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Lichen-forming members of the Lecanoromycetes. 2. Pleopsidium chlorophanum, Acarosporomycetidae, Acarosporales, Acarosporaceae (photo by E. Timdal). 3. Candelariella lutella, Candelariaceae (photo by E. Timdal). 4. Phyllobaeis imbricata. Close-up of fruiting bodies, Ostropomycetidae, Baeomycetaceae (photo by R. Lü cking). 5. Ophioparma ventosa, Ophioparmaceae (photo by E. Timdal). 6. Leptogium burgessii. Close-up of fruiting bodies, Lecanoromycetidae,
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New and interesting records of Ascomycota in Bulgaria
Soil fungi have been widely studied, but the effects of heavy metal contamination at various levels as well as the abundance and diversity of heavy metal tolerant fungi in the contaminated paddy soils are still unknown. The purpose of this study is to analyze the adaptability of fungi at different levels of heavy metal contamination to identify spe...
Dimelaena tibetica is described as a species new to science, characterized by a grayish yellow surface, usually with a covering of white pruina, a crustose thallus, areolate at center, radiate-plicate at margin, adnate apothecia and lacking gyrophoric acid. It differs from other usnic acid-containing Dimelaena species by its plane marginal lobes an...
Citations
... Ascomycota and Basidiomycota were identified as the dominant phyla in both healthy and infected K. valerianoides plants, mirroring the fungal distribution observed in rhizosphere soil. Ascomycetes was the most prevalent taxon, as it plays an important ecological role as a decomposer [53]. Previous studies have demonstrated that endophytic fungi primarily originate from soil fungi and gain entry into plants through roots, stems, and leaves [37]. ...
Background
Rhizosphere and endophytic fungi play important roles in plant health and crop productivity. However, their community dynamics during the continuous cropping of Knoxia valerianoides have rarely been reported. K. valerianoides is a perennial herb of the family Rubiaceae and has been used in herbal medicines for ages. Here, we used high-throughput sequencing technology Illumina MiSeq to study the structural and functional dynamics of the rhizosphere and endophytic fungi of K. valerianoides.
Results
The findings indicate that continuous planting has led to an increase in the richness and diversity of rhizosphere fungi, while concomitantly resulting in a decrease in the richness and diversity of root fungi. The diversity of endophytic fungal communities in roots was lower than that of the rhizosphere fungi. Ascomycota and Basidiomycota were the dominant phyla detected during the continuous cropping of K. valerianoides. In addition, we found that root rot directly affected the structure and diversity of fungal communities in the rhizosphere and the roots of K. valerianoides. Consequently, both the rhizosphere and endophyte fungal communities of root rot-infected plants showed higher richness than the healthy plants. The relative abundance of Fusarium in two and three years old root rot-infected plants was significantly higher than the control, indicating that continuous planting negatively affected the health of K. valerianoides plants. Decision Curve Analysis showed that soil pH, organic matter (OM), available K, total K, soil sucrase (S_SC), soil catalase (S_CAT), and soil cellulase (S_CL) were significantly related (p < 0.05) to the fungal community dynamics.
Conclusions
The diversity of fungal species in the rhizosphere and root of K. valerianoides was reported for the first time. The fungal diversity of rhizosphere soil was higher than that of root endophytic fungi. The fungal diversity of root rot plants was higher than that of healthy plants. Soil pH, OM, available K, total K, S_CAT, S_SC, and S_CL were significantly related to the fungal diversity. The occurrence of root rot had an effect on the community structure and diversity of rhizosphere and root endophytic fungi.
... We also used blastn to extract nucLSU, mitSSU, RPB1, and RPB2 genes with GenBank sequences JQ301589, KJ766480, KJ766831, and KJ766963, respectively, as queries. These four genes were used for phylogenetic placement using the Evolutionary Placement Algorithm as implemented in T-BAS v2.3 with the Lecanoromycetes v2 reference tree (see Supplementary Figure S1) (Miadlikowska et al. 2006;Carbone et al. 2017Carbone et al. , 2019. ...
Lichen-forming fungi are a diverse and ecologically important group of obligate mutualistic symbionts. Due to difficulties with maintaining them in culture and their extremely slow growth, lichenologists are increasingly opting for metagenomic sequencing followed by symbiont genome separation using bioinformatic pipelines. However, without knowing the true genome size of the lichen-forming fungus, we cannot quantify the completeness of the genome assembly and the efficacy of the bioinformatic filtering. To address this issue, we report here the first whole-genome assembly for the lichen-forming fungus Ramalina farinacea (L.) Ach. sequenced with Oxford Nanopore long-read technology alongside direct measurements of its genome size using flow cytometry. The assembly showed high contiguity (N50 = 1.55 Mbp) and gene set completeness (BUSCO = 95.8%). The highly robust genome size obtained of 33.61 Mbp/1C (CV% = 2.98) showed our assembly covered 97% of the entire genome. Our results demonstrate that accurate genome size measurements can be obtained directly from lichen thalli and used to provide a benchmark for assessing true cytometric completeness of metagenome-derived assemblies.
