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New species of Bacidia from the Russian Far East. A & B, Bacidia areolata: A, TS apothecium; B, ascus with spores. C & D, B. elongata: C, TS apothecium; D, spore. E & F, B. kurilensis: E, TS apothecium; F, ascus with spores. G & H, B. sachalinensis: G, TS apothecium; H, ascus with spores. Scales: A, C & G = 50 µm; E = 100 µm; B, D, F & H = 20 µm. In colour online.
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The molecular phylogeny of Bacidia s.s. in the Russian Far East was investigated using 62 nucleotide sequences from the ITS nrDNA region, 22 of which were newly obtained. Phylogenetic reconstructions employed Bayesian inference and maximum likelihood searches using MrBayes and RAxML. In addition, ITS2 secondary structures added further support usin...
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... microscope with an attached AxioCam MRc5 camera and processed with the Zeiss ZEN2012 image program. Images of the external features of the species were obtained from a Zeiss Stemi-2000 CS microscope with an attached AxioCam MRc5 camera and processed with the Zeiss AxioVision image program. The photomicrographs with detail of exciple structures in Fig. 4C were taken with a Zeiss AxioScope A1 compound microscope equipped with a Canon 60D digital camera. Spore and apothecium measurements are given as mean ðxÞ ± 1SD with outliers in parentheses. All other measurements are given as minimum, mean ðxÞ and maximum values. In those cases where not enough measurements were available for the ...
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... Five to eight apothecia were used from fresh material not older than five years, and thallus fragments were removed to minimize the risk of contamination by, for example, lichenicolous fungi. The same five target loci (three RNA-coding genes (nrITS, nrLSU, and mtSSU) and two protein-coding genes (RPB1 and RPB2)) as in Gerasimova et al. (2021a) have been selected for PCR; amplification, purification and sequencing were performed as described in Gerasimova et al. (2018). Cycling conditions included initial denaturation at 95°C for 2 min, 5 cycles of 95°C for 40 s, 54°C for 60 s, 72°C for 90 s, 33 cycles of 95°C for 40 s, 54°C for 60 s, 72°C for 90 s, and a final extension step at 72°C for 7 min. ...
... The Lichenologist 283 Table 4. Main characters separating taxa of Bacidia rubella s. lat. group. Information for Bacidia fraxinea and B. rubella are given by Ekman (1996), Ekman & Nordin (1993), Smith et al. (2009; B. iberica and B. parathalassica are from Llop (2007) and Aragón & Martínez (2003); B. thyrrenica from Llop et al. (2007); B. obtecta and B. elongata are from Gerasimova et al. (2018Gerasimova et al. ( , 2021b. Measurements for Caucasian taxa are newly provided (see taxa with 'Caucasus' in brackets after the species name. ...
... The main groups obtained from single and concatenated data in both ML and BI analyses are congruent and correspond to those obtained from the previous phylogenies (Ekman 2001;Gerasimova et al. 2018Gerasimova et al. , 2021b. Furthermore, similar to previous results, our phylogenies revealed two highly supported major clades in the two-and three-locus phylogenies. ...
During a study of the incompletely known lichen flora of the Caucasus, we analyzed 237 specimens of corticolous Bacidia s. str. collected in the Northern and Southern Caucasus, including Armenia, Azerbaijan, Georgia, and Russia. Of these, 54 specimens belonging to 11 species of Bacidia s. str. were selected for molecular studies, representing the observed morphological variability of the genus. We obtained 142 sequences from three RNA-coding genes (nrITS, nrLSU, and mtSSU) and two protein-coding genes ( RPB 1 and RPB 2). The single and concatenated datasets were complemented with Bacidia s. str. sequences from GenBank and subjected to Bayesian inference and two maximum likelihood analyses (RAxML and IQ-TREE). The resulting trees yielded highly concordant topologies of the groups and corresponded with previous results, supporting two main clades correlating with apothecia pigmentation. Our analyses are the first to reveal the presence of Bacidia heterochroa in the Caucasus. An exceptionally high degree of morphological plasticity was found in the Rubella and Suffusa groups. As a result of morphological examination and phylogenetic results, B. caucasica (Suffusa group) was described as new to science. Furthermore, two putative taxa in the Rubella group, Bacidia inconspicua ined. and B. maritima ined., were introduced. This study furthers our understanding and documentation of the understudied lichen flora of the Caucasus, bringing the total number of Bacidia species for the region to 13.
... Phylogenetic analysis resulted in B. friesiana of Korea (ON352609 and ON352610) being nested with the sequences of Russia (MH539765), supported by a bootstrap value of 100 and a posterior probability of 1.00 for the branch (Fig. 2). Bacidia friesiana was previously reported from Europe, North America and Russian Far East (Smith et al. 2009;Gerasimova et al. 2018). This is a new record to Korea. ...
... Phylogenetic relationships amongst available species in the genus Bacidia, based on a Maximum Likelihood analysis of the dataset of ITS sequences. The tree was rooted with the sequences of the genus Biatora, based onGerasimova et al. (2018). Maximum Likelihood bootstrap values ≥ 70% and posterior probabilities ≥ 95% are shown above internal branches. ...
A new species, Bacidia fuscopallida Lee & Heo and four new records, B. ekmaniana R. C. Harris, Ladd & Lendemer, B. friesiana (Hepp) Körb., B. heterochroa (Müll. Arg.) Zahlbr. and B. suffusa (Fr.) A. Schneid., are described from South Korea. Bacidia fuscopallida differs from B. diffracta S. Ekman, the most similar species, by warted but non-granular thallus, paler and smaller apothecia without pruina, proper exciple without crystals, over 11-septate ascospores and smaller pycnidia and pycnoconidia. Bacidia ekmaniana is recorded new to Asia, B. heterochroa is reported new to northeastern Asia and B. friesiana and B. suffusa are new to Korea. Molecular analyses employing internal transcribed spacer (ITS) sequences strongly support the classification of the five species of Bacidia . A surrogate key is provided to assist in the identification of all 19 taxa in Bacidia of Korea.
