Mention fungi, and most people will probably think of the mushrooms they pick in fall, or maybe the yeast they add when baking or making wine. Others will perhaps recall last week’s mouldy bread – or cucumbers gone bad in the refrigerator. Indeed, mycologists have studied these fungi as sources of food and fermentation but also decay and disease for centuries.
Sampling soil and sediments for fungal diversity not far from Göteborg, Sweden. Photo by Henrik Nilsson
But while we’re used to thinking of fungi as organisms that form physical structures such as fruiting bodies, or yeast-like life forms that we can grow in our kitchens or laboratories, it is gradually becoming clear that fungi don’t readily assort into only these two groups. DNA sequencing studies of environmental substrates such as soil are finding massive evidence of large groups of fungi that do not seem to form fruiting bodies and that we seem unable to grow in the lab – but that are there nonetheless. These groups are often called “dark fungi,” in analogy with the concept of “dark matter” in astronomy – something we know is out there, but that we cannot directly observe right now.
A new study in MycoKeys contrasts the accumulation of fungal species recovered using traditional mycological approaches with those recovered using environmental DNA sequencing over time. Even when allowing for various kinds of biases, the authors found that species discovery through environmental sequencing vastly outpaces traditional species recovery in a strongly increasing trend over the last five years. The authors conclude that dark fungi form a defining feature of the fungal kingdom.
Field work on the Tibetan Plateau. Photo by Wengang Kang
“And that’s where it gets interesting”, Henrik Nilsson at the University of Gothenburg, Sweden, and the lead author of the study, says. “Under the current rules of nomenclature, these fungi cannot be given scientific names – they cannot be described formally. And species and groups that cannot be named formally, well, they tend to fall between the cracks. They’re typically not considered in nature conservation initiatives. They are often left out from efforts to estimate the evolutionary history of fungi, and their ecological roles and associations are largely overlooked when we try to figure out how mass and energy flow in ecosystems. They’re essentially treated as if they didn’t exist.”
Examining minute fungal fruiting bodies not far from Stockholm, Sweden. Photo by Kristina Stenmarck
Second author Martin Ryberg at the University of Uppsala, Sweden chimes in, “And it’s not like we’re adding the few missing pieces to an otherwise nearly complete jigsaw puzzle. It seems to be the other way around. We’re talking about tens of large groups of fungi – and thousands upon thousands of species, some of which seem to be so common that we have yet to find a soil sample from which they’re absent. Indeed, we’re talking about what could well prove to be the dominant life style in the fungal kingdom.”
The mycological community has been debating whether the rules of fungal nomenclature should be modified to allow formal description of these dark fungi. So far, the matter has not been resolved in the affirmative. “I think our study shows that it’s time to stop that debate, like, right away,” Nilsson says. “What we should be debating is how we should describe them. What criteria must be fulfilled for a dark fungus to be given a formal scientific name? Clearly, formation of a fruiting body or growth in the laboratory can’t be part of those criteria.”
Field work in New Caledonia. Photo by Sten Anslan
Co-author Alice Retter of the University of Vienna, Austria explains, “We figured we’d kickstart the how debate by listing criteria that we think make sense – criteria that would be stringent enough to allow for only particularly well-vetted dark fungi to be described, upholding a high level of scientific rigor and reproducibility in the process. We blended our own observations with suggestions from the mycological community, culled from depositing a preprint of the manuscript at bioRxiv. We’re certainly not claiming that our suggestions form the final word in the debate. It’s more like they’re the first. We’re thinking that the mycological community will jointly be able to come up with a set of sound guiding principles on the matter – and here comes an initial set of well-meaning observations for nucleation.”
Field work in the German Alps. Photo by Vanessa Schulz
The authors advocate gentle modifications to the nomenclatural rules governing the naming of fungi to allow giving formal names to at least the most well-documented species and groups of dark fungi. The suggested modifications would, at present, exclude many rare or otherwise less well-documented dark fungi from formal description.
“But you don’t have to have a theory of everything to have a theory of something,” senior author Kessy Abarenkov of the Tartu Natural History Museum, Estonia asserts. “By establishing rules for what’s needed to describe dark fungi, and specifying when we’ll have to refrain from describing such species at present, mycologists can do what they do best: doggedly gather enough research data to warrant naming of the dark fungi, group by group, and species by species. It’s what mycology has excelled at for hundreds of years. It’s just the setting that’s a bit new.”
Drying soil samples immediately upon collection under field conditions in Norway. Photo by Sten Anslan
Sten Anslan, University of Tartu, continues: “Much is at stake, obviously. The current rules governing the naming of fungi have served mycology well for a long time. We don’t want to upend or overthrow them. But we fear that if they’re not updated in this particular regard, there’s a risk that they grow increasingly obsolete over time. Having a book of rules that govern maybe only some few percent of the organisms it was originally conceived to govern – the fungal kingdom – would seem untenable in the long run.”
