Tag: biodiversity

Novel tech for research & protection of marine biodiversity: Pensoft joins EU project ANERIS

Pensoft joins the ANERIS consortium as an expert in science communication with the goal to engage stakeholders and build an active community

Coastal and marine biodiversity has been declining at an alarming rate in recent years due to anthropogenic activity, climate change, ocean acidification and other factors. 

To help protect and preserve these precious ecosystems, the new research project under the name of ANERIS (operAtional seNsing lifE technologies for maRIne ecosystemS) and coordinated by the Institute of Marine Sciences (ICM-CSIC) was launched under the Horizon Europe program.

ANERIS aims to contribute to improving the understanding, monitoring and protection of these ecosystems through technological, scientific and methodological innovation in the fields of marine life-sensing and monitoring.

Pensoft is joining the ANERIS consortium as a leader of WP6 Exploitation, Communication and Networking. The Pensoft team is to develop and implement sustainable communication and dissemination strategies, which will ensure the impactful knowledge exchange between partners and external stakeholders.

In addition, Pensoft is responsible for the development of a long-lasting brand identity of the project, which shall be reached by establishing and maintaining a user-friendly and eye-appealing public website. The overall visual identity of ANERIS will be supported by a set of innovatively-designed promotional materials. 

The project

ANERIS launched in January 2023 and will be running until December 2026 with the support of EUR 10 million of funding provided by the European Union’s Horizon Europe program and the work on the project officially kicked off with the project’s first consortium meeting, which took place on the 8th and 9th of March 2023 in Barcelona, Spain. 

The joint mission of the ANERIS partners for the next four years is to build the next generation of marine-sensing instruments and infrastructure for systematic routine measurements and monitoring of oceanic and coastal life, and their rapid interpretation and dissemination to all interested stakeholders.

In total, ANERIS aims to pioneer 11 novel technologies rerelated to marine ecosystem monitoring, data processing and dissemination:

  • NANOMICS – NAnopore sequeNcing for Operational Marine genomICS
  • MARGENODAT – workflows for the MARine GENOmics DAta managemenT
  • SLIM-2.0 – A Virtual Environment for genomic data analysis (ANERIS extended version)
  • EMUAS – Expandable Multi-imaging Underwater Acquisition System
  • AIES-ZOO – Automatic Information Extraction System for ZOOplankton images
  • AIES-PHY – Automatic Information Extraction System for PHYtoplankton images
  • ATIRES – Automatic underwaTer Image REstoration System
  • AIES-MAC – Automatic Information Extraction System for MACroorganisms
  • AMAMER – Advanced Multiplatform App for Marine lifE Reporting
  • AMOVALIH – Advanced Marine Observations VALidation-Identification system based on Hybrid intelligence
  • AWIMAR – Adaptive Web Interfaces for MARine life reporting, sharing and consulting

These technologies will be validated across four ANERIS case studies which aim to bridge the gaps between existing technologies and incorporate them into a functional technological framework:

  • High-temporal resolution marine life monitoring in research infrastructure observatories;
  • Improved spatial and temporal resolution of marine life monitoring based on genomics;
  • Large scale marine participatory actions;
  • Merging imaging and genomic information in different monitoring scenarios.

The final goal of the project through the creation and validation of these novel technologies and involving academia, industry, governments and civil society, is to build up the concept of Operational Marine Biology (OMB) to provide faster, higher quality, reliable, and accessible marine and coastal life data. OMB opens the door for near-real-time marine observations, data interpretation and decision making based on that data.

International Consortium

The interdisciplinary ANERIS consortium consists of 25 partnering organisations from 13 countries around Europe, the Mediterranean basin and Israel, bringing diverse expertise spanning from robotics, biooptics, marine biology and genomics, to programming and sustainability.

Many partners represent acclaimed scientific institutions with rich experience in collaboration in EU projects, specifically in the fields of marine research.

Full list of partners:

Visit the ANERIS website on https://www.aneris.eu/. You can also follow the project on Twitter (@ANERISproject), LinkedIn (/ANERIS Project) and Instagram (@aneris_project).

Don Quixote gives his name to a new plant species only known from La Mancha, Spain

“In the present biodiversity crisis scenario, it is critical that we do not neglect basic scientific disciplines like taxonomy, since cataloguing biodiversity is a fundamental step towards its preservation.”

The knowledge of biodiversity in allegedly well-known places is not as complete as one would expect and its detailed study by researchers continues to offer surprises, is what we find out in a new study of the flora of south-central Spain. 

Now, Spanish botanists from Pablo de Olavide University (Seville, Spain) have described a new plant species of the papyrus family (Cyperaceae) restricted to the La Mancha region in south-central Spain. This region is in fact well-known for classic literary fans, who might recognise the name as the main setting in Miguel de Cervantes’ (1547–1616) masterpiece Don Quixote.

Artistic recreation depicting Don Quixote and his squire Sancho Panza with the iconic La Mancha windmills, and a Carex quixotiana’s habitat.
Image by Faro Míguez.

The epic novel, which tells the story of the life and journeys of Alonso Quijano, a Spanish hidalgo (nobleman), who becomes the knight-errant Don Quixote de la Mancha, is commonly considered to be one of the greatest literary works ever written, with its number of editions and translations thought to be only surpassed by those of the Bible.

