Category: MycoKeys

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
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.

***

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

New fungus found to cause cankers and declines in pistachio trees in Sicily, Italy

Starting in the spring of 2010, farmers from Sicily – the major pistachio production area of Italy – have been reporting a previously unknown disease on the trees. Characterised by cankers and declines, it sometimes leads to the collapse of the entire plant.

When the research team led by Salvatore Vitale, Centro di Ricerca Difesa e Certificazione, Italy, studied plants from a total of 15 pistachio orchards in Catania, Agrigento and Caltanissetta provinces, they identified cankers associated with vascular necrosis and tree decline on twigs, branches and stems, alongside abundant gummosis. There were also localised, sunken lesions with several central cracks. These lesions would deepen into the woody tissue, where discolouration and necrotic tissue were also present.

Additionally, the scientists conducted a series of pathogenicity tests on 5-year-old potted pistachio plants (Pistacia vera), which successfully reproduced the field observations. As a result, a previously unknown pathogenic fungus, which colonises the woody plant tissue, has been isolated.

*Timelapse of the symptoms reproduced in a potted plant.*

The aetiology of the disease and the description of the new species, named Liberomyces pistaciae, are published in the open access journal MycoKeys. Despite cankers and subsequent decline of pistachio trees having been observed in Sicily for several years, the paper is the first work to successfully determine the causal agent.

“On the basis of the high disease incidence and the frequency of this species observed in several orchards in the last years, we believe that L. pistaciae represents amenace to pistachio production in Sicily,” say the researchers.

*Symptoms caused by the newly described pathogenic fungus observed in the field.*

Out of the 15 surveyed orchards, the scientists detected the presence of the fungus in ten of them. Most of the observations occurred in the winter period and during late spring, but the authors found the pathogen in asymptomatic trees as well, which suggests that the fungus has a dormant growth phase.

When already symptomatic, the plants begin to exudate gum. Often, the bark on their trunks and/or branches would scale, appearing as if cracking and peeling. The initial pale circular areas present in the bark turn dark and sunken with time. Later, the infected patches were seen to expand in all directions, yet faster along the main axis of the stems, branches and twigs. When the scientists examined beneath the bark, they saw discoloured and necrotic tissues. Once the trunk of the tree is encircled by a canker, they report, the whole plant collapses.

Other symptoms include canopy decline as well as wilting and dying inflorescences and shoots growing from infected branches or twigs.

The newly described fungus is characterised with slowly growing colonies. With time, they turn from white to pale to dark brown with a whitish slightly lobed margin.

The researchers warn that essential hazard for the further spread and promotion of the infection is the use and distribution of infected propagation material taken from nurseries and mechanical injuries or pruning wounds.

Further research and studies are currently in progress aiming to extend the survey to other areas in order to eventually formulate effective disease management strategies.

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Original source:

Vitale S, Aiello D, Guarnaccia V, Luongo L, Galli M, Crous PW, Polizzi G, Belisario A, Voglmayr H (2018) Liberomyces pistaciae sp. nov., the causal agent of pistachio cankers and decline in Italy. MycoKeys 40: 29-51. https://doi.org/10.3897/mycokeys.40.28636

The Alps are home to more than 3,000 lichens

Historically, the Alps have always played an emblematic role, being one of the largest continuous natural areas in Europe. With its numerous habitats, the mountain system is easily one of the richest biodiversity hotspots in Europe.

Lichens are curious organisms comprising a stable symbiosis between a fungus and one or more photosynthetic organisms, for example green algae and/or cyanobacteria. Once the symbiosis is established, the new composite organism starts to function as a whole new one, which can now convert sunlight into essential nutrients and resist ultraviolet light at the same time.