Getting ready for DNA extraction from soil samples. Photo by Sten Anslan
Marisol Sanchez-Garcia of the Swedish Agricultural University concludes: “The nomenclatural aspects of dark fungi will presumably be discussed at some length at next year’s international mycological congress in Maastricht, the Netherlands. We’re hopeful that the mycological community will reach meaningful agreement on integration of the dark fungi into the rules of nomenclature. After all, mycologists are used to negotiating and solving non-trivial questions on a day-to-day basis, and this one is hardly any different. Being part of tackling a huge, more or less unknown group of organisms where precious little is set in stone and where the rules will have to be adapted over time for the endeavour to stay attuned to recent developments, well, that’s what makes being a mycologist so interesting and rewarding in my eyes.”
Research article:
Nilsson RH, Ryberg M, Wurzbacher C, Tedersoo L, Anslan S, Põlme S, Spirin V, Mikryukov V, Svantesson S, Hartmann M, Lennartsdotter C, Belford P, Khomich M, Retter A, Corcoll N, Gómez Martinez D, Jansson T, Ghobad-Nejhad M, Vu D, Sanchez-Garcia M, Kristiansson E, Abarenkov K (2023) How, not if, is the question mycologists should be asking about DNA-based typification. MycoKeys 96: 143-157. https://doi.org/10.3897/mycokeys.96.102669
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.
In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.
“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”
explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.
“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”
he adds.
At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.
Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL.
As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions.
Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.
Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.
On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.
“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”
All journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
In support of transparency and openness in scholarly publishing and academia, the scientific publisher and technology provider Pensoft joined the Journal Comparison Service (JCS) initiative by cOAlition S, an alliance of national funders and charitable bodies working to increase the volume of free-to-read research.
As a result, all journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
The JCS was launched to aid libraries and library consortia – the ones negotiating and participating in Open Access agreements with publishers – by providing them with everything they need to know in order to determine whether the prices charged by a certain journal are fair and corresponding to the quality of the service.
According to cOAlition S, an increasing number of libraries and library consortia from Europe, Africa, North America, and Australia have registered with the JCS over the past year since the launch of the portal in September 2021.
While access to the JCS is only open to librarians, individual researchers may also make use of the data provided by the participating publishers and their journals.
This is possible through an integration with the Journal Checker Tool, where researchers can simply enter the name of the journal of interest, their funder and affiliation (if applicable) to check whether the scholarly outlet complies with the Open Access policy of the author’s funder. A full list of all academic titles that provide data to the JCS is also publicly available. By being on the list means a journal and its publisher do not only support cOAlition S, but they also demonstrate that they stand for openness and transparency in scholarly publishing.
“We are delighted that Pensoft, along with a number of other publishers, have shared their price and service data through the Journal Comparison Service. Not only are such publishers demonstrating their commitment to open business models and cultures but are also helping to build understanding and trust within the research community.”
said Robert Kiley, Head of Strategy at cOAlition S.
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About cOAlition S:
On 4 September 2018, a group of national research funding organisations, with the support of the European Commission and the European Research Council (ERC), announced the launch of cOAlition S, an initiative to make full and immediate Open Access to research publications a reality. It is built around Plan S, which consists of one target and 10 principles. Read more on the cOAlition S website.
About Plan S:
Plan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. Read more on the cOAlition S website.
The FAIR Data Place – the key and final product of the partnership – is meant to provide scientists with all types of biodiversity data “at their fingertips”
The Horizon 2020 – funded project BiCIKL has reached its halfway stage and the partners gathered in Plovdiv (Bulgaria) from the 22nd to the 25th of October for the Second General Assembly, organised by Pensoft.
The BiCIKL project will launch a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in the biodiversity and life sciences based on open science practices through access to data, tools and services.
BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 research infrastructures and their databases. The 3-year European Commission-supported initiative kicked off in 2021 and involves 14 key natural history institutions from 10 European countries.
BiCIKL is keeping pace as expected with 16 out of the 48 final deliverables already submitted, another 9 currently in progress/under review and due in a few days. Meanwhile, 21 out of the 48 milestones have been successfully achieved.
Prof. Lyubomir Penev (BiCIKL’s project coordinator Prof. Lyubomir Penev and CEO and founder of Pensoft) opens the 2nd General Assembly of BiCIKL in Plovdiv, Bulgaria.
The hybrid format of the meeting enabled a wider range of participants, which resulted in robust discussions on the next steps of the project, such as the implementation of additional technical features of the FAIR Data Place (FAIR being an abbreviation for Findable, Accessible, Interoperable and Reusable).
This FAIR Data Place online platform – the key and final product of the partnership and the BiCIKL initiative – is meant to provide scientists with all types of biodiversity data “at their fingertips”.
This data includes biodiversity information, such as detailed images, DNA, physiology and past studies concerning a specific species and its ‘relatives’, to name a few. Currently, the issue is that all those types of biodiversity data have so far been scattered across various databases, which in turn have been missing meaningful and efficient interconnectedness.
Additionally, the FAIR Data Place, developed within the BiCIKL project, is to give researchers access to plenty of training modules to guide them through the different services.
Halfway through the duration of BiCIKL, the project is at a turning point, where crucial discussions between the partners are playing a central role in the refinement of the FAIR Data Place design. Most importantly, they are tasked with ensuring that their technologies work efficiently with each other, in order to seamlessly exchange, update and share the biodiversity data every one of them is collecting and taking care of.