The new species, now scientifically known as Carex quixotiana, belongs to sedges of the genus Carex, a group of herbs included in the papyrus family (Cyperaceae). The classification (taxonomy) of these plants is difficult, as it is a highly diverse and widely distributed genus, whose species are frequently hard to tell apart. In fact, C. quixotiana has itself evaded the eyes of expert botanists for decades, because of its close resemblance to related species.

“Cryptic species are frequent in complex plant groups, such as sedges, and integrative studies encompassing different data sources (e.g. morphology, molecular phylogeny, chromosome number, ecological requirements) are needed to unravel systematic relationships and accurately describe biodiversity patterns,”

says Dr. Martín-Bravo, senior author of the paper.

After a preliminary genetic study pointed to something odd about specimens of what was later to be known as Carex quixotiana, the authors set off on exhaustive field collecting campaigns across La Mancha. As they studied additional populations of the plant in further detail, using morphology, phylogenetics, and chromosome number, the scientists confirmed that they were looking at a species previously unknown to science. Understandably, the distribution range of the newly discovered species, restricted to the mountain ranges surrounding La Mancha (Sierra Madrona and Montes de Toledo), made the authors think about Cervantes’ masterpiece.

So far only known from 16 populations, Carex quixotiana prefers habitats with high water availability, such as small streams, wet meadows and riverside (riparian) forests. 

Since little is known about the species’ demographics, including the number of mature individuals in the wild, further investigation is required to determine its conservation status. However, based on what they have learnt so far about the species, the authors of the present study assume that:

“it is an Iberian endemic with a relatively small number of populations and distribution range, which would benefit from legal protection and inclusion in in-situ/ex-situ conservation programmes.”

“In the present biodiversity crisis scenario, it is critical that we do not neglect basic scientific disciplines like taxonomy, since cataloguing biodiversity is a fundamental step towards its preservation and, thus, sustainable management,”

say the researchers.

In conclusion, the scientists point to their results as yet another proof of how much there is still to learn about Earth’s biodiversity, even when it comes to supposedly well-known organisms, such as flowering plants, and countries, whose flora is presumed to be fully documented. The “Flora Iberica”, for example, which covers Spain and Portugal, has only recently been finalised, the team reminds us.

Close-up images of reproductive parts (inflorescences known as spikes) of the newly described species Carex quixotiana. Photo by Modesto Luceño.

Research article:

Benítez-Benítez C, Jiménez-Mejías P, Luceño M, Martín-Bravo S (2023) Carex quixotiana (Cyperaceae), a new Iberian endemic from Don Quixote’s land (La Mancha, S Spain). PhytoKeys 221: 161-186. https://doi.org/10.3897/phytokeys.221.99234

Follow PhytoKeys on Facebook and Twitter.

Two striking new species of carnivorous plants discovered in the Andes of Ecuador

The two new species of butterworts were discovered in poorly explored, remote areas in the Amotape-Huancabamba zone, a biodiversity hotspot in southern Ecuador.

A team of botanists from Ecuador, Germany, and the United States has described two new species of carnivorous plants with striking appearance. They are part of the butterworts (genus Pinguicula), a group of flowering plants with about 115 species that can catch and digest small insects with their sticky leaves. Whereas the majority of butterwort species is distributed in the northern hemisphere, these new species were discovered in the high Andes of southern Ecuador, close to the border with Peru.

Pinguicula ombrophila sp. nov. Photograph by Álvaro J. Pérez.

Carnivorous plants use animals (usually small insects) as an additional source of nutrients to compensate the nutrient deficiency of the substrate they’re growing in. This gives them a competitive advantage over other plants and enables them to thrive in challenging habitats. The tropical high Andes have a variety of such habitats, for example marshland and rocky slopes covered in constant rain and clouds.

The two new species described in the study, Pinguicula jimburensis and Pinguicula ombrophila, were found on the shore of a highland lagoon at 3400 m and on a nearly vertical rock face at 2900 m, respectively. Their small-scale habitats lie within the so-called Amotape-Huancabamba zone, which encompasses large portions of southern Ecuador and northern Peru. This area is characterized by exceptional biodiversity, due in part to the fact that the rugged terrain and varied climate of the Andes provide so many microhabitats.

Pinguicula jimburensis sp. nov. Photograph by Kabir Montesinos.

“And as small and scattered as the species’ suitable habitats are, so is the species composition,”

says senior author Tilo Henning of Leibniz Center for Agricultural Landscape Research (ZALF), who is a specialist in this plant family in this region.

His colleague Álvaro Pérez of the Pontifica Universidad Catolica del Ecuador and his team were the first to discover the plants. They then got in touch with Henning.

“Both of these new species are only known from a single location, where only a few dozens of plant individuals occur in each case.”

For one of them, only one population with about 15 mature individuals was discovered, making it vulnerable even if it is hidden in an isolated, difficult-to-access area. This narrow endemism (limited distribution in a particular area) is typical of the Amotape-Huancabamba zone, and there are many more new plant and animal species awaiting discovery, Henning says.

