The next generation fungal diversity researcher

Integrative taxonomy of Metarhizium anisopliae species complex, based on phylogenomics combined with morphometrics, metabolomics, and virulence data

Metarhizium anisopliae (Clavicipitaceae, Hypocreales) is a globally distributed entomopathogenic fungus, which has been largely studied and used in agriculture for its potent entomopathogenicity. Since its taxonomic establishment as a member of Metarhizium, many closely related taxa have been described with highly similar morphology (cryptic species). A holotype specimen of M. anisopliae is not extant, and the ex-neotype strain (CBS 130.71) does not form a monophyletic clade with other strains, up to now, recognized as M. anisopliae sensu stricto. In this study, we have conducted an integrative taxonomic treatment of M. anisopliae sensu lato by including the ex-neotype strain of M. anisopliae, other unknown strains from our collections identified as M. anisopliae s. lat., as well as other known species that have been previously delimited as closely related but distinct to M. anisopliae. By including whole-genome sequencing, morphometric analysis, LC-MS based metabolomics, and virulence assays, we have demonstrated that M. anisopliae s. str. should also include M. lepidiotae (synonym), and that M. anisopliae s. str. differentiates from the other species of the complex by its metabolome and less severe entomopathogenicity. New taxa, namely M. hybridum, M. neoanisopliae and M. parapingshaense spp. nov., are proposed. The novel taxa proposed here have strong phylogenomics support, corroborated by fine-scale differences in the length/width of conidia/phialides, while the metabolomics and virulence data still largely overlap. We have also demonstrated via population genomics data the existence of local clonal lineages, particularly the one corresponding to the persistence of a biocontrol candidate strain that has been used in the field application for three years. This study showcases the utility of combining various data sources for accurate delimitation of species within an important group of fungal biocontrol agents against pest insects.

Innovative infrastructure to access Brazilian fungal diversity using deep learning

In the present investigation, we employ a novel and meticulously structured database assembled by experts, encompassing macrofungi field-collected in Brazil, featuring upwards of 13,894 photographs representing 505 distinct species. The purpose of utilizing this database is twofold: firstly, to furnish training and validation for convolutional neural networks (CNNs) with the capacity for autonomous identification of macrofungal species; secondly, to develop a sophisticated mobile application replete with an advanced user interface. This interface is specifically crafted to acquire images, and, utilizing the image recognition capabilities afforded by the trained CNN, proffer potential identifications for the macrofungal species depicted therein. Such technological advancements democratize access to the Brazilian Funga, thereby enhancing public engagement and knowledge dissemination, and also facilitating contributions from the populace to the expanding body of knowledge concerning the conservation of macrofungal species of Brazil.

A case study on the application of spore sampling for the monitoring of macrofungi

Fungi play a vital role in ecosystem functioning, yet significant knowledge gaps persist in understanding their diversity and distribution leading to uncertainties about their threat status and extinction risk. This is partly owed to the difficulty of monitoring fungi using traditional fruiting body surveys. The present study evaluates airborne environmental DNA (eDNA) sampling as a monitoring tool with a focus on grassland macrofungi. We applied active and passive air sampling methods, complemented by extensive field surveys of waxcap and clavarioid fungi-species groups of high relevance for conservation. Twenty-nine species were recorded during the field surveys, 19 of which were also detectable by ITS2 metabarcoding of the collected samples. An additional 12 species from the studied genera were identified exclusively in air eDNA. We found that the patterns of species detection and read abundance in air samples reflected the abundance and occurrence of fruiting bodies on the field. Dispersal kernels fitted for the three dominant species predicted rapidly decreasing spore concentrations with increasing distance from fruitbodies. Airborne assemblages were dominated by a high diversity of common species, while rare and threatened red-listed species were under-represented, which underscores the difficulty in detecting rare species, not only in conventional surveys. Considering the benefits and drawbacks of air sampling and fruitbody surveys, we conclude that air sampling serves as a cost- and time-efficient tool to characterize local macrofungal communities, providing the potential to facilitate and improve future fungal monitoring efforts.