By Year 3 of the BiCIKL project, the partners agree, when those infrastructures and databases become efficiently interconnected to each other, scientists studying the Earth’s biodiversity across the world will be in a much better position to build on existing research and improve the way and the pace at which nature is being explored and understood. At the end of the day, knowledge is the stepping stone for the preservation of biodiversity and humankind itself.
The Biodiversity Knowledge Hub is no longer existing on paper only! We are opening the 2nd day of the #BiCIKL_H2020 General Assembly looking at the prototype of the BKH created by the @LifeWatchERIC team. It's so exciting to see projects taking shape! 🤩 #Plovdivpic.twitter.com/RidzwBpxZx
“Needless to say, it’s an honour and a pleasure to be the coordinator of such an amazing team spanning as many as 14 partnering natural history and biodiversity research institutions from across Europe, but also involving many global long-year collaborators and their infrastructures, such as Wikidata, GBIF, TDWG, Catalogue of Life to name a few,”
said BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft.
“I see our meeting in Plovdiv as a practical demonstration of our eagerness and commitment to tackle the long-standing and technically complex challenge of breaking down the silos in the biodiversity data domain. It is time to start building freeways between all biodiversity data, across (digital) space, time and data types. After the last three days that we spent together in inspirational and productive discussions, I am as confident as ever that we are close to providing scientists with much more straightforward routes to not only generate more biodiversity data, but also build on the already existing knowledge to form new hypotheses and information ready to use by decision- and policy-makers. One cannot stress enough how important the role of biodiversity data is in preserving life on Earth. These data are indeed the groundwork for all that we know about the natural world”
Prof. Lyubomir Penev added.
Christos Arvanitidis (CEO of LifeWatch ERIC) at the 2nd General Assembly of the BiCIKL project.
“The point is: do we want an integrated structure or do we prefer federated structures? What are the pros and cons of the two options? It’s essential to keep the community united and allied because we can’t afford any information loss and the stakeholders should feel at home with the Project and the Biodiversity Knowledge Hub.”
Joe Miller, Executive Secretary and Director at GBIF, commented:
“We are a brand new community, and we are in the middle of the growth process. We would like to already have answers, but it’s good to have this kind of robust discussion to build on a good basis. We must find the best solution to have linkages between infrastructures and be able to maintain them in the future because the Biodiversity Knowledge Hub is the location to gather the community around best practices, data and guidelines on how to use the BiCIKL services… In order to engage even more partners to fill the eventual gaps in our knowledge.”
Joana Pauperio (biodiversity curator at EMBL-EBI) atthe 2nd General Assembly of the BiCIKL project.
“BiCIKL is leading data infrastructure communities through some exciting and important developments”
said Dr Guy Cochrane, Team Leader for Data Coordination and Archiving and Head of the European Nucleotide Archive at EMBL’s European Bioinformatics Institute (EMBL-EBI).
“In an era of biodiversity change and loss, leveraging scientific data fully will allow the world to catalogue what we have now, to track and understand how things are changing and to build the tools that we will use to conserve or remediate. The challenge is that the data come from many streams – molecular biology, taxonomy, natural history collections, biodiversity observation – that need to be connected and intersected to allow scientists and others to ask real questions about the data. In its first year, BiCIKL has made some key advances to rise to this challenge,”
“As a partner, we, at the Biodiversity Information Standards – TDWG, are very enthusiastic that our standards are implemented in BiCIKL and serve to link biodiversity data. We know that joining forces and working together is crucial to building efficient infrastructures and sharing knowledge.”
The project will go on with the first Round Table of experts in December and the publications of the projects who participated in the Open Call and will be founded at the beginning of the next year.
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Learn more about BiCIKL on the project’s website at: bicikl-project.eu
For the 37th time, experts from across the world to share and discuss the latest developments surrounding biodiversity data and how they are being gathered, used, shared and integrated across time, space and disciplines.
Between 17th and 21st October, about 400 scientists and experts took part in a hybrid meeting dedicated to the development, use and maintenance of biodiversity data, technologies, and standards across the world.
For the 37th time, the global scientific and educational association Biodiversity Information Standards (TDWG) brought together experts from all over the globe to share and discuss the latest developments surrounding biodiversity data and how they are being gathered, used, shared and integrated across time, space and disciplines.
This was the first time the event happened in a hybrid format. It was attended by 160 people on-site, while another 235 people joined online.
The TDWG 2022 conference saw plenty of networking and engaging discussions with as many as 160 on-site attendees and another 235 people, who joined the event remotely.
“It’s wonderful to be in the Balkans and Bulgaria for our Biodiversity Information and Standards (TDWG) 2022 conference! Everyone’s been so welcoming and thoughtfully engaged in conversations about biodiversity information and how we can all collaborate, contribute and benefit,”
“Our TDWG mission is to create, maintain and promote the use of open, community-driven standards to enable sharing and use of biodiversity data for all,”
she added.
Prof Lyubomir Penev (Pensoft) and Deborah Paul (TDWG) at TDWG 2022.
