pipan

Karst groundwater dependent ecosystems (KGDEs) represent an important asset worldwide due to their ecological and socioeconomic values. In the contribution the main KGDEs of the Dinaric karst in Slovenia are presented. The main hydrological processes (i.e., extent, duration and frequency of groundwater inflow), the main biota and indicator communities, and the factors limiting the evolution of species (e.g., darkness) were identified. An overview of rare, endemic and charismatic species was also shown including Proteus anguinus, Marifugia cavatica, Monolistra racovitzae racovitzae and others. Due to its location in an area of very high geographical diversity and between different climate types, the Slovenian Dinaric karst is one of the hotspots of subterranean biodiversity on a global scale. The interaction between orographic, climatic, hydrological and edaphic conditions, as well as the fact that the area served as a hub for different species and as a refuge during the ice ages, are crucial for the very high biodiversity in this area. Due to deforestation in prehistoric times, man has even contributed to the diversification of the flora by creating space for the appearance or spread of habitats that are now considered natural (e.g., dry grasslands). An important factor in maintaining a particularly rich diversity of karst flora and fauna is also the low human impact and the very well preserved landscape in its natural state. KGDE sites in Slovenia with the greatest known species diversity are the Postojna -Planina and Škocjanske Jame cave systems, Cerkniško and Planinsko Polje, and the intermittent lakes of Pivka. Characterization of KGDEs is a prerequisite for a better understanding of the processes that control them, their biological function, and their vulnerability. The ecohydrological characterization of KGDEs of Slovenian Dinaric karst can serve as a pilot study for other karst regions with high biodiversity.

Photo credit: B Kogovšek, N Ravbar, Adobe Stock.