... Much of our current understanding on photobiont-mycobiont partnerships comes from studies involving a few lichen species or geographical areas 17,19,23,24,[33][34][35][36][37][38] . However, mycobiont-photobiont partnerships do not happen in isolation, they are part of a larger web of interactions supporting the assembly and maintenance of communities, and understanding them requires a systemic approach. ...
Symbiosis is a major engine of evolutionary innovation underlying many extant complex organisms. Lichens are a paradigmatic example that offers a unique perspective on the role of symbiosis in ecological success and evolutionary diversification. Lichen studies have produced a wealth of information regarding the importance of symbiosis, but they frequently focus on a few species, limiting our understanding of large-scale phenomena such as guilds. Guilds are groupings of lichens that assist each other’s proliferation and are intimately linked by a shared set of photobionts, constituting an extensive network of relationships. To characterize the network of lichen symbionts, we used a large data set (n=206\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$n=206$$\end{document} publications) of natural photobiont-mycobiont associations. The entire lichen network was found to be modular, but this organization does not directly match taxonomic information in the data set, prompting a reconsideration of lichen guild structure and composition. The multiscale nature of this network reveals that the major lichen guilds are better represented as clusters with several substructures rather than as monolithic communities. Heterogeneous guild structure fosters robustness, with keystone species functioning as bridges between guilds and whose extinction would endanger global stability.
... Our attention was initially drawn to seven recently described classes of Ascomycota, [6][7][8][9][10][11] none of which had been previously resolved with respect to evolutionary relationships, using various taxon and locus samplings. 3,4,7,8,[12][13][14][15][16][17][18][19][20] We obtained genomes from 15 representatives of each of these ''orphan'' classes by genome sequencing from both culture and metagenome-assembled genomes (MAGs). We augmented this sampling by targeting several other fungal lineages treated as ''incertae sedis'' or previously undersampled in genome-scale studies. ...
Ascomycota account for about two-thirds of named fungal species.¹ Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.² Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.³,⁴,⁵ However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous “orphan” ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.
... Of the molecular markers tested so far, the highest taxonomic resolution resides in sequences covering the 18S-ITS-28S segment of the nuclear ribosomal DNA and partial sequences of the largest subunit of RNA polymerase II (rpb1), which allow separating even very clo-80 sely related species, including those hidden among so called complex species (Kohout et al. 2014;Krüger et al. 2012;Stockinger et al. 2014). Moreover, recent analyses indicated that phylogenies of members of the Glomeraceae reconstructed from concatenated 85 sequences of the two unlinked loci (18S-ITS-28S+rpb1) were more robust than those obtained based on these loci analyzed separately (Błaszkowski et al. 2021a(Błaszkowski et al. , 2021b, in agreement with the opinions of many researchers dealing with other fungal groups (Alves-90 Silva et al. 2020;Matheny 2005;Miadlikowska et al. 2006Miadlikowska et al. , 2014Salvador-Montoya et al. 2020). However, members of other families of the Glomeromycota have not been tested in this respect so far. ...
Three new species of arbuscular mycorrhizal fungi of the genus Diversispora (phylum Glomeromycota) were described based on their morphology and molecular phylogeny. The phylogeny was inferred from the analyses of the partial 45S rDNA sequences (18S-ITS-28S) and the largest subunit of RNA polymerase II (rpb1) gene. These species were associated in the field with plants colonizing maritime sand dunes of the Baltic Sea in Poland and formed mycorrhiza in single-species cultures.
... At higher taxonomic ranks, lichen mycobiontphotobiont associations are quite stable, where whole lichen families or even orders have preferences for specific genera of photobionts (Miadlikowska et al. 2006). The most common, by far, is Trebouxia (Trebouxiophyceae), followed by Nostoc (Cyanobacteria), Trentepohlia (Ulvophyceae), and Asterochloris (Trebouxiophyceae; dePriest 2004, Miadlikowska et al. 2006). ...
... At higher taxonomic ranks, lichen mycobiontphotobiont associations are quite stable, where whole lichen families or even orders have preferences for specific genera of photobionts (Miadlikowska et al. 2006). The most common, by far, is Trebouxia (Trebouxiophyceae), followed by Nostoc (Cyanobacteria), Trentepohlia (Ulvophyceae), and Asterochloris (Trebouxiophyceae; dePriest 2004, Miadlikowska et al. 2006). However, these photobionts are rarely found in Verrucariaceae, a family in which most of the amphibious lichens (both freshwater and marine) belong. ...
