Category: MycoKeys

Pensoft’s ARPHA Publishing Platform integrates with OA Switchboard to streamline reporting to funders of open research

By the time authors open their inboxes to the message their work is online, a similar notification will have also reached their research funder.

Image credit: OA Switchboard.

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.

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Follow OA Switchboard on Twitter and Linkedin.

Cultivated and wild bananas in northern Viet Nam threatened by а devastating fungal disease

For over 100 years, Fusarium, one of the most important fungal plant pathogens, has affected banana production worldwide.

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.

Using DNA analyses and morphological characterization, an international team of researchers from Viet Nam (Plant Resources Center, Vietnam National University of Agriculture), Belgium (Meise Botanic Garden, KU Leuven, Bioversity Leuven, MUCL) and the Netherlands (Naturalis Biodiversity Center) investigated the identity of the Fusarium wilt infections. They recently published their joint research in the open-access, peer-reviewed journal MycoKeys.

The study shows that approximately 3 out of 4 Fusarium infections 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

A year of biodiversity: Top 10 new species of 2021 from Pensoft journals, Part 1

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”.

Published in: MycoKeys

9. The master of disguise

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 one of 13 new species of leaf insects described in our journal ZooKeys this 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.

Published in: ZooKeys

8. The Neil Gaiman spider

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.

Published in: ZooKeys

7. The deadly Chinese-goddess snake

Bungarus suzhenae was 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.

Published in: ZooKeys

6. The ephemeral fairy lanterns

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.

Published in: PhytoKeys

Part 2 coming soon – stay tuned!

Lifting the veil over mysterious desert truffles: Terfezia’s ecology and diversity towards cultivation

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

New species of fungus sticking out of beetles named after the COVID-19 quarantine

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.

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

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Follow lead author Dr. Danny Haelewaters on Twitter (@dhaelewa) and visit his website at: https://www.dannyhaelewaters.com/.

New pathogen threatens fennel yield in Italy

A new fungal genus and species Ochraceocephala foeniculi causes fennel yield losses of about 20-30% for three different cultivars. It damages the crops with necrotic lesions on the crown, root and stem.
International research group makes the first step in handling the new fennel disease by publishing their paper in the open-access journal Mycokeys.

A new fennel fungal disease caused by a new genus and species – Ochraceocephala foeniculi, was observed for the first time in 2017 on 5% of the “Apollo” fennel cultivar grown in the sampled localities in Catania province, Italy. Now, it has spread to 2 more cultivars: “Narciso” and “Pompeo”, causing crop losses of around 20-30%. The new pathogen damages the fennel with necrotic lesions on the crown, root and stem.

Fennel, a crop native in arid and semi-arid regions of southern Europe and the Mediterranean area is massively used as a vegetable, herb and seed spice in food, pharmaceutical, cosmetic and healthcare industries with Italy taking the world-leading production. It is an important and widely cultivated crop in Sicily (southern Italy).

Symptoms caused by Ochraceocephala foeniculi on fennel plants
Symptoms caused by Ochraceocephala foeniculi on fennel plants
Credits: Dalia Aiello
License: CC-BY 4.0

Worldwide, fennel crops are affected by several fungal diseases. In Italy, amongst soilborne diseases, there have been reports of brown rot and wilt caused by Phytophthora megasperma and crown rot caused by Didymella glomerata.

International research group, led by Ms. Dalia Aiello from the University of Catania, made the first step in handling the new fennel disease by identifying the causal agent obtained from symptomatic plants and publishing the results of their research in the open-access journal Mycokeys.

In order to understand the origin of the causal agent, scientists collected 30 samples during several surveys in the affected areas in Sicily, and studied the consistently grown fungal colonies from symptomatic tissues.

“The fungal species obtained from symptomatic tissues was identified based on morphological characters and molecular phylogenetic analyses of an ITS-LSU-SSU rDNA matrix, resulting in the description of the fennel pathogen as a new genus and species, Ochraceocephala
foeniculi,”

shares Dr. Dalia Aiello.

According to the pathogenicity tests, O. foeniculi causes symptoms on artificially inoculated plants of the same cultivar. Preliminary evaluation of fennel germplasm, according to the susceptibility to the new disease, shows that some cultivars (“Narciso”, “Apollo” and “Pompeo”) are more susceptible and some are less susceptible (“Aurelio”, “Archimede” and “Pegaso”), but this is a subject yet to be confirmed by additional investigations. More studies are required in order to plan further effective disease management strategies.