“We are proud to have been selected to be the hosts of this year’s TDWG annual conference and are definitely happy to have joined and observed so many active experts network and share their know-how and future plans with each other, so that they can collaborate and make further progress in the way scientists and informaticians work with biodiversity information,”
said Pensoft’s founder and CEO Prof. Lyubomir Penev.
“As a publisher of multiple globally renowned scientific journals and books in the field of biodiversity and ecology, at Pensoft we assume it to be our responsibility to be amongst the first to implement those standards and good practices, and serve as an example in the scholarly publishing world. Let me remind you that it is the scientific publications that present the most reliable knowledge the world and science has, due to the scrutiny and rigour in the review process they undergo before seeing the light of day,”
he added.
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In a nutshell, the main task and dedication of the TDWG association is to develop and maintain standards and data-sharing protocols that support the infrastructures (e.g., The Global Biodiversity Information Facility – GBIF), which aggregate and facilitate use of these data, in order to inform and expand humanity’s knowledge about life on Earth.
It is the goal of everyone at TDWG to let scientists interested in the world’s biodiversity to do their work efficiently and in a manner that can be understood, shared and reused.
It is the goal of everyone volunteering their time and expertise to TDWG to enable the scientists interested in the world’s biodiversity to do their work efficiently and in a manner that can be understood, shared and reused by others. After all, biodiversity data underlie everything we know about the natural world.
If there are optimised and universal standards in the way researchers store and disseminate biodiversity data, all those biodiversity scientists will be able to find, access and use the knowledge in their own work much more easily. As a result, they will be much better positioned to contribute new knowledge that will later be used in nature and ecosystem conservation by key decision-makers.
On Monday, the event opened with welcoming speeches by Deborah Paul and Prof. Lyubomir Penev in their roles of the Chair of TDWG and the main host of this year’s conference, respectively.
The opening ceremony continued with a keynote speech by Prof. Pavel Stoev, Director of the Natural History Museum of Sofia and co-host of TDWG 2022.
Prof. Pavel Stoev (Natural History Museum of Sofia) with a presentation about the known and unknown biodiversity of Bulgaria during the opening plenary session of TDWG 2022.
He walked the participants through the fascinating biodiversity of Bulgaria, but also the worrying trends in the country associated with declining taxonomic expertise.
He finished his talk with a beam of hope by sharing about the recently established national unit of DiSSCo, whose aim – even if a tad too optimistic – is to digitise one million natural history items in four years, of which 250,000 with photographs. So far, one year into the project, the Bulgarian team has managed to digitise more than 32,000 specimens and provide images to 10,000 specimens.
The plenary session concluded with a keynote presentation by renowned ichthyologist and biodiversity data manager Dr. Richard L. Pyle, who is also a manager of ZooBank – the key international database for newly described species.
Keynote presentation by Dr Richard L. Pyle (Bishop Museum, USA) at the opening plenary session of TDWG 2022.
In his talk, he highlighted the gaps in the ways taxonomy is being used, thereby impeding biodiversity research and cutting off a lot of opportunities for timely scientific progress.
“There are simple things we can do to change how we use taxonomy as a tool that would dramatically improve our ability to conduct science and understand biodiversity. There is enormous value and utility within existing databases around the world to understand biodiversity, how threatened it is, what impacts human activity has (especially climate change), and how to optimise the protection and preservation of biodiversity,”
he said in an interview for a joint interview by the Bulgarian News Agency and Pensoft.
“But we do not have easy access to much of this information because the different databases are not well integrated. Taxonomy offers us the best opportunity to connect this information together, to answer important questions about biodiversity that we have never been able to answer before. The reason meetings like this are so important is that they bring people together to discuss ways of using modern informatics to greatly increase the power of the data we already have, and prioritise how we fill the gaps in data that exist. Taxonomy, and especially taxonomic data integration, is a very important part of the solution.”
Pyle also commented on the work in progress at ZooBank ten years into the platform’s existence and its role in the next (fifth) edition of the International Code of Zoological Nomenclature, which is currently being developed by the International Commission of Zoological Nomenclature (ICZN).
“We already know that ZooBank will play a more important role in the next edition of the Code than it has for these past ten years, so this is exactly the right time to be planning new services for ZooBank. Improvements at ZooBank will include things like better user-interfaces on the web to make it easier and faster to use ZooBank, better data services to make it easier for publishers to add content to ZooBank as part of their publication workflow, additional information about nomenclature and taxonomy that will both support the next edition of the Code, and also help taxonomists get their jobs done more efficiently and effectively. Conferences like the TDWG one are critical for helping to define what the next version of ZooBank will look like, and what it will do.”
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During the week, the conference participants had the opportunity to enjoy a total of 140 presentations; as well as multiple social activities, including a field trip to Rila Monastery and a traditional Bulgarian dinner.
TDWG 2022 conference participants document their species observations on their way to Rila Monastery.
While going about the conference venue and field trip localities, the attendees were also actively uploading their species observations made during their stay in Bulgaria on iNaturalist in a TDWG2022-dedicated BioBlitz. The challenge concluded with a total of 635 observations and 228 successfully identified species.
Amongst the social activities going on during TDWG 2022 was a BioBlitz, where the conference participants could uploade their observations made in Bulgaria on iNaturalist and help each other successfully identify the specimens.