Habitat Protection Approaches Facilitate Conservation of Overlooked Fungal Diversity - A Case Study From the Norwegian Coastal Heathland System

European coastal heathlands are distinct ecosystems shaped by land use tradition and they have experienced an 80% area reduction from their historical maximum. These mosaics of mires and wind exposed patches have ericaceous shrub dominated vegetation, and soils within coastal heathlands are characterized by low pH and high levels of recalcitrant debris. Using a culture-based approach with molecular identification of isolates, we characterized root-associated fungal communities of six ericaceous species in eight heathland localities along Norway's western coast. Site-level alpha diversity ranged from 21-38 OTUs, while the total estimated gamma diversity for culturable heathland root fungi was 190-231 OTUs. Most species recovered are previously reported at low abundance in Norway, suggesting the biodiversity in this community is underreported, rather than novel for science. The fungi recovered were primarily Ascomycota, specifically endophytic Phialocephala, and Pezicula, and no host specificity was observed in the communities. The fungal communities exhibited high turnover and low nestedness, both between ericaceous hosts and across heathland sites. We observed no spatial patterns in fungal betadiversity, and this heterogeneity may be a product of the unique historic land use practices at each locality creating a distinct mycofloral "fingerprint". Robust diversity estimates will be key for managing fungal biodiversity in coastal heathlands. Our results indicate that sampling schemes that maximize the number of host plants sampled per site, rather than the number of cultures per plant yield improved alpha diversity estimates. Similarly, gamma diversity estimates are improved by maximizing the total number of localities sampled, rather than increasing the number of plants sampled per locality. We argue that while the current protected status of coastal heathland habitats and restoration efforts have knock-on effects for the conservation of fungal biodiversity, fungi have a vital functional role in the ecosystem and holistic conservation plans that consider fungal biodiversity would be beneficial.

An overview of the history, current contributions and future outlook of iNaturalist in Australia

Citizen science initiatives and the data they produce are increasingly common in ecology, conservation and biodiversity monitoring. Although the quality of citizen science data has historically been questioned, biases can be detected and corrected for, allowing these data to become comparable in quality to professionally collected data. Consequently, citizen science is increasingly being integrated with professional science, allowing the collection of data at unprecedented spatial and temporal scales. iNaturalist is one of the most popular biodiversity citizen science platforms globally, with more than 1.4 million users having contributed over 54 million observations. Australia is the top contributing nation in the southern hemisphere, and in the top four contributing nations globally, with over 1.6 million observations of over 36000 identified species contributed by almost 27000 users. Despite the platform’s success, there are few holistic syntheses of contributions to iNaturalist, especially for Australia. Here, we outline the history of iNaturalist from an Australian perspective, and summarise, taxonomically, temporally and spatially, Australian biodiversity data contributed to the platform. We conclude by discussing important future directions to maximise the usefulness of these data for ecological research, conservation and policy.

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

Draft genome sequences of five Calonectria species from Eucalyptus plantations in China, Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa

Draft genome sequences of five Calonectria species [including Calonectria aciculata, C. crousiana, C. fujianensis, C. honghensis and C. pseudoturangicola], Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa are presented. Species of Calonectria are the causal agents of Eucalyptus leaf blight disease, threatening the growth and sustainability of Eucalyptus plantations in China. Celoporthe dispersa is the causal agent of stem canker in native Syzygium cordatum and exotic Tibouchina granulosa in South Africa. Sporothrix phasma was first discovered in the infructescences of Protea laurifolia and Protea neriifolia in South Africa. Alectoria sarmentosa is fruticose lichen belongs to the alectorioid clade of the family Parmeliaceae. The availability of these genome sequences will facilitate future studies on the systematics, population genetics, and genomics of these fungi.

Conservation mycology in Australia and the potential role of citizen science

Fungi are undoubtedly important for ecosystem functioning; however, they have been omitted or given scant attention in most biodiversity policy documents, management plans, and formal conservation schedules throughout the world. This oversight may be due to a general lack of awareness in the scientific community and compounded by a scarcity of mycology-associated curricula at the tertiary level and a lack of mycologists in research institutions. Although molecular techniques advance the systematic cataloging of fungi and facilitate insights into fungal communities, the scarcity of professional mycologists in the environmental sciences hampers conservation efforts. Conversely, citizen science initiatives are making significant contributions to the mycology discipline by increasing awareness and extending the scope of fungal surveys. Future research by professional and amateur mycologists into the distribution of fungi and their function in ecosystems will help identify wider and more effective conservation goals.

Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal "from the floor" to allow DNA sequences as types of names

We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus9: 167-175,2018) and Thines et al. (IMA Fungus9: 177-183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code (Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code. We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with "false negatives" surpassing "false positives"; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Code that would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatus status of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as "nom. seq." (nomen sequentiae). Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungi following evaluation based on strict quality control of the underlying studies based on established rules or recommendations.