With the description of these two new species, the number of Pinguicula species recorded in Ecuador has tripled, as previously only P. calyptrata was known, discovered by none other than Alexander von Humboldt. The authors are convinced that there are many more new species awaiting formal scientific recognition, but admit that lately it has been a race against time.

“The results presented in this study show that the assessment of the Neotropical biodiversity is far from complete. Even in well-known groups such as the carnivorous plants, new taxa are continuously discovered and described, in particular from remote areas that become accessible in the course of the unlimited urban sprawl,” Henning, Pérez, and their colleagues write in a scientific article dedicated to the new plants that was published in the peer-reviewed journal PhytoKeys. “This is both encouraging and worrying at the same time“.

“Relentless urban sprawl and the accompanying destruction of habitats pose a massive threat to biodiversity in general, and to the tightly-knit and specialized organisms that depend on their fragile microhabitats in particular,”

Henning points out.

Although the two new species are relatively safe from direct human interference – as they both occur within protected areas – human-induced climate change is increasingly affecting ecosystems regardless of location, especially those that rely on regular precipitation, such as mountain wetlands.

The dependence on a constant climate is even reflected in the name of one of the two new species: Pinguicula ombrophila means “rain-loving butterwort”, as the plant prefers very wet conditions, receiving moisture from the waterlogged paramo-soil and enjoying the frequent rain and fog typical for this area.

Pinguicula ombrophila sp. nov. Photograph by Álvaro J. Pérez.

Additional information:

The expedition to Cerro Plateado in 2016 was supported by Secretaría de Educación Superior, Ciencia, Tecnología e Innovación de la República del Ecuador (SENESCYT, Arca de Noé Initiative; S. R. Ron and O.Torres–Carvajal, Principal Investigators) and in 2021 by the International Palm Society (IPS) Endowment Fund and by Claes Persson (University of Gothenburg), the expedition also received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 865787, GLOBAL project). The Open Access Fund of the Leibniz Association covered the publication costs for the article.

Original source:

Pérez ÁJ, Tobar F, Burgess KS, Henning T (2023) Contributions to Ecuadorian butterworts (Lentibulariaceae, Pinguicula): two new species and a re-evaluation of Pinguicula calyptrata. PhytoKeys 222: 153-171. https://doi.org/10.3897/phytokeys.222.98139

You can also follow PhytoKeys on Twitter and Facebook.

Southern Flying Squirrel rediscovered in Honduras after 43 years

The Southern Flying Squirrel (Glaucomys volans) was spotted in an area where forestry and silvicultural activities are carried out for the sustainable exploitation of pine logging and timber.

The presence of The Southern Flying Squirrel (Glaucomys volans) was documented in Honduras for the first time after 43 years. The record is from a site of the forest management plan called “Las Lechuzas”, municipality of Concordia, department of Olancho.

Apart from this newly confirmed location, the species has also been recorded in Zambrano, department of Francisco Morazán in 1935, in Gracias, department of Lempira, and finally in the Department of paradise in 1979. Based on these records, Honduras is considered the southernmost distribution known for this species.

G.volans before it started to glide to the oaks. Photograph by MATC.

The discovery was possible thanks to a project of El Aserradero Sansone, a company focused on sustainable forestry activities in Honduras, and is published in a research article in the peer-reviewed journal Check List.

This finding confirmed that there is at least one population of G. volans in the country, at the Las Lechuzas site, which is currently also the southernmost locality known in its global distribution.

The species has been assessed as Least Concern by the IUCN (meaning it has stable populations), but is considered Data Deficient on the Red List of Honduran species.  Considering the low number of records and the high rate of destruction of pine forests in Honduras, G. volans is a priority for conservation in the country.

Part of the team that helped to encounter the squirrel. Photograph by MATC.

In support of the conservation of the biodiversity of Las Lechuzas, the company Sansone is now committed to giving priority to the conservation of G. volans in the area. The use of artificial shelters for G. volans is also being studied, as the animal is at greater risk when its nests are disturbed.

Based on recommendations suggested in the study, Sansone will work to increase the quantity and quality of tree seedlings that will grow in the canopy and educate people in the community about the need to protect pine ecosystems and rare animals. Additionally, within the 3,139.62 ha of the management plan of Las Lechuzas, there are 836.63 ha that have been declared as hydrological protection zones. Currently, there is no record of G. volans in any protected area of Honduras.

“As a professional with an experience of 43 years, I capitalize on the detection of the Flying Squirrel as an event that opens the doors to the true dimension posed by the Honduran forest law in the proper administrative management. That includes biodiversity conservation and protection and rationality of the protection of natural resources. The latter turns out to be of greater importance in view of the strong social pressures in favor of the conversion of the use of forest land destined for extensive agriculture and livestock, as well as the environmental impacts caused by climate change that is being sustained by the mismanagement of our resources,”

says José Muñoz, one of the authors in the study.

About El Aserradero Sansone:

El Aserradero Sansone was founded in 1957, characterized by compliance with the laws of Honduras, especially those related to forest management. It has developed an evolutionary and progressive process of achievements in the implementation of management plans, including such related to the evaluation of environmental impacts.