“Biodiversity provides the support systems for all life on Earth. Yet the natural world is in peril, and we face biodiversity and climate emergencies. The consequences of these include accelerating extinction, increased risk from zoonotic disease, degradation of natural capital, loss of sustainable livelihoods in many of the poorest yet most biodiverse countries of the world, challenges with food security, water scarcity and natural disasters, and the associated challenges of mass migration and social conflicts.
Solutions to these problems can be found in the data associated with natural science collections. DiSSCo is a partnership of the institutions that digitise their collections to harness their potential. By bringing them together in a distributed, interoperable research infrastructure, we are making them physically and digitally open, accessible, and usable for all forms of research and innovation.
At present rates, digitising all of the UK collection – which holds more than 130 million specimens collected from across the globe and is being taken care of by over 90 institutions – is likely to take many decades, but new technologies like machine learning and computer vision are dramatically reducing the time it will take, and we are presently exploring how robotics can be applied to accelerate our work.”
In his turn, Dr Donat Agosti, CEO and Managing director at Plazi – a not-for-profit organisation supporting and promoting the development of persistent and openly accessible digital taxonomic literature – said:
“All the data about biodiversity is in our libraries, that include over 500 million pages, and everyday new publications are being added. No person can read all this, but machines allow us to mine this huge, very rich source of data. We do not know how many species we know, because we cannot analyse with all the scientists in this library, nor can we follow new publications. Thus, we do not have the best possible information to explore and protect our biological environment.”
Dr Donat Agosti demonstrating the importance of publishing biodiversity data in a structured and semantically enhanced format in one of his presentations at TDWG 2022.
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At the closing plenary session, Gail Kampmeier – TDWG Executive member and one of the first zoologists to join TDWG in 1996 – joined via Zoom to walk the conference attendees through the 37-year history of the association, originally named the Taxonomic Databases Working Group, but later transformed to Biodiversity Information Standards, as it expanded its activities to the whole range of biodiversity data.
“While this presentation is about TDWG’s history as an organisation, its focus will be on the heart of TDWG: its people. We would like to show how the organisation has evolved in terms of gender balance, inclusivity actions, and our engagement to promote and enhance diversity at all levels. But more importantly, where do we—as a community—want to go in the future?”,
Then, in the final talk of the session, Deborah Paul took to the stage to present the progress and key achievements by the association from 2022.
🤩Year in review by @idbdeb at #TDWG2022: many wonderful achievements & even more in the works!🙌 E.g.✅Memorandum of Understanding with Genomic Standards Consortium ✅new Mineralogy Task Group ✅new vision & mission statement ✅collaboration with @GBIF on the new data model.. 1/ pic.twitter.com/RZx8hlePOm
Deborah Paul reminds that – apart from the conference abstracts – the TDWG journal: Biodiversity Information Science and Standards (BISS) also welcomes full-lenght articles that demonstrate the development or application of new methods and approaches in biodiversity informatics.
Launched in 2017 on the Pensoft’s publishing platform ARPHA, the journal provides the quite unique and innovative opportunity to have both abstracts and full-length research papers published in a modern, technologically-advanced scholarly journal. In her speech, Deborah Paul reminded that BISS journal welcomes research articles that demonstrate the development or application of new methods and approaches in biodiversity informatics in the form of case studies.
Amongst the achievements of TDWG and its community, a special place was reserved for the Horizon 2020-funded BiCIKL project (abbreviation for Biodiversity Community Integrated Knowledge Library), involving many of the association’s members.
Having started in 2021, the 3-year project, coordinated by Pensoft, brings together 14 partnering institutions from 10 countries, and 15 biodiversity under the common goal to create a centralised place to connect all key biodiversity data by interlinking a total of 15 research infrastructures and their databases.
Deborah Paul also reported on the progress of the Horizon 2020-funded project BiCIKL, which involves many of the TDWG members. BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 key research infrastructures and their databases.
In fact, following the week-long TDWG 2022 conference in Sofia, a good many of the participants set off straight for another Bulgarian city and another event hosted by Pensoft. The Second General Assembly of BiCIKL took place between 22nd and 24th October in Plovdiv.
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You can also explore highlights and live tweets from TDWG 2022 on Twitter via #TDWG2022.
The Pensoft team at TDWG 2022 were happy to become the hosts of the 37th TDWG conference.
By the time authors – who have acknowledged third-party financial support in their research papers submitted to a journal using the Pensoft-developed publishing platform: ARPHA – open their inboxes to the congratulatory message that their work has just been published and made available to the wide world, a similar notification will have also reached their research funder.
This automated workflow is already in effect at all journals (co-)published by Pensoft and those published under their own imprint on the ARPHA Platform, as a result of the new partnership with the OA Switchboard: a community-driven initiative with the mission to serve as a central information exchange hub between stakeholders about open access publications, while making things simpler for everyone involved.
All the submitting author needs to do to ensure that their research funder receives a notification about the publication is to select the supporting agency or the scientific project (e.g. a project supported by Horizon Europe) in the manuscript submission form, using a handy drop-down menu. In either case, the message will be sent to the funding body as soon as the paper is published in the respective journal.