A common fruticose lichen in the Alps (Flavocetraria nivalis). Photo: Dr Peter O. Bilovitz — *A common fruticose lichen in the Alps (Flavocetraria nivalis).*
*Photo: Dr Peter O. Bilovitz*

Being able to grow on a wide range of surfaces – from tree bark to soil and rock, lichens are extremely useful as biomonitors of air quality, forest health and climate change.

Nevertheless, while the Alps are one of the best studied parts of the world in terms of their biogeography, no overview of the Alpine lichens had been provided up until recently, when an international team of lichenologists, led by Prof. Pier Luigi Nimis, University of Trieste, Italy, concluded their 15-year study with a publication in the open access journal MycoKeys.

Sunrise in the Julian Alps. Photo: Dr Pier Luigi Nimis — *Sunrise in the Julian Alps.*
*Photo: Dr Pier Luigi Nimis*

The scientists’ joint efforts produced the first ever checklist to provide a complete critical catalogue of all lichens hitherto reported from the Alps. It comprises a total of 3,138 entries, based on data collected from eight countries – Austria, France, Germany, Italy, Liechtenstein, Monaco, Slovenia and Switzerland. In their research paper, the authors have also included notes on the lichens’ ecology and taxonomy.

A common lichen in the Alps (Xanthoria elegans). Photo: Dr Tomi Trilar — *A common lichen in the Alps (Xanthoria elegans).*
*Photo: Dr Tomi Trilar*

They point out that such catalogue has been missing for far too long, hampering research all over the world. The scientists point out that this has been “particularly annoying”, since the data from the Alps could have been extremely useful for comparisons between mountainous lichen populations from around the globe. It turns out that many lichens originally described from the Alps have been later identified in other parts of the world.

“It was a long and painstaking work, which lasted almost 15 years, revealing a surprisingly high number of yet to be resolved taxonomic problems that will hopefully trigger further research in the coming years,” say the authors.

“We think that the best criterion to judge whether a checklist has accomplished its task for the scientific community is the speed of it becoming outdated,” they conclude paradoxically.

The new checklist is expected to serve as a valuable tool for retrieving and accessing the enormous amount of information on the lichens of the Alps

A widespread alpine lichen (Thamnolia vermicularis). Photo: Dr Peter O. Bilovitz — *A widespread alpine lichen (Thamnolia vermicularis).*
*Photo: Dr Peter O. Bilovitz*

that has accumulated over centuries of research. It offers a basis for specimen revisions, critical re-appraisal of poorly-known species and further exploration of under-explored areas. Thus, it could become a catalyst for new, more intensive investigations and turn into a benchmark for comparisons between mountains systems worldwide.

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Original source:

Nimis PL, Hafellner J, Roux C, Clerc P, Mayrhofer H, Martellos S, Bilovitz PO (2018) The lichens of the Alps – an annotated checklist. MycoKeys 31: 1-634. https://doi.org/10.3897/mycokeys.31.23568

Lichenologists at work in the Carnic Alps. Photo: Dr Pier Luigi Nimis — *Lichenologists at work in the Carnic Alps.*
*Photo: Dr Pier Luigi Nimis*

Underwater mushrooms: Curious lake fungi under every turned over stone

While fungi are well known for being essential in cycling carbon and nutrients, there are only about 100,000 described species in contrast to the 1.5 to 3 millions, assumed to exist on Earth. Of these, barely 3000 fungi belong to aquatic habitats. In fact, freshwater fungi have been researched so little, it is only now that an international research team provide the first lake-wide fungal diversity estimate in the open access journal MycoKeys.

Over the spring and the early summer of 2010, a large team of scientists, led by Dr Christian Wurzbacher and Dr Norman Warthmann, affiliated with the Leibniz-Institute of Freshwater Ecology and Inland Fisheries and the Berlin Center for Genomics in Biodiversity Research, Germany (currently at University of Gothenburg, Sweden, and the Australian National University, Australia, respectively), collected a total of 216 samples from 54 locations, encompassing eight different habitats within Lake Stechlin in North-East Germany.