In this sense, the environmental importance in the management of natural resources has continued to promote evolution, defining the need to venture into aspects related to the conservation of flora and fauna as well as the incidence of climatic and environmental factors in the administration of natural resources. Within this responsibility, the last challenge that the company Sansone is welcoming with great optimism lies in adhering to the international criteria and indicators of the forest certification process through the principles of FSC (Forest Stewardship Council) and through the GFA company of Hamburg, Germany.

Research article:

Turcios-Casco MA, Hernández GS, Mancía FE, Molinero CF, Muñoz J, López CM, Ordóñez-Garza N (2023) Unseen for 43 years! A new occurrence of Glaucomys volans (Linnaeus, 1758) (Rodentia, Sciuridae) in Honduras. Check List 19(1): 133-139. https://doi.org/10.15560/19.1.133

You can also follow Check List on Twitter and Facebook.

Unraveling nature’s chorus: AI detects bird sounds in Taiwan’s montane forests

Researchers developed an AI tool which identifies 169 species native to Taiwan from the sound of their calls.

Spectacular subtropical montane forest scenery in Yushan National Park. Credit: Ms. Wen-Ling Tsai

Montane forests, known as biodiversity hotspots, are among the ecosystems facing threats from climate change. To comprehend potential impacts of climate change on birds in these forests, researchers set up automatic recorders in Yushan National Park, Taiwan, and developed an AI tool for species identification using bird sounds. Their goal is to analyze status and trends in animal activity through acoustic data.

Prof. Hsueh-Wen Chang and Ph.D. Candidate Shih-Hung Wu from National Sun Yat-Sen University, Taiwan, Dr. Ruey-Shing Lin, Assistant Researcher Jerome Chie-Jen Ko from the Endemic Species Research Institute, and Ms. Wen-Ling Tsai from Yushan National Park Headquarters have published a paper in the open access journal Biodiversity Data Journal, detailing their use of AI to detect 6 million bird songs.

Compared to traditional observation-based methods, passive acoustic monitoring using automatic recorders to capture wildlife sounds provides cost-effective, long-term, and systematic alternative for long-term biodiversity monitoring.

The authors deployed six recorders in Yushan National Park, Taiwan, a subtropical montane forest habitat with elevations ranging from 1,200 to 2,800 meters. From 2020 to 2021, they recorded nearly 30,000 hours of audio files with abundant biological information.

An automatic recorder was installed on a tree to capture the surrounding soundscape. Credit: Ph.D. Candidate Shih-Hung Wu

However, analyzing this vast dataset is challenging and requires more than human effort alone.

To tackle this challenge, the authors utilized deep learning technology to develop an AI tool called SILIC that can identify species by sound.

SILIC can quickly pinpoint the precise timing of each animal call within the audio files. After several optimizations, the tool is now capable of recognizing 169 species of wildlife native to Taiwan, including 137 bird species, as well as frogs, mammals, and reptiles.

In this study, authors used SILIC to extract 6,243,820 vocalizations from seven montane forest bird species with a high precision of 95%, creating the first open-access AI-analyzed species occurrence dataset available on the Global Biodiversity Information Facility. This is the first open-access dataset with species occurrence data extracted from sounds in soundscape recordings by artificial intelligence.

The Gray-chinned Minivet (left) displays a secondary non-breeding season peak (right) which is possibly related to flocking behavior. Credit: Shih-Hung Wu, Ph.D. Candidate

The dataset unveils detailed acoustic activity patterns of wildlife across both short and long temporal scales. For instance, in diel patterns, the authors identify a morning vocalization peak for all species. On an annual basis, most species exhibit a single breeding season peak; however, some, like the Gray-chinned Minivet, display a secondary non-breeding season peak, possibly related to flocking behavior.

As the monitoring projects continue, the acoustic data may help to understand changes and trends in animal behavior and population across years in a cost-effective and automated manner.

The sound of Gray-chinned Minivet. Credit: Ph.D. Candidate Shih-Hung Wu

The authors anticipate that this extensive wildlife vocalization dataset will not be valuable only for the National Park’s headquarters in decision-making.

“We expect our dataset will be able to help fill the data gaps of fine-scale avian temporal activity patterns in montane forests and contribute to studies concerning the impacts of climate change on montane forest ecosystems,”

they say.

Original source:

Wu S-H, Ko JC-J, Lin R-S, Tsai W-L, Chang H-W (2023) An acoustic detection dataset of birds (Aves) in montane forests using a deep learning approach. Biodiversity Data Journal 11: e97811. https://doi.org/10.3897/BDJ.11.e97811

You can also follow Biodiversity Data Journal on Twitter and Facebook.

Endangered vulture returns to Bulgaria after being extinct for 36 years

Preliminary results from the releases of Cinereous Vultures (Aegypius monachus) were published in the Biodiversity Data Journal.

The Cinereous Vulture (Aegypius monachus) – also known as Black Vulture, Monk Vulture or Eurasian Black Vulture – is the largest bird of prey in Europe.

Globally classified as Near Threatened, its populations in southern Europe, once abundant, have been experiencing a dramatic decline since the late 1800s. So dramatic, in fact, that by the mid-1900s, these birds had already been nowhere to be seen throughout most of their distributional range across the Old Continent. In Bulgaria, the species has been considered locally extinct since 1985.