“At Pensoft, we are delighted to announce our integration with the OA Switchboard, as this workflow is yet another excellent practice in scholarly publishing that supports transparency in research. Needless to say, funding and financing are cornerstones in scientific work and scholarship, so it is equally important to ensure funding bodies are provided with full, prompt and convenient reports about their own input.”
comments Prof Lyubomir Penev, CEO and founder of Pensoft and ARPHA.
“Research funders are one of the three key stakeholder groups in OA Switchboard and are represented in our founding partners. They seek support in demonstrating the extent and impact of their research funding and delivering on their commitment to OA. It is great to see Pensoft has started their integration with OA Switchboard with a focus on this specific group, fulfilling an important need,”
adds Yvonne Campfens, Executive Director of the OA Switchboard.
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About the OA Switchboard:
A global not-for-profit and independent intermediary established in 2020, the OA Switchboard provides a central hub for research funders, institutions and publishers to exchange OA-related publication-level information. Connecting parties and systems, and streamlining communication and the neutral exchange of metadata, the OA Switchboard provides direct, indirect and community benefits: simplicity and transparency, collaboration and interoperability, and efficiency and cost-effectiveness.
About Pensoft:
Pensoft is an independent academic publishing company, well known worldwide for its novel cutting-edge publishing tools, workflows and methods for text and data publishing of journals, books and conference materials.
All journals (co-)published by Pensoft are hosted on Pensoft’s full-featured ARPHA Publishing Platform and published in a way that ensures their content is as FAIR as possible, meaning that it is effortlessly readable, discoverable, harvestable, citable and reusable by both humans and machines.
Fusarium is one of the most important fungal plant pathogens, affecting the cultivation of a wide range of crops. All over the world, thousands of farmers suffer agricultural losses caused by Fusarium oxysporum f. sp. cubense (referred to as Foc for short), which directly affects their income, subsistence, and nourishment.
As a soil-borne fungus, Foc invades the root system, from where it moves into the vascular tissue that gradually deteriorates, until eventually the plant dies. What makes it particularly hard to deal with is that, even 20 years after all infected plants and tissue are removed, spores of it still remain in the soil.
One industry significantly affected by Foc is global banana export, largely dependent on the cultivation of members of the Cavendish subgroup, which are highly susceptible to some of the Foc strains.
For over 100 years, the fungus has affected banana production worldwide. Researchers predict it will continue spreading intensively in Asia, affecting important banana-producing countries such as China, the Philippines, Pakistan, and Viet Nam.
For Viet Nam, predictions on the impact of Foc for the future are dramatic: an estimated loss in the banana production area of 8% within the next five years, and up to 71% within the next 25 years. In particular, the recent rise of the novel TR4 strain has resulted in worldwide anxiety about the future of the well-known Cavendish banana and many other cultivars. Fusarium oxysporum f. sp. cubense is, however, not limited to TR4 or other well-known strains, like Race 1 or Race 2; it is a species complex that plant pathologists are yet to fully disentangle.
In Viet Nam, like in the rest of Asia, Africa, Latin America, and the Caribbean, most bananas are consumed and traded locally, supporting rural livelihood. This means that any reduction in crop harvest directly affects local people’s income and nourishment.
It has thus become necessary to find out what are the individual species causing the Fusarium wilt among Vietnamese bananas. Only by understanding which species are infecting the cultivated bananas can concrete measures be taken to control the future spreading of the disease to other regions.
The study shows that approximately 3 out of 4 Fusariuminfections of the northern Vietnamese bananas are caused by the species F. tardichlamydosporum, which can be regarded as the typical Race 1 infections. Interestingly, Foc TR4 is not yet a dominant strain in northern Viet Nam, as the species causing the disease – F.odoratissimum – only accounts for 10% of the Fusarium infections. A similar proportion of Fusarium infections is caused by the species Fusarium cugenangense – considered to cause Race 2 infections among bananas.More importantly, Fusarium wilt was not only found in cultivated bananas: the disease seemed to also affect wild bananas. This finding indicates that wild bananas might function as a sink for Fusarium wilt from where reinfections towards cultivars could take place.
Research article:
Le Thi L, Mertens A, Vu DT, Vu TD, Anh Minh PL, Duc HN, de Backer S, Swennen R, Vandelook F, Panis B, Amalfi M, Decock C, Gomes SIF, Merckx VSFT, Janssens SB (2022) Diversity of Fusarium associated banana wilt in northern Viet Nam. MycoKeys 87: 53-76. https://doi.org/10.3897/mycokeys.87.72941
With 2022 round the corner, we thought we’d start off the celebrations by looking back to some the most memorable discoveries of 2021. And what a year it has been! Many new species made their debuts on the pages of Pensoft journals – here’s our selection of the most exciting animals, plants and fungi that we published in 2021.
With 2022 round the corner, we thought we’d start off the celebrations by looking back to some the most memorable discoveries of 2021. And what a year it has been! Many new species made their debuts on the pages of Pensoft journals – here’s our selection of the most exciting animals, plants and fungi that we published in 2021.
10. The delicious wild oak mushroom
It’s amazing that edible species, long known to local communities, can still present a novelty for science. This was the case with Cantharellus veraecrucis, a chanterelle from – that’s right, Veracruz, Mexico.