... Chemistry: all thallus spot tests negative, no secondary metabolites detected (Ekman 1996). Molecular support: a single ITS sequence (isolate DLH35 from UoA-CC-84), is most similar to Bacidia circumspecta GenBank Accessions AF282124 (Sweden, 97% percent identity, 12 positions different, 479 bp overlap, Ekman 2001) and MH539764 (Russia, 96% percent identity, 21 positions different, 549 bp overlap, Gerasimova et al. 2018). These differences are smaller than the difference between the two previously accessioned sequences (23 positions different, 476 bp overlap). ...
Here we provide one of the first detailed studies of lichen and allied fungi diversity in a continental North American city (Edmonton, Alberta, Canada), including an annotated checklist, images of all species, dichotomous keys, and local distribution maps. Edmonton is the northernmost city in North America with a population of over one million, and an industrial and transportation gateway for much of northern Canada. Lichen-based biomonitoring could be a tool to track airborne pollutants resulting from Edmonton’s growing populace and industrial activity. The first step towards such a program is documenting the diversity and distribution of lichens in the city. To accomplish this, we conducted a city-wide, systematic survey of 191 sites focused on epiphytes growing on deciduous boulevard trees. We augmented that survey with surveys of rare trees, opportunistic collections from river valley and ravine habitats, herbarium collections, phylogenetic analyses of a subset of collections, and observations submitted to online nature-reporting applications. We present ITS sequence barcode data for 33 species, phylogenetic analyses for Candelariaceae, Endocarpon, Flavopunctelia, the Lecanora dispersa group, Lecidella, Peltigera, Physconia, and Punctelia, and detailed descriptions of 114 species in 47 genera and 23 families. Two species are hypothesized to be new to North America (Endocarpon aff. unifoliatum, Lecidella albida), twelve more are new to Alberta (Amandinea dakotensis, Bacidia circumspecta, Candelaria pacifica, Candelariella antennaria, Heterodermia japonica, Lecania naegelii, Lecanora sambuci, Lecanora stanislai, Lecidea erythrophaea, Peltigera islandica, Phaeocalicium aff. tremulicola, and the introduced Xanthoria parietina), and five are putative new species to science (Physcia aff. dimidiata, Physcia aff. stellaris, Phaeocalicium sp., Phaeocalicium aff. tremulicola, Lichenaceae sp.). Illustrations are provided for all species to aid in verification and public outreach. Species richness was highest in foliose lichens (48), followed by crustose and calicioid lichens and allied fungi (41), with the lowest richness in fruticose lichens (25). We did a preliminary assessment of the suitability of species for citizen-science biomonitoring by assessing their distribution across the city, perceptibility to the public, identification accuracy, and, for a subset, how consistently species were surveyed by trained novices. Compared to other urban areas where lichen diversity has been studied, Edmonton is relatively species-rich in calicioids and Peltigera. Promising bioindicators may be limited to chlorolichens, including Caloplaca spp., Evernia mesomorpha, Flavopunctelia spp., Phaeophyscia orbicularis, Physcia adscendens, Physcia aipolia group, Physcia aff. stellaris, Usnea spp., and Xanthomendoza fallax. Other genera that may be responsive to pollutants such as Cladonia and Peltigera were almost exclusively restricted to river valley and ravine ecosystems, limiting their application as bioindicators. Some species commonly used as biomonitors elsewhere were too rare, small, poorly developed, or obscured by more common species locally (e.g., Candelaria concolor s.l., Xanthomendoza hasseana). The low overlap with lists of biomonitoring species from other regions of North America illustrates the necessity of grounding monitoring in knowledge of local diversity. Future augmentation of this list should focus on enhanced sampling of downed wood-, conifer-, and rock-dwelling lichens, particularly crustose species. The next step in developing a biomonitoring program will require modelling species’ responses to known air quality and climatic gradients.
... Lichen species within Bacidia occur in almost all substrates, habitats and climatic zones of the world, but are abundant and diverse in sheltered habitats, such as tree bark, in moist areas of boreal, temperate and especially tropical regions (Kirk et al., 2008). Bacidia in the strict sense is consequently characterized by acicular spores and a well-developed, prosoplectenchymatic proper exciple composed of radiating, abundantly furcate and rarely anastomosed hyphae with heavily gelatinized cell walls and cell lumina that become compressed and narrower with age (Gerasimova et al., 2018;Kistenich et al., 2018). Species of this genus also produce one or more pigments in the apothecia. ...
... This study reports it as a new record to the lichen biota of Pakistan. (Gerasimova et al., 2018). In the phylogram, newly generated sequences from Pakistani collections clustered with B. suffusa specimens and formed a sister group relationship with B. areolata Gerasimova & A. Beck (Fig. 3). ...
... It is the frequently pruinose species having long ascospores. In the phylogram, Bacidia suffusa made sister branch to B. areolata reported form Russia (Gerasimova et al., 2018), which is morphologically different from Pakistani specimen in having smooth, cracked to areolate thallus and small ascospores. ...
... In the first molecular study on Bacidia s. str. from the Russian Far East (RFE), taxon sampling was expanded (Gerasimova et al. 2018). Four new species were described, and these are currently considered endemic. ...
... This study was based on fresh collections of Bacidia gathered by the authors in the field from 2013 to 2015 in the southern part of the Russian Far East (Primorskiy and Khabarovskiy Krai), and on Sakhalin and the Kurile Islands (as indicated in Gerasimova et al. (2018)). The second author collected the Bacidia obtecta specimens on