Thanks to the re-introduction initiative that was started in 2015 by three Bulgarian non-governmental organisations: the leading and oldest environmental protection NGO in Bulgaria: Green Balkans, the Fund for Wild Flora and Fauna and the Birds of Prey Protection Society, the species is now back in the country.

The project, aptly named  “Vultures Back to LIFE“, where the Vulture Conservation Foundation (Switzerland), EuroNatur (Germany) and Junta de Extremadura (Spain) are also partners, has been co-financed by the LIFE+ financial instrument of the European Commission.

By mid-2022, the team imported a total of 72 individuals from Spain and European zoos, before releasing them in strategically-chosen sites in the Eastern Balkan Mountains and the Vrachanski Balkan Nature Park in Northwestern Bulgaria. 

The team brought 63 immatures from Spain, where the birds had been found in distress and rehabilitated in aviaries. The other nine juveniles were captive-bred in zoos, and then released by means of hacking, which involves an artificial nest, from where the fledglings can gradually ‘’take off” to a life in the wild.

The re-introduction campaign to date is presented in a research article, published in the open-access Biodiversity Data Journal. There, the scientists led by Ivelin Ivanov (Green Balkans), report on and discuss the effectiveness and challenges of the different release methods and offer tips on the conservation and re-introduction. 

For example, hacking proved to be inefficient for establishing an entirely new core (or nucleus) population of Cinereous Vultures in the Balkan Mountains in Bulgaria. It did not work for supplementing a small settled group of individuals either.

A Cinereous Vulture on a hacking platform.
Photo by Hristo Peshev, Fund for Wild Flora and Fauna.

Instead, the team recommend the aviary method and delayed release, where captive-bred birds are introduced to the new locality after a period of acclimatisation, where the birds can gain life experience to the local environment.

 “The Cinereous Vulture re-introduction establishment phase in Bulgaria in the two first release sites is running according to the plan, and the first results are satisfactory,” 

the scientists comment.

“Two distinct nuclei are now created, and the species started breeding, which might be a reason to up-list it in the Red Data Book of Bulgaria from ’Extinct’ to ‘Critically Endangered.’”

These two newly created breeding nuclei of the Cinereous Vulture in Bulgaria are the second and third of their kind in the Balkan Peninsula. 

“Following a dramatic decline throughout the 20th century for decades, the species had remained in only one breeding colony in Dadia-Lefkimi-Soufli Forest National Park in north-eastern Greece. Now, exchange between the three colonies will facilitate the exchange of individuals, ensure long-term stability, and give rise to the regional population,”

the authors of the study say.

However, the team points out that further monitoring and modelling and adaptive management are indispensable for the long-term persistence of the new national population. Now that there is already evidence that the imported vultures have been successfully breeding in Bulgaria, there is one step left before it can be officially confirmed that the Cinereous Vulture species has successfully re-established in the country. This conclusion can only be made after the core breeding populations begin to produce about ten chicks every year and after the locally fledged individuals begin to reproduce on their own. Such results are expected by 2030.

The re-introduction of the Cinereous Vulture is the latest in a series of conservation projects focused on birds of prey in Bulgaria. 

First, in a programme that started in 2009, the Griffon Vulture was successfully re-introduced in Bulgaria after about 50 years of “extinction”. In fact, the team took a lot of the know-how and methods used in that project to apply in the present project. The success story was published in a research paper in the Biodiversity Data Journal in 2021.

The incredible return of Griffon Vulture to Bulgaria’s Eastern Balkan Mountains

In fact, the very same day in 2021 saw two publications in the Biodiversity Data Journal that reported on re-introduction successes involving birds of prey in Bulgaria, which had gone missing for decades. The second instance was the discovery of the first nesting Saker Falcons in twenty years  

When conservation work pays off: After 20 years, the Saker Falcon breeds again in Bulgaria

Both scientific publications are part of a dynamic ‘living’ collection, titled “Restoration of species of conservation importance”, whose aim is to collate publicly available research studies reporting on the reintroduction and/or restocking of animal and plant species of conservation importance around the world. The collection was inspired by the “International Scientific Conference on Restoration of Conservation-Reliant Species and Habitats” held in Sofia, Bulgaria, in 2020.

“The restoration of species is one of the most important conservation tools in the context of constantly intensified human-driven global biodiversity loss. The reintroduction/restocking activities are related to significant research and data gathering before and during the work process, which ensures their sustainable success,”

explain the collection editors.

Research article: 

Ivanov I, Stoynov E, Stoyanov G, Kmetova–Biro E, Andevski J, Peshev H, Marin S, Terraube J, Bonchev L, Stoev IP, Tavares J, Loercher F, Huyghe M, Nikolova Z, Vangelova N, Stanchev S, Mitrevichin E, Tilova E, Grozdanov A (2023) First results from the releases of Cinereous Vultures (Aegypius monachus) aiming at re-introducing the species in Bulgaria – the start of the establishment phase 2018–2022. Biodiversity Data Journal 11: e100521. https://doi.org/10.3897/BDJ.11.e100521

You can also follow Biodiversity Data Journal on Twitter and Facebook.

