Molecular-Based Diversity Studies and Field Surveys Are Not Mutually Exclusive: On the Importance of Integrated Methodologies in Mycological Research

Cazabonne, Jonathan; Bartrop, Lachlan; Dierickx, Glen; Gafforov, Yusufjon; Hofmann, Tina A.; Martin, Thomas E.; Piepenbring, Meike; Rivas‐Ferreiro, Mauro; Haelewaters, Danny

doi:10.3389/ffunb.2022.860777

Cited by 12 publications

(10 citation statements)

References 154 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The study identified dominant fungi such as Ascomycota, Basidiomycota, and Mucoromycota at the phyla level, though many ASVs were unidentified; this could partly be due to the unavailability of reference sequences in the used UNITE database [57] or possible novelty of the organisms. A report of severe underestimation and underrepresentation of fungal diversity has been previously established [58]. The presence of Ascomycota in all the cultivars may indicate their dominance in the community [29,59], suggesting it to be the core endophytic organism in the plant.…”

Section: Discussionmentioning

confidence: 90%

Chemical Characterization and Metagenomic Identification of Endophytic Microbiome from South African Sunflower (Helianthus annus) Seeds

et al. 2023

View full text Add to dashboard Cite

Helianthus annus (sunflower) is a globally important oilseed crop whose survival is threatened by various pathogenic diseases. Agrochemical products are used to eradicate these diseases; however, due to their unfriendly environmental consequences, characterizing microorganisms for exploration as biocontrol agents are considered better alternatives against the use of synthetic chemicals. The study assessed the oil contents of 20 sunflower seed cultivars using FAMEs-chromatography and characterized the endophytic fungi and bacteria microbiome using Illumina sequencing of fungi ITS 1 and bacteria 16S (V3–V4) regions of the rRNA operon. The oil contents ranged between 41–52.8%, and 23 fatty acid components (in varied amounts) were found in all the cultivars, with linoleic (53%) and oleic (28%) acids as the most abundant. Ascomycota (fungi) and Proteobacteria (bacteria) dominated the cultivars at the phyla level, while Alternaria and Bacillus at the genus level in varying abundance. AGSUN 5102 and AGSUN 5101 (AGSUN 5270 for bacteria) had the highest fungi diversity structure, which may have been contributed by the high relative abundance of linoleic acid in the fatty acid components. Dominant fungi genera such as Alternaria, Aspergillus, Aureobasidium, Alternariaste, Cladosporium, Penicillium, and bacteria including Bacillus, Staphylococcus, and Lactobacillus are established, providing insight into the fungi and bacteria community structures from the seeds of South Africa sunflower.

show abstract

Section: Discussionmentioning

confidence: 90%

Chemical Characterization and Metagenomic Identification of Endophytic Microbiome from South African Sunflower (Helianthus annus) Seeds

et al. 2023

View full text Add to dashboard Cite

show abstract

“…Moreover, certain groups of fungi have few morphological characteristics, and some species may exhibit cryptic diversity or high phenotypic plasticity (e.g., Slepecky and Starmer 2009 ; Haelewaters et al 2018 ; Hapuarachchi et al 2019 ; Van Caenegem et al 2023a ). These observations highlight the need to combine morphological and molecular data whenever possible when dealing with singleton-based species—in line with using integrated methodologies to study fungal diversity (Cazabonne et al 2022 ).…”

Section: Limitations and Risks Of Singleton-based Speciesmentioning

confidence: 89%

Singleton-based species names and fungal rarity: Does the number really matter?

Cazabonne,

Walker,

Lesven

et al. 2024

IMA Fungus

Self Cite

View full text Add to dashboard Cite

Fungi are among the least known organisms on earth, with an estimated number of species between 1.5 and 10 million. This number is expected to be refined, especially with increasing knowledge about microfungi in undersampled habitats and increasing amounts of data derived from environmental DNA sequencing. A significant proportion of newly generated sequences fail to match with already named species, and thus represent what has been referred to as fungal “dark taxa”. Due to the challenges associated with observing, identifying, and preserving sporophores, many macro- and microfungal species are only known from a single collection, specimen, isolate, and/or sequence—a singleton. Mycologists are consequently used to working with “rare” sequences and specimens. However, rarity and singleton phenomena lack consideration and valorization in fungal studies. In particular, the practice of publishing new fungal species names based on a single specimen remains a cause of debate. Here, we provide some elements of reflection on this issue in the light of the specificities of the fungal kingdom and global change context. If multiple independent sources of data support the existence of a new taxon, we encourage mycologists to proceed with formal description, irrespective of the number of specimens at hand. Although the description of singleton-based species may not be considered best practice, it does represent responsible science in the light of closing the Linnean biodiversity shortfall.

show abstract

“…Similarly, arguments exist for expediting taxonomic processes by employing new approaches such as DNA metabarcoding (Kress & Erickson, 2012) and environmental DNA analysis (Yan et al, 2018). However, these approaches have their own limitations (Cazabonne et al, 2022; de Carvalho et al, 2005). Citizen scientists are often limited in their ability to identify cryptic taxa to species‐level (e.g.…”

Section: Discussionmentioning

confidence: 99%

Biological knowledge shortfalls impede conservation efforts in poorly studied taxa—A case study of Laboulbeniomycetes

Haelewaters,

Matthews,

Wayman

et al. 2023

Journal of Biogeography

Self Cite

View full text Add to dashboard Cite

Most empirical research on biological shortfalls has focused on vertebrate taxa. This is important given many species in poorly studied groups such as invertebrates, plants, and fungi are predicted to possess high conservation risk. Here, we focus on Laboulbeniomycetes: a class of microfungi that are understudied. We examined four shortfalls: Linnean (knowledge gaps in species diversity), Wallacean (knowledge gaps in distributions), Latimerian (knowledge gaps in species persistence), and the newly introduced Scottian (knowledge gaps in species conservation assessments) shortfalls. The Linnean shortfall in Laboulbeniomycetes is hard to predict due to inconsistent species description rates. Analysis of distribution patterns indicates Laboulbeniomycetes are likely to experience an extremely high Wallacean shortfall, with many species having highly disjunct known distributions. Latimerian shortfall analysis shows over half (51%) of Laboulbeniomycetes have not been recorded in >50 years, while the group has a collective Scottian shortfall of 100%, given none of the 2454 described species have received an IUCN threat assessment. We suggest continued study of natural history collections, expanded citizen science programmes, and machine‐learning identification approaches as important tools for reducing knowledge shortfalls in both Laboulbeniomycetes and poorly studied taxa more generally.

show abstract

Molecular-Based Diversity Studies and Field Surveys Are Not Mutually Exclusive: On the Importance of Integrated Methodologies in Mycological Research

Cited by 12 publications

References 154 publications

Chemical Characterization and Metagenomic Identification of Endophytic Microbiome from South African Sunflower (Helianthus annus) Seeds

Chemical Characterization and Metagenomic Identification of Endophytic Microbiome from South African Sunflower (Helianthus annus) Seeds

Singleton-based species names and fungal rarity: Does the number really matter?

Biological knowledge shortfalls impede conservation efforts in poorly studied taxa—A case study of Laboulbeniomycetes

Contact Info

Product

Resources

About