Crustose Verrucariaceae lichens form a distinctive black belt on seashores all over the world. This lifestyle is apparently enabled by a specific set of photobionts. However, their diversity is understudied. We sampled these lichens from the northern Patagonian Pacific coast of Chile. Using molecular markers, we identified both mycobionts and photobionts. The lichens, belonging to the genus Hydropunctaria and Wahlenbergiella group, hosted solely Ulvophycean photobionts. Pseudendoclonium submarinum (Kornmanniaceae, Ulvales) was the most common, but representatives of other closely related, yet undescribed, lineages were also found. Undulifilum symbioticum gen. et sp. nov. is described within the Kornmanniaceae based on culture morphology and DNA sequence data. Furthermore, the free-living macroscopic genus Urospora (Acrosiphoniaceae, Ulotrichales) is reported as a lichen photobiont for the first time and is the first of its kind in the order. These results indicate that undescribed algal diversity is waiting to be uncovered in seashore lichens.
... Currently our knowledge of the phylogeny of Lecidella is limited, with only a few studies including representatives from this genus [43][44][45][46][47][48][49]. While these few studies support the monophyly of Lecidella and its placement in Lecanoraceae, none have included a broader taxonomic sampling to address the evolutionary relationships of species within the genus. ...
... ex Tuck.) A. Schneid., B. rosella and B. rubella (Hoffm.) A. Massal. (James et al. 2006;Miadlikowska et al. 2006Miadlikowska et al. , 2014Reese Naesborg et al. 2007;Ekman et al. 2008;Kistenich et al. 2018). ...
To clarify deep relationships among species lineages within Bacidia s. str., and to investigate the robustness of the deeper branches, we combined data from three traditionally used RNA-coding genes (nrITS, nrLSU and mtSSU) with two protein-coding genes ( RPB 1 and RPB 2). The multigene phylogeny contained 48 newly generated sequences from the Russian Far East and all Bacidia s. str. sequences from GenBank (131 sequences). We subjected the alignments for the single and concatenated data sets to Bayesian inference (BI) and two maximum likelihood (ML) analyses (RAxML and IQ-TREE). The topologies of phylogenetic trees recovered from BI and ML analyses were highly concordant. The multilocus phylogeny of Bacidia s. str. was congruent with previous results based on nrITS sequences from the Russian Far East but with considerably higher support values for most of the deeper branches. A correlation between the recovered clades and apothecial pigments in the upper part of the hymenium and lateral exciple was observed. Based on morphological and molecular evidence, Bacidia obtecta is described as new to science. It was recovered as the sister lineage of B. elongata . The two species are alike in having up to four enlarged lumina cells along the exciple edge, but B. obtecta differs in the abundant crystals found in the upper hymenium and lateral exciple, and by having spores with fewer septa.
... org/ about. php), which was used as the basis for the classification of the kingdom Fungi James et al. 2006;Miadlikowska et al. 2006;Schoch et al. 2006Schoch et al. , 2009a. Most of the recently published fungal monographs have also used multilocus phylogenies, Fig. 9 (continued) such as the monographs on Alternaria (Woudenberg et al. 2015), Diademaceae , Didymellaceae (Chen et al. 2017), freshwater Dothideomycetes (Shearer et al. 2009;Dong et al. 2020), Massarineae , Trypetheliaceae (Lücking et al. 2016) amongst others. ...
The species is one of the basic units of biological classification. Both species concepts and recognition are essential topics in taxonomic studies and other biological research. In the first part of this review, we briefly discuss the taxonomic history of the class Dothideomycetes. In the second part of the paper, we review four commonly used species concepts, focusing on morphological, ecological, biological and phylogenetic criteria and their applicability in the taxonomy of Dothideomycetes. The application and utility of the four criteria is discussed with examples in the genera Ascochyta, Cercospora and Neofusicoccum. Some problems and challenges of studying Dothideomycetes are analyzed and basic guidelines for classifying species under the above criteria are provided.
... Fuscopannaria viridescens P. M. Jørg. & Zhurb., the only tripartite species in a large cyanolichen genus (Jørgensen & Zhurbenko 2002;Nelson & Wheeler 2013), could be postulated to have been derived from photobiont switch, as also proposed to have taken place in the genus Peltigera (Miadlikowska et al. 2006). Another remarkable example is from Gibbosporina didyma Elvebakk et al., where cephalodia form small chlorobiont thalli which produce apothecia, almost like the adverse situation of a cephalodium on a green thallus ). ...
Gibbosporina cyanea is described here as new to science, based on its holotype collected in Sri Lanka in the 1860s. The species is a bipartite cyanolichen in contrast to all other known Gibbosporina species, which are tripartites. The species appears to have evolved through cephalodia emancipation followed by divergence. Phyllidia indicate a cephalodiate evolutionary origin with a continued function similar to vegetative propagules. The species is considered to represent a relatively young speciation within an evolutionary old genus and G. sphaerospora is discussed as a possible candidate for being its closest known relative based on spore morphology. As the species appears to be so different from the remaining Gibbosporina species, it is compared here to representatives of other related palaeotropical cyanogenera, such as Leightoniella , Lepidocollema , Pannaria and Physma . Perispore structure is shown to be a useful character in separating these genera, including distinct clades of the non-monophyletic genera Physma and Lepidocollema. Leightoniella zeylanensis is reported here as new to Japan, and it is concluded that Pannaria lurida needs to be restudied in India and Sri Lanka.