Holotype of Ochraceocephala foeniculi
Credits: Mr. Hermann Voglmayr
License: CC-BY 4.0

“On the basis of the disease incidence and severity observed in the field, we believe that this disease represents a serious threat to fennel crop in Sicily and may become a major problem also to other areas of fennel production if accidentally introduced,”

concludes Dr. Dalia Aiello.
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Original source: Aiello D, Vitale A, Polizzi G, Voglmayr H (2020) Ochraceocephala foeniculi gen. et sp. nov., a new pathogen causing crown rot of fennel in Italy. MycoKeys 66: 1-22. https://doi.org/10.3897/mycokeys.66.48389

Data mining applied to scholarly publications to finally reveal Earth’s biodiversity

At a time when a million species are at risk of extinction, according to a recent UN report, ironically, we don’t know how many species there are on Earth, nor have we noted down all those that we have come to know on a single list. In fact, we don’t even know how many species we would have put on such a list.

The combined research including over 2,000 natural history institutions worldwide, produced an estimated ~500 million pages of scholarly publications and tens of millions of illustrations and species descriptions, comprising all we currently know about the diversity of life. However, most of it isn’t digitally accessible. Even if it were digital, our current publishing systems wouldn’t be able to keep up, given that there are about 50 species described as new to science every day, with all of these published in plain text and PDF format, where the data cannot be mined by machines, thereby requiring a human to extract them. Furthermore, those publications would often appear in subscription (closed access) journals.

The Biodiversity Literature Repository (BLR), a joint project ofPlazi, Pensoft and Zenodo at CERN, takes on the challenge to open up the access to the data trapped in scientific publications, and find out how many species we know so far, what are their most important characteristics (also referred to as descriptions or taxonomic treatments), and how they look on various images. To do so, BLR uses highly standardised formats and terminology, typical for scientific publications, to discover and extract data from text written primarily for human consumption.

By relying on state-of-the-art data mining algorithms, BLR allows for the detection, extraction and enrichment of data, including DNA sequences, specimen collecting data or related descriptions, as well as providing implicit links to their sources: collections, repositories etc. As a result, BLR is the world’s largest public domain database of taxonomic treatments, images and associated original publications.

Once the data are available, they are immediately distributed to global biodiversity platforms, such as GBIF–the Global Biodiversity Information Facility. As of now, there are about 42,000 species, whose original scientific descriptions are only accessible because of BLR.

The very basic principle in science to cite previous information allows us to trace back the history of a particular species, to understand how the knowledge about it grew over time, and even whether and how its name has changed through the years. As a result, this service is one avenue to uncover the catalogue of life by means of simple lookups.

So far, the lessons learned have led to the development of TaxPub, an extension of the United States National Library of Medicine Journal Tag Suite and its application in a new class of 26 scientific journals. As a result, the data associated with articles in these journals are machine-accessible from the beginning of the publishing process. Thus, as soon as the paper comes out, the data are automatically added to GBIF.

While BLR is expected to open up millions of scientific illustrations and descriptions, the system is unique in that it makes all the extracted data findable, accessible, interoperable and reusable (FAIR), as well as open to anybody, anywhere, at any time. Most of all, its purpose is to create a novel way to access scientific literature.

To date, BLR has extracted ~350,000 taxonomic treatments and ~200,000 figures from over 38,000 publications. This includes the descriptions of 55,800 new species, 3,744 new genera, and 28 new families. BLR has contributed to the discovery of over 30% of the ~17,000 species described annually.

Prof. Lyubomir Penev, founder and CEO of Pensoft says,

“It is such a great satisfaction to see how the development process of the TaxPub standard, started by Plazi some 15 years ago and implemented as a routine publishing workflow at Pensoft’s journals in 2010, has now resulted in an entire infrastructure that allows automated extraction and distribution of biodiversity data from various journals across the globe. With the recent announcement from the Consortium of European Taxonomic Facilities (CETAF) that their European Journal of Taxonomy is joining the TaxPub club, we are even more confident that we are paving the right way to fully grasping the dimensions of the world’s biodiversity.”

Dr Donat Agosti, co-founder and president of Plazi, adds:

“Finally, information technology allows us to create a comprehensive, extended catalogue of life and bring to light this huge corpus of cultural and scientific heritage – the description of life on Earth – for everybody. The nature of taxonomic treatments as a network of citations and syntheses of what scientists have discovered about a species allows us to link distinct fields such as genomics and taxonomy to specimens in natural history museums.”

Dr Tim Smith, Head of Collaboration, Devices and Applications Group at CERN, comments:

“Moving the focus away from the papers, where concepts are communicated, to the concepts themselves is a hugely significant step. It enables BLR to offer a unique new interconnected view of the species of our world, where the taxonomic treatments, their provenance, histories and their illustrations are all linked, accessible and findable. This is inspirational for the digital liberation of other fields of study!”