During the rainy season, locals harvest this mushroom from tropical oak forests to sell it or enjoy it as a delicacy; this is probably why they’ve dubbed it “Oak mushroom”.
If you ever see a leaf insect, there’s a good chance you won’t notice it – these little critters are masters of camouflaging.
This picture was taken in 2014, when Jérôme Constant and Joachim Bresseel from the Royal Belgian Institute of Natural Sciences were enjoying a night walk in Vietnam’s Nui Chua National Park. It wasn’t until this year, though, that this beauty got its own scientific name: Cryptophyllium nuichuaense. Named after the park where it was found, it is oneof 13 new species of leaf insects described in our journal ZooKeysthis February.
This leaf insect, like many others, is endemic to Vietnam. This is why the researchers who found itcall for the creation of more protected areas in order to keep this precious biodiversity intact.
Unlike most spiders, trapdoor spiders don’t use silk to make a web. Instead, they live in burrows lined with silk that they cover with a “trapdoor”. They are relatively widely spread, but you’d rarely encounter one out in the open, because they spend most of their lives underground.
This is probably why arachnologists and spider lovers the world over got so excited when Dr. Rebecca Godwin (Piedmont University, GA) and Dr. Jason Bond (University of California, Davis, CA) described 33 new species of trapdoor spiders from the genus Ummidia – in addition to the 27 already known.
Dr. Rebecca Godwin talks to L. Brian Patrick about her discovery of 33 new species of trapdoor spiders on his podcast New Species.
One of the 33 is Ummidia neilgaimani, named after fantasy and horror writer Neil Gaiman. A particular favorite of Dr. Godwin, Gaiman is the author of a number of books with spider-based characters. His novel American Gods features a character based on the West African spider god Anansi and a World Tree “one hour south of Blacksburg,” not far from the type locality of this species. He’s also part of the documentary Sixteen Legs, in his own words “An amazing film about Tasmanian cave spider sex.”
“I think anything we can do to increase people’s interest in the diversity around them is worthwhile and giving species names that people recognize but that still have relevant meaning is one way to do that,” says Dr. Godwin.
Bungarus suzhenaewas only described as a new species this year, but its reputation preceded it – in a bad way. Researchers were already familiar with a notorious black-and-white banded krait that bit herpetologists on expeditions in Myanmar and China – in one infamous case, to death. After extensive morphological and phylogenetical analysis, the researchers were finally able to confirm it as new to science.
The story behind B. suzhenae’s name is interesting, too: it was named after a character from the traditional Chinese myth ‘Legend of White Snake’. The powerful snake goddess Bai Su Zhen is to this day regarded as a symbol of true love and good-heartedness in China.
Snakebites from kraits – including this one – are known to have a high mortality. This is why the new knowledge on B. suzhenae and its description as a new species are essential to the research on its venom and an important step in the development of antivenom and improved snakebite treatment.
Commonly known as “fairy lanterns”, plants of the genus Thismia are very rare and small in size. They are mycoheterotrophic, which means they live in close association with fungi from which they acquire most of their nutrition. They’re also very elusive, growing in dark, remote rainforests, and visible only when they emerge to flower and set seed after heavy rain.
In fact, researchers were only able to find one specimen of the new T. sitimeriamiae, which they discovered in the Terengganu State of Malaysia – the rest of the population had been destroyed by wild boars.
Just discovered, T. sitimeriamiae may already be threatened by extinction – which is why the research team that discovered it suggest that this exceptionally rare plant is classified as Critically Endangered.
Developing below the soil surface, desert truffles are hard to find. Recently, researchers of the University of Évora updated the number of known species of the desert truffle genus Terfezia occurring in Portugal from three to ten species. They thoroughly characterized their ecological preferences, adding new knowledge on Terfezia’s cryptic lifestyle. These findings are of major importance, as desert truffles have a high economic value. The study was published in the open-access journal MycoKeys.
In a caring, symbiotic relationship, mycorrhizal fungi live and feed in the roots of specific plants, while providing water and nutrients to their ‘companion’. In arid and semi-arid environments, mycorrhization processes are essential to the survival of both plants and fungi. Moreover, the fungus’ hyphal network, which spreads within the soil connecting several plant individuals, is of utmost importance to enhancing soil quality and fertility.
Researchers of the University of Évora in Portugal, led by biologist Celeste Santos e Silva, worked on Terfezia fungi, the most diverse and species-rich genus among desert truffles. Their study, published in the open-access journal MycoKeys, might prove particularly valuable to rural populations in the Mediterranean basin, where desert truffles, highly valued in local markets, are an important food source. Increasingly turning into an exquisite component of the Mediterranean diet, Terfezia products can also be very profitable. Furthermore, these fungi are essential for soil conservation, preventing erosion and desertification.
Desert truffles.
After 8 years of exhaustive field exploration in search of desert truffles and many hours in the molecular biology lab, the researchers noted some previously unknown trends in the ecology of Terfezia species. They recorded seven species that were new to Portugal, including two that are new to science – Terfezia lusitanica and Terfezia solaris-libera. This brings the number of Terfezia species known to be growing in the country to ten. Particularly important was the discovery of a broader ecological range for many of the studied species (e.g. Terfezia grisea). Adding valuable information about their possible hosts, symbionts and ecological constraints, these findings help open new opportunities for truffle cultivation.