Pensoft joins EU-funded project SOLO, supporting the EU Mission “A Soil Deal for Europe”

Apart from communication, dissemination and data management tasks, within SOLO, Pensoft is also responsible for the development of the key project output: the SOLO platform

The issue at hand

As the foundation of our food systems, healthy soils are essential for life on Earth. They provide clean water and habitats for biodiversity while contributing to climate resilience and support our cultural heritage and landscapes and are the basis of our economy and prosperity.

Soils are under multiple pressures, including climate change, urbanisation, pollution, overexploitation, nutrient mining and biodiversity loss with the European Commission estimating that under current management practices, it’s between 60% and 70% of our soils that are unhealthy.

The ‘deal’ with soils

The EU Mission “A Soil Deal for Europe” aims to address these issues by:

  • funding an ambitious research and innovation programme with a strong social science component;

  •  putting in place an effective network of 100 living labs and lighthouses to co-create knowledge, test solutions and demonstrate their value in real-life conditions;

  • developing a harmonised framework for soil monitoring in Europe;

  •  raising people’s awareness on the vital importance of soils.

Achieving those objectives requires a direct involvement of a wide range of stakeholders, bringing together multiple perspectives in ecological, environmental, economic and social contexts.

The project

SOLO launched in December 2022 and will be running until November 2027 with the support of 5 million euros provided by the European Union’s Horizon Europe program. 

SOLO will identify current knowledge gaps, drivers, bottlenecks, and novel research and innovation approaches to be considered in the European Soil Mission research and innovation roadmap.

The project aims to create a knowledge hub for soil health research and innovation that will last beyond the project’s lifespan by establishing strategic partnerships and by implementing a participatory and transparent process.

The project will implement Think Tanks, one for each Mission objective, with the aim of co-creating knowledge and identifying the knowledge gaps, drivers, bottlenecks, and novel approaches in terms of research and innovation.

The Think Tanks will consist of groups of experts who will together tackle the issues regarding soil health, set out in the EU Mission ‘A Soil Deal for Europe’.
Together with an open digital platform, based on Pensoft’s ARPHA Writing Tool, the Think Tanks will function as an operational tool for implementing a participatory process that will last beyond SOLO’s lifespan.

The project will engage users at regional, national and European level to support the co-design of comprehensive research and innovation roadmaps for the Soil Mission and identify knowledge gaps and novel avenues for European soil research and innovation in the context of the Soil Mission objectives. 

Furthermore, SOLO will identify, describe and assess the drivers and barriers to soil health in Europe, develop dynamic roadmaps as effective research and innovation agendas for the Soil Mission with a particular focus on the integration and synthesis across sectors.

The 3rd Global Soil Biodiversity Conference (March 2023; Dublin, Ireland) saw several talks by researchers involved in the SOLO project, while communication materials provided additional information to the delegates who stopped by the Pensoft exhibition stand.

You can find out more about the project on the Soils for Europe (SOLO) website: soils4europe.eu. Stay up to date with the project’s progress on Twitter (@soils4europe) and LinkedIn (/Soils-for-Europe).

UPDATE: The Soils for Europe journal is NOW LIVE at: https://journal.soils4europe.eu/.


The innovative open-access digital publishing platform provides a forum for open review and co-creation of the European Mission Soil research and innovation roadmaps in support of more integrative and encompassing policies aiming to achieve improvements in soil health and a thriving environment for soil-related research in Europe.

The consortium

SOLO’s consortium comprises a European network of established professionals from the academic and non-academic fields from various backgrounds, who have agreed to work collaboratively to fulfil the objectives set by the EU Mission “A Soil Deal for Europe” which aims to create a shared research and innovation vision that will accelerate Europe’s trajectory towards sustainable soil management and restoration as part of a wider, green transition in rural and urban areas.

Full list of partners:
  1. National Resources Institute Finland
  2. University of Leipzig
  3. Pesticide Action Network
  4. Agroecology Europe
  5. Leitat Technological Centre
  6. Netherlands Institute of Ecology
  7. Leibniz Centre for Agricultural Landscape Research
  8. Lund University
  9. Pensoft Publishers
  10. University of Évora
  11. Institute of Advanced Studies Kőszeg
  12. National Observatory of Athens
  13. Norwegian University of Life Sciences
  14. University of Antwerp
  15. University of Trento
  16. Fraunhofer Society
  17. ICLEI European Secretariat GMBH

Redefining nature-based decision-making: Pensoft joins EU project SELINA

“Ecosystem services is one of the topics that Pensoft has been involved in for over 10 years,” points out COO Prof Pavel Stoev.

Ambitious goals have been set by the European Union, in order to tackle the biodiversity conservation challenges over the coming decade. No less ambitious are the goals of the Horizon Europe project SELINA, which is one of the current major initiatives looking in the same direction. 

SELINA (Science for Evidence-based and Sustainable Decisions about Natural Capital) is a transdisciplinary project aimed at promoting the conservation of biodiversity, enhancing ecosystem conditions, and supporting the sustainable use of the environment through evidence-based decision-making.

As an experienced science communicator and open-science publisher, Pensoft will be leading the project’s communication and dissemination activities.

“Ecosystem services is one of the topics that Pensoft has been involved in for more than 10 years, so it was only natural for us to continue our work as a communicator of scientific information in the ambitious SELINA project as well,”

says Prof Pavel Stoev, COO at Pensoft.