Having recovered samples on three occasions over the course of the study, their aim was to test how habitat specificity affects the fungal community and whether fungal groups would reflect the availability of particulate organic matter as substrate. Unlike previous studies of aquatic fungi that compared water samples among different lakes or seasons, theirs would compare the diversity among habitats within a single lake. This included the study of fungi living in the water and the sediments, as well as fungi living on the surfaces of plants and other animals.

As a result, the scientists concluded that every type of habitat, i.e. sediments, biofilms, and submerged macrophytes (large aquatic plants), has a specific fungal community that varies more than initially expected. Of these, lake biofilms, representing a group of microorganisms, whose cells stick to each other, and cling together to a surface, turned out to be the hotspots for aquatic fungi.

“Our study provides the first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition,” the scientists summarise. “Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body.”

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Original source:

Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https://doi.org/10.3897/mycokeys.16.9646

Top 50 most wanted fungi: New search function zooms in on the dark fungal diversity

There are many millions of undescribed fungi, and public DNA sequence databases contain thousands of fungal sequences that cannot be assigned to any known fungal group with confidence. Many of these sequences have defied robust taxonomic assignment for more than 10 years.

Frustrated at this situation, an international group of researchers presents a search functionin the UNITE database for molecular identification of fungi. Its aim is to highlight the fungi we know the least about, and invite the scientific community to resolve their taxonomic affiliation. The effort seeks to bridge the substantial knowledge gap between fungal taxonomy and molecular ecology through a list, the authors refer to as the “50 Most Wanted Fungi”. Their work is presented in a new research paper published in the open-access journal MycoKeys.

Some 100,000 species of fungi have been described formally, although current estimates put the number of extant fungal species to at least 6 million. There is clearly no shortage of research venues in the study of fungi – but are there other shortages? The vast dark fungal diversity unravelled with molecular techniques hints that the interaction between fungal taxonomy and DNA sequencing of environmental substrates such as soil and water is not necessarily optimal.

“There is no taxonomic feedback loop in place to highlight the presence of these enigmatic lineages to the mycological community, and they often end up in sequence databases for years without attracting significant research interest,” explain the authors. “More than 10 years in some cases, as a matter of fact.”

Therefore, the researchers, led by Dr Henrik Nilsson, University of Gothenburg, now present a search function that produces lists of approximately genus-level clusters of fungal DNA sequences whose taxonomic affiliation we know next to nothing about. These lists are recomputed on a monthly basis, accounting for any updates and additions contributed by the scientific community in between each iteration. Community participation is encouraged, and the UNITE database has extensive support for third-party annotation.

By putting the spotlight on these fungal lineages, Dr Nilsson and colleagues hope to speed up the study and formal description of the underlying species. To support researchers focusing on select groups of fungi or environments, a set of keyword-filtered lists is provided. This allows researchers to zoom in on unknown fungi recovered, for example, from the built environment or aquatic habitats.

Commenting on their choice of a name for the list, the researchers clarify that the underlying fungi are not guilty of any crime. “Indeed, nothing can be said of the way they make a living. It is simply not known. We make no claim as to the importance of these fungi from whatever point of view – ecological, economic, or otherwise,” they stress. “We do make claim to their uniqueness, though, because it is frustrating, in the year 2016, not to be able to assign a name to a fungal sequence even at the phylum level.”

“We hope that the present publication will serve to put the spotlight on these uncharted parts of the fungal tree of life, and we invite the reader to examine them through our online tools or otherwise,” they conclude.

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Original source:

Nilsson RH, Wurzbacher C, Bahram M, Coimbra VRM, Larsson E, Tedersoo L, Eriksson J, Duarte Ritter C, Svantesson S, Sánchez-García M, Ryberg M, Kristiansson E, Abarenkov K (2016) Top 50 most wanted fungi. MycoKeys 12: 29-40. doi: 10.3897/mycokeys.12.7553