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Additional information:

BLR is a joint project led by Plazi in partnership with Pensoft and Zenodo at CERN.

Currently, BLR is supported by a grant from Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin.

Medicinal mushroom newly reported from Thailand helps reveal optimum growth conditions

Globally recognised medicinal mushroom is reported for the first time in Thailand. The study also presents the first assessment of the optimum growth conditions for the species.

A species of globally recognised medicinal mushroom was recorded for the first time in Thailand. Commonly referred to as lingzhi, the fungus (Ganoderma tropicum) was collected from the base of a living tree in Chiang Rai Province, Northern Thailand. Additionally, the study reports the first assessment of the optimum conditions needed for the species to grow its mycelia (the vegetative part of a fungus consisting of a branching network of fine, thread-like structures) and spread its colony.

The discoveries are published in the open-access journal MycoKeys by a research team from the Chinese Academy of Sciences, University of Chinese Academy of Sciences, World Agroforestry Centre, Kunming Institute of Botany (China) and Center of Excellence in Fungal Research, Mae Fah Luang University (Thailand), led by Thatsanee Luangharn.

Over the last centuries, the studied mushroom and its related species in the genus Ganoderma have been used extensively in traditional Asian medicines due to their natural bioactive compounds, including polysaccharides, triterpenoids, sterols, and secondary metabolites, which are used in the treatment of various diseases. Other compounds derived from lingzhi, such as the studied species, also demonstrate antimicrobial activities. The medicinal use of these mushrooms is recognised by the World Health Organization and they are featured in the Chinese Pharmacopoeia.

The studied mushroom belongs to a group known to be parasitic or pathogenic on a wide range of tree species. The species is characterised with strongly laccate fruiting bodies and a cap with distinctly dark brown base colour and reddish shades. It grows to up to 7-12 cm in length, 4-8 cm in width and is up to 1.5 cm thick. While the mushroom has so far been widely reported from tropical areas, including mainland China, Taiwan and South America, it had never been recorded from Thailand.

During their research, the scientists found that mycelial production for Ganoderma tropicum is most successful on Potato Dextrose Agar, Malt Extract Agar, and Yeast extract Peptose Dextrose Agar, at a temperature of 25-28 °C and 7-8 pH. Unfortunately, mushroom fruiting was not achieved in the experiment.

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Original source:

Luangharn T, Karunarathna SC, Mortimer PE, Hyde KD, Thongklang N, Xu J (2019) A new record of Ganoderma tropicum (Basidiomycota, Polyporales) for Thailand and first assessment of optimum conditions for mycelia production. MycoKeys 51: 65-83. https://doi.org/10.3897/mycokeys.51.33513

FAIR biodiversity data in Pensoft journals thanks to a routine data auditing workflow

Data audit workflow provided for data papers submitted to Pensoft journals.

To avoid publication of openly accessible, yet unusable datasets, fated to result in irreproducible and inoperable biological diversity research at some point down the road, Pensoft takes care for auditing data described in data paper manuscripts upon their submission to applicable journals in the publisher’s portfolio, including Biodiversity Data Journal, ZooKeys, PhytoKeys, MycoKeys and many others.

Once the dataset is clean and the paper is published, biodiversity data, such as taxa, occurrence records, observations, specimens and related information, become FAIR (findable, accessible, interoperable and reusable), so that they can be merged, reformatted and incorporated into novel and visionary projects, regardless of whether they are accessed by a human researcher or a data-mining computation.

As part of the pre-review technical evaluation of a data paper submitted to a Pensoft journal, the associated datasets are subjected to data audit meant to identify any issues that could make the data inoperable. This check is conducted regardless of whether the dataset are provided as supplementary material within the data paper manuscript or linked from the Global Biodiversity Information Facility (GBIF) or another external repository. The features that undergo the audit can be found in a data quality checklist made available from the website of each journal alongside key recommendations for submitting authors.

Once the check is complete, the submitting author receives an audit report providing improvement recommendations, similarly to the commentaries he/she would receive following the peer review stage of the data paper. In case there are major issues with the dataset, the data paper can be rejected prior to assignment to a subject editor, but resubmitted after the necessary corrections are applied. At this step, authors who have already published their data via an external repository are also reminded to correct those accordingly.