“We have already collaborated with many of the partners within the earlier EC Horizon 2020 project ESMERALDA, which concluded with the launch of a pan-European network of scientific institutions engaged with biodiversity conservation and ecosystem services.

In addition, Pensoft has been strongly connected to the community through the scholarly journal One Ecosystem, which is supported by Ecosystem Services Partnership, and offers an opportunity for scientists in the field to publish their results in a new and innovative way.”

he adds.

The project

SELINA was launched in July 2022 and will run for 5 years. Having received EUR 13 million in funding, the project is seen as an unprecedented opportunity for smart, cost-effective, and nature-based solutions to historic societal challenges such as climate change, biodiversity loss, and food security. 

One of the project’s main objectives is to identify biodiversity, ecosystem condition, and ecosystem service factors that can be successfully integrated into decision-making processes in both the public and private sectors. 

To achieve this objective, SELINA will develop, test, and integrate new and existing knowledge, including methodological approaches to improve biodiversity, ecosystem condition, and ecosystem service information uptake by decision-makers. 

In addition, the project will utilise EU-wide workshops and multi-disciplinary Communities of Practice involving a wide range of stakeholders, including scientists, policymakers, business leaders, and civil society organisations. 

The project will also organise Demonstration Projects on biodiversity, ecosystem condition, and ecosystem service integration in decision-making and co-create a Compendium of Guidance that will allow stakeholders to make full use of the project’s results and fit-for-purpose recommendations with real-world applications in policy-making and business decisions. 

International consortium

SELINA project brings together experts from 50 partnering organisations across all European Union member states, Norway, Switzerland, Israel, and the United Kingdom.

The project comprises a Pan-European and transdisciplinary network of professionals from the academic and non-academic sectors with various (inter)disciplinary backgrounds – including ecologists, economists, social scientists – who have agreed to work collaboratively to support transformative change based on evidence-based decision-making related to the management of natural resources.

Find out more about the project on the SELINA website: project-selina.eu/.

Stay up to date with the project’s progress on Twitter, Facebook, Linkedin and YouTube.

BiCIKL Project supports article collection in Biodiversity Data Journal about use of linked data

Welcomed are taxonomic and other biodiversity-related research articles, which demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data

The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) will support free of charge publications* submitted to the dedicated topical collection: “Linking FAIR biodiversity data through publications: The BiCIKL approach” in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data, so that they can be easily harvested, distributed and re-used to generate new knowledge. 

BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc. to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles.

Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem.

The new article collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions, and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

To be eligible for the collection, a manuscript must comply with at least two of the conditions listed below. In the submission form, the author needs to specify the condition(s) applicable to the manuscript. The author should provide the explanation in a cover letter, using the Notes to the editor field.

All submissions must abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics. 

The data used in the articles must comply with the Data Quality Checklist and Fair Data Checklist available in the Authors’ instructions of the journal.

Conditions for publication in the article collection:

  • The authors are expected to use explicit Globally Unique Persistent and Resolvable Identifiers (GUPRI) or other persistent identifiers (PIDs), where such are available, for the different types of data they use and/or cite in the manuscripts (specimens IDs, sequence accession numbers, taxon name and taxon treatment IDs, image IDs, etc.)

  • Global taxon reviews in the form of “cyber-catalogues” are welcome if they contain links of the key data elements (specimens, sequences, taxon treatments, images, literature references, etc.) to their respective records in external repositories. Taxon names in the text should not be hyperlinked. Instead, under each taxon name in the catalogue, the authors should add external links to, for example, Catalogue of Life, nomenclators (e.g. IPNI, MycoBank, Index Fungorum, ZooBank), taxon treatments in Plazi’s TreatmentBank or other relevant trusted resources.

  • Taxonomic papers (e.g. descriptions of new species or revisions) must contain persistent identifiers for the holotype, paratypes and at least most of the specimens used in the study.

  • Specimen records that are used for new taxon descriptions or taxonomic revisions and are associated with a particular Barcode Identification Number (BIN) or Species Hypothesis (SH) should be imported directly from BOLD or PlutoF, respectively, via the ARPHA Writing Tool data-import plugin.

  • More generally, individual specimen records used for various purposes in taxonomic descriptions and inventories should be imported directly into the manuscript from GBIF, iDigBio, or BOLD via the ARPHA Writing Tool data-import plugin. 

  • In-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome in any taxonomic revision or catalogue. The in-text citations should be hyperlinked to the original treatment data at TreatmentBank.

  • Hyperlinking other terms of importance in the article text to their original external data sources or external vocabularies is encouraged.

  • Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s linked data tables guidelines.

  • Theoretical or methodological papers on linking FAIR biodiversity data are eligible for the BiCIKL collection if they provide real examples and use cases.

  • Data papers or software descriptions are eligible if they use linked data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.

  • Articles that contain nanopublications created or added during the authoring process in Biodiversity Data Journal. A nanopublication is a scientifically meaningful assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, for example biotic relationship between taxa, or habitat preference of a taxon. The in-built workflow ensures the linkage and its persistence, while the information is simultaneously human-readable and machine-interpretable.
  • Manuscripts that contain or describe any other novel idea or feature related to linked or semantically enhanced biodiversity data will be considered too.