“It is very difficult to identify all specimens given that the Terfezia species look so much alike, and molecular biology was absolutely fundamental here”, explains the researcher. “The technique was essential to update and solve problems about their taxonomy and the relationship between the species in the genus.”
Furthermore, the discoveries are also expected to positively impact the local communities by stimulating agriculture produce, business and even employment.
Desert truffle production explained. Video by University of Évora
Knowledge gained in this research about the conditions in which different Terfezia species grow is an important step to desert truffle cultivation: the fungi are hard to find in the wild, which is why it would make a big difference – including financially – for local communities if they figure out a way to grow truffles themselves.
Within the project “Mycorrhization of Cistus spp with Terfezia arenaria (Moris) Trappe and its application in the production of desert truffles” (ALT20-03-0145-FEDER-000006), the researchers took a step forward towards achieving mycorrhizal association of desert truffles with perennial plants (rock roses), which would allow their mass production for various sectors such as food, medicine and soil recovery. This new form of production, assures the MED researcher and leader of the project, “will make it possible to create more jobs, reversing the current trend towards desertification in rural areas, while being a great tool for ecosystem recovery and restoration”.
Research article:
Santos-Silva C, Louro R, Natário B, Nobre T (2021) Lack of knowledge on ecological determinants and cryptic lifestyles hinder our understanding of Terfezia diversity. MycoKeys 84: 1-14. https://doi.org/10.3897/mycokeys.84.71372
A major comprehensive study on Herpomycetales and Laboulbeniales, two orders of unique ectoparasitic fungi associated with insects and other arthropods (class Laboulbeniomycetes) in Belgium and the Netherlands was published in the open-access, peer-reviewed scholarly journal MycoKeys.
A major comprehensive study on Herpomycetales and Laboulbeniales, two orders of unique ectoparasitic fungi associated with insects and other arthropods (class Laboulbeniomycetes) in Belgium and the Netherlands was published in the open-access, peer-reviewed scholarly journal MycoKeys.
Having surveyed arthropod fauna using pitfall traps and an illuminated white screen at night, and with the help of a network of entomologists, Dr. Danny Haelewaters (Purdue University, University of South Bohemia and Ghent University) and Dr. André De Kesel (Botanic Garden Meise) provide identification details about a total of 140 fungal species. The list includes nine species that are reported for the first time for either of the two countries and two newly described species.
Interestingly, one of the novel fungi was described during the 2020 global quarantine period, imposed to curb the COVID-19 pandemic. This prompted the researchers to dedicate the newly discovered species to this extraordinary time. In the annals of science, the species will be going by the name of Laboulbenia quarantenae.
— Dr. Danny Haelewaters ?????️? (@dhaelewa) July 7, 2020
Laboulbenia quarantenae grows externally on the body of ground beetles belonging to the species Bembidion biguttatum and is thus far only found at the Botanic Garden Meise in Belgium. This new fungus is considered to be very rare compared to Laboulbenia vulgaris, another, well-documented species that is more commonly found on the same host. So far, there has been no evidence that L. quarantenae parasitizes other host species.
Extreme close-up of the thalli of a fungus in the genus Hesperomyces (H. virescens sensu lato) parasitizing a harlequin ladybird (Harmonia axyridis). Image by Gilles San. Drawing by André De Kesel.
Herpomycetales and Laboulbeniales–unlike common mushrooms–do not form branching thread-like hyphae, nor a mycelium. Rather, they grow a single three-dimensional thallus of a few thousand cells sticking out of the body of the host organism. While some species of Laboulbeniales, like Laboulbenia quarantenae, are superficially attached to their host, others are more invasive, such as Hesperomyces halyziae, the second fungus newly described in this study. These fungi produce a haustorium, which is a hyphal outgrowth used to penetrate the tissues of their arthropod hosts, so that they can reach to the primary body cavity and the circulatory fluid in there. By doing so, it is thought that the parasites can both increase surface area for nutrient uptake and tighten their grip on their host.
In their study, the scientists hypothesize that, because of their invasive nature, these haustorial parasites maintain close interactions with their hosts in a process referred to as an “evolutionary arms race”. This means that whenever the host evolves a defence mechanism against the fungus, the parasite promptly evolves in its own turn, and adapts accordingly. Eventually, specialization leads to the evolution of new species.
The present study compiles all available data from Belgium and the Netherlands and serves as an appropriate starting point for an updated checklist of thallus-forming fungi in the class Laboulbeniomycetes found across Europe. Such a checklist is an ongoing project meant to summarize decades of research and will undoubtedly continue to uncover significant fungal diversity. The last update of this piece of knowledge dates back to 1991.
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Original source:
Haelewaters D, De Kesel A (2020) Checklist of thallus-forming Laboulbeniomycetes from Belgium and the Netherlands, including Hesperomyces halyziae and Laboulbenia quarantenae spp. nov. MycoKeys 71: 23-86. https://doi.org/10.3897/mycokeys.71.53421