“It all started back in 2010, when we joined forces with GBIF on a quite advanced idea in the domain of biodiversity: a data paper workflow as a means to recognise both the scientific value of rich metadata and the efforts of the the data collectors and curators. Together we figured that those data could be published most efficiently as citable academic papers,” says Pensoft’s founder and Managing director Prof. Lyubomir Penev.
“From there, with the kind help and support of Dr Robert Mesibov, the concept evolved into a data audit workflow, meant to ‘proofread’ the data in those data papers the way a copy editor would go through the text,” he adds.
“The data auditing we do is not a check on whether a scientific name is properly spelled, or a bibliographic reference is correct, or a locality has the correct latitude and longitude”, explains Dr Mesibov. “Instead, we aim to ensure that there are no broken or duplicated records, disagreements between fields, misuses of the Darwin Core recommendations, or any of the many technical issues, such as character encoding errors, that can be an obstacle to data processing.”

At Pensoft, the publication of openly accessible, easy to access, find, re-use and archive data is seen as a crucial responsibility of researchers aiming to deliver high-quality and viable scientific output intended to stand the test of time and serve the public good.

CASE STUDY: Data audit for the “Vascular plants dataset of the COFC herbarium (University of Cordoba, Spain)”, a data paper in PhytoKeys

To explain how and why biodiversity data should be published in full compliance with the best (open) science practices, the team behind Pensoft and long-year collaborators published a guidelines paper, titled “Strategies and guidelines for scholarly publishing of biodiversity data” in the open science journal Research Ideas and Outcomes (RIO Journal).

New family of fungi threatens a UNESCO-listed 8-century-old cathedral in Portugal

The Old Cathedral of Coimbra [right], the Santa Maria chapel [left, top] and the artwork from which the scientists retrieved the studied fungi [left, bottom]. Photo by Miguel Mesquita.
To be listed as UNESCO World Heritage requires special care and protection of valuable cultural monuments and pieces of Art from threats such as biodeterioration caused by microcolonial black fungi. The culprits lodge their branch-like structures (hyphae) deep into the stone forming fissures and cracks and also produce polysaccharides that trigger corrosion.

These fungi are well known for their unique resistance to hostile environmental conditions, including extreme temperatures, high solar and UV radiation, severe droughts and low abundance of nutrients. As a result, they survive in hot and cold deserts, saltpans, acidic and hydrocarbon-contaminated sites and exposed rocks surfaces. All of this makes them a particular challenge to conservationists and biologists who care for historic monuments.

During a multi-disciplinary scientific survey at the 8-century-old cathedral Sé Velha de Coimbra (Old Cathedral of Coimbra), which is the only Romanesque cathedral in Portugal to have survived relatively intact since the Reconquista times, scientists retrieved a peculiar slow-growing microcolonial black fungus.

What João Trovão of the University of Coimbra (Portugal) and his colleagues were looking at turned out to be a species of a whole new family (Aeminiaceae) in the order of the sooty mould fungi. The new species, its new genus and the novel family are described in the open-access journal MycoKeys.

This is a colony of the newly described black fungus species Aeminium ludgeri. Photo by João Trovão.

To define the new group of fungi, the researchers first scraped off samples from a deteriorated limestone artwork in the “Santa Maria” chapel and then conducted an extensive and integrative analysis, based on morphological, physiological, ecological characters and DNA sequences.

As for the origin of the previously unknown fungus, the scientists hypothesise that the species had ‘arrived’ at the Old Cathedral of Coimbra with the limestone used during its construction. Coming from the unique nearby areas of Ançã and Portunhos, such limestone has been used on several of the “Our Ladies of the O” statues, as well as in the portal of the Royal Hospital in Santiago de Compostela (Spain). Currently, these fungi are considered endemic to the limestone quarries in the Iberian Peninsula.

“Regarding stone monuments exposed to the environment, microcolonial black fungi are considered one of the main culprits for the phenomenon of stone biodeterioration, being responsible for severe aesthetic, biochemical and biophysical alterations,” comment the scientists.

“It is, therefore, crucial to gather deeper knowledge regarding their biodiversity and their biological, ecological and physiological unique characteristics, in order to span our knowledge regarding these fungi and, at the same time, allow the development and improvement of tools to protect stone monuments from their deteriorative effects.”

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Original source:

Trovão J, Tiago I, Soares F, Paiva DS, Mesquita N, Coelho C, Catarino L, Gil F, Portugal A (2019) Description of Aeminiaceae fam. nov., Aeminium gen. nov. and Aeminium ludgeri sp. nov. (Capnodiales), isolated from a biodeteriorated art-piece in the Old Cathedral of Coimbra, Portugal. MycoKeys 45: 57-73. https://doi.org/10.3897/mycokeys.45.31799