Naming the untouchable – environmental sequences and niche partitioning as taxonomical evidence in fungi

Khan, Faheema Kalsoom; Kluting, Kerri L.; Tångrot, Jeanette; Urbina, Héctor; Ammunét, Tea; Sahraei, Shadi Eshghi; Rydén, Martin; Ryberg, Martin; Rosling, Anna

doi:10.1186/s43008-020-00045-9

Cited by 23 publications

(20 citation statements)

References 64 publications

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“…There has been much discussion in the mycological community on using metagenomic DNA from environmental samples as holotypes and in general for taxon naming [ 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 ]. In addition, the first studies on naming DNA-based taxa have already been published, e.g., De Beer et al [ 111 ], Lücking and Moncada [ 112 ], Kalsoom Khan et al [ 113 ]. The ITS1 and ITS2 phylotypes attributed to Zanclospora represent either new lineages or already described species that have not yet been sequenced.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny, Global Biogeography and Pleomorphism of Zanclospora

et al. 2021

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Zanclospora (Chaetosphaeriaceae) is a neglected, phialidic dematiaceous hyphomycete with striking phenotypic heterogeneity among its species. Little is known about its global biogeography due to its extreme scarcity and lack of records verified by molecular data. Phylogenetic analyses of six nuclear loci, supported by phenotypic data, revealed Zanclospora as highly polyphyletic, with species distributed among three distantly related lineages in Sordariomycetes. Zanclospora is a pleomorphic genus with multiple anamorphic stages, of which phaeostalagmus-like and stanjehughesia-like are newly discovered. The associated teleomorphs were previously classified in Chaetosphaeria. The generic concept is emended, and 17 species are accepted, 12 of which have been verified with DNA sequence data. Zanclospora thrives on decaying plant matter, but it also occurs in soil or as root endophytes. Its global diversity is inferred from metabarcoding data and published records based on field observations. Phylogenies of the environmental ITS1 and ITS2 sequences derived from soil, dead wood and root samples revealed seven and 15 phylotypes. The field records verified by DNA data indicate two main diversity centres in Australasia and Caribbean/Central America. In addition, environmental ITS data have shown that Southeast Asia represents a third hotspot of Zanclospora diversity. Our data confirm that Zanclospora is a rare genus.

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Section: Discussionmentioning

confidence: 99%

Phylogeny, Global Biogeography and Pleomorphism of Zanclospora

et al. 2021

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“…We then grouped ASVs into phylogeny-based species hypotheses (SHs) using a Poisson tree process model (PTP; Zhang et al 2013), based on a phylogenetic tree built from the reads. Denoised ASVs were generated from the dataset using the procedure established in Kalsoom- Khan et al (2020) after assessing general read quality and ensuring that the majority of reads fell within the expected length (1-2 kb). Raw sequence reads were filtered and trimmed using the tool cutadapt (version 1.18; Martin 2011) to demultiplex reads based on the forward and reverse barcodes, to keep only reads with both primers present, and to remove the actual primer sequences from the reads.…”

Section: Bioinformatic Sequence Analysesmentioning

confidence: 99%

“…The maximum likelihood tree contained multiple issues including nonfungal lineages and possible chimeras. Class-level taxonomic assignments with a SIN-TAX confidence value of 0.8 or higher were added to the ASV name in the tree file using a customized script (Kalsoom Khan et al 2020) in order to aid pruning of nonfungal lineages from the initial phylogenetic tree. A series of alignments and trees were generated by stepwise removal of ASVs that were determined to be non-fungal based on SINTAX taxonomy assignment and their placement in the tree.…”

Section: Bioinformatic Sequence Analysesmentioning

confidence: 99%

Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa

Meidl¹,

Furneaux²,

Tchan³

et al. 2021

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Forests and woodlands in the West African Guineo-Sudanian transition zone contain many tree species that form symbiotic interactions with ectomycorrhizal (ECM) fungi. These fungi facilitate plant growth by increasing nutrient and water uptake and include many fruiting body-forming fungi, including some edible mushrooms. Despite their importance for ecosystem functioning and anthropogenic use, diversity and distribution of ECM fungi is severely under-documented in West Africa. We conducted a broad regional sampling across five West African countries using soil eDNA to characterize the ECM as well as the total soil fungal community in gallery forests and savanna woodlands dominated by ECM host tree species. We subsequently sequenced the entire ITS region and much of the LSU region to infer a phylogeny for all detected soil fungal species. Utilizing a long read sequencing approach allows for higher taxonomic resolution by using the full ITS region, while the highly conserved LSU gene allows for a more accurate higher-level assignment of species hypotheses, including species without ITS-based taxonomy assignments. We detect no overall difference in species richness between gallery forests and woodlands. However, additional gallery forest plots and more samples per plot would have been needed to firmly conclude this pattern. Based on both abundance and richness, species from the families Russulaceae and Inocybaceae dominate the ECM fungal soil communities across both vegetation types. The community structure of both total soil fungi and ECM fungi was significantly influenced by vegetation types and showed strong correlation within plots. However, we found no significant difference in fungal community structure between samples collected adjacent to different host tree species within each plot. We conclude that within plots, the fungal community is structured more by the overall ECM host plant community than by the species of the individual host tree that each sample was collected from.

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“…Adding environmental DNA-samples to our basidiome data could be a next step to clarify the situation (cf. Kalsoom Khan et al 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Polypore fungi as a flagship group to indicate changes in biodiversity – a test case from Estonia

2021

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Polyporous fungi, a morphologically delineated group of Agaricomycetes (Basidiomycota), are considered well studied in Europe and used as model group in ecological studies and for conservation. Such broad interest, including widespread sampling and DNA based taxonomic revisions, is rapidly transforming our basic understanding of polypore diversity and natural history. We integrated over 40,000 historical and modern records of polypores in Estonia (hemiboreal Europe), revealing 227 species, and including Polyporus submelanopus and P. ulleungus as novelties for Europe. Taxonomic and conservation problems were distinguished for 13 unresolved subgroups. The estimated species pool exceeds 260 species in Estonia, including at least 20 likely undescribed species (here documented as distinct DNA lineages related to accepted species in, e.g., Ceriporia, Coltricia, Physisporinus, Sidera and Sistotrema). Four broad ecological patterns are described: (1) polypore assemblage organization in natural forests follows major soil and tree-composition gradients; (2) landscape-scale polypore diversity homogenizes due to draining of peatland forests and reduction of nemoral broad-leaved trees (wooded meadows and parks buffer the latter); (3) species having parasitic or brown-rot life-strategies are more substrate-specific; and (4) assemblage differences among woody substrates reveal habitat management priorities. Our update reveals extensive overlap of polypore biota throughout North Europe. We estimate that in Estonia, the biota experienced ca. 3–5% species turnover during the twentieth century, but exotic species remain rare and have not attained key functions in natural ecosystems. We encourage new regional syntheses on long studied fungal groups to obtain landscape-scale understanding of species pools, and for elaborating fungal indicators for biodiversity assessments.

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Naming the untouchable – environmental sequences and niche partitioning as taxonomical evidence in fungi

Cited by 23 publications

References 64 publications

Phylogeny, Global Biogeography and Pleomorphism of Zanclospora

Phylogeny, Global Biogeography and Pleomorphism of Zanclospora

Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa

Polypore fungi as a flagship group to indicate changes in biodiversity – a test case from Estonia

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