We recommend authors to get acquainted with these two papers before they decide to submit a manuscript to the collection: 

Here are several examples of research questions that might be explored using semantically enriched and linked biodiversity data: 

(1) How does linking taxon names or Operational Taxonomic Units (OTUs) to related external data (e.g. specimen records, sequences, distributions, ecological & bionomic traits, images) contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?

(2) How could the production and publication of taxon descriptions and inventories – including those based mostly on genomic and barcoding data – be streamlined? 

(3) How could general conclusions, assertions and citations in biodiversity articles be expressed in formal, machine-actionable language, either to update prior work or express new facts (e.g. via nanopublications)? 

(4) How could research data and narratives be re-used to support more extensive and data-rich studies? 

(5) Are there other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR biodiversity data?

All manuscripts submitted to the Biodiversity Data Journal have their data audited by data scientists prior to the peer review stage.

Once published, specimen records data are being exported in Darwin Core Archive to GBIF.

The data and taxon treatments are also exported to several additional data aggregators, such as TreatmentBank, the Biodiversity Literature Repository, and SiBILS amongst others. The full-text articles are also converted to Linked Open Data indexed in the OpenBiodiv Knowledge Graph.

All articles will need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section.

* The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at € 650. Authors of larger manuscripts will need to cover the surplus charge (€10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net.

Follow the BiCIKL Project on Twitter and Facebook. Join the conservation on via #BiCIKL_H2020.

You can also follow Biodiversity Data Journal on Twitter and Facebook.

BiCIKL keeps on adding project outcomes in own collection in RIO Journal

The publications so far include the grant proposal; conference abstracts, a workshop report, guidelines papers and deliverables submitted to the Commission.

The dynamic open-science project collection of BiCIKL, titled “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” (doi: 10.3897/rio.coll.105), continues to grow, as the project progresses into its third year and its results accumulate ever so exponentially. 

Following the publication of three important BiCIKL deliverables: the project’s Data Management Plan, its Visual identity package and a report, describing the newly built workflow and tools for data extraction, conversion and indexing and the user applications from OpenBiodiv, there are currently 30 research outcomes in the BiCIKL collection that have been shared publicly to the world, rather than merely submitted to the European Commission.

Shortly after the BiCIKL project started in 2021, a project-branded collection was launched in the open-science scholarly journal Research Ideas and Outcomes (RIO). There, the partners have been publishing – and thus preserving – conclusive research papers, as well as early and interim scientific outputs.

The publications so far also include the BiCIKL grant proposal, which earned the support of the European Commission in 2021; conference abstracts, submitted by the partners to two consecutive TDWG conferences; a project report that summarises recommendations on interoperability among infrastructures, as concluded from a hackathon organised by BiCIKL; and two Guidelines papers, aiming to trigger a culture change in the way data is shared, used and reused in the biodiversity field. 

In fact, one of the Guidelines papers, where representatives of the Consortium of European Taxonomic Facilities (CETAF), the Society for the Preservation of Natural History Collections (SPNHC) and the Biodiversity Heritage Library (BHL) came together to publish their joint statement on best practices for the citation of authorities of scientific names, has so far generated about 4,000 views by nearly 3,000 unique readers.

At the time of writing, the top three of the most read papers in the BiCIKL collection is completed by the grant proposal and the second Guidelines paper, where the partners – based on their extensive and versatile experience – present recommendations about the use of annotations and persistent identifiers in taxonomy and biodiversity publishing. 

Access to data and services along the entire data and research life cycle in biodiversity science.
The figure was featured in the BiCIKL grant proposal, now made available from the BiCIKL project collection in RIO Journal.

What one might find quite odd when browsing the BiCIKL collection is that each publication is marked with its own publication source, even though all contributions are clearly already accessible from RIO Journal. 

So, we can see many project outputs marked as RIO publications, but also others that have been published in the likes of F1000Research, the official journal of TDWG: Biodiversity Information Science and Standards, and even preprints servers, such as BiohackrXiv. 

This is because one of the unique features of RIO allows for consortia to use their project collection as a one-stop access point for all scientific results, regardless of their publication venue, by means of linking to the original source via metadata. Additionally, projects may also upload their documents in their original format and layout, thanks to the integration between RIO and ARPHA Preprints. This is in fact how BiCIKL chose to share their latest deliverables using the very same files they submitted to the Commission.

“In line with the mission of BiCIKL and our consortium’s dedication to FAIRness in science, we wanted to keep our project’s progress and results fully transparent and easily accessible and reusable to anyone, anywhere,” 

explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft. 

“This is why we opted to collate the outcomes of BiCIKL in one place – starting from the grant proposal itself, and then progressively adding workshop reports, recommendations, research papers and what not. By the time BiCIKL concludes, not only will we be ready to refer back to any step along the way that we have just walked together, but also rest assured that what we have achieved and learnt remains at the fingertips of those we have done it for and those who come after them,” he adds.

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You can keep tabs on the BiCIKL project collection in RIO Journal by subscribing to the journal newsletter or following @RIOJournal on Twitter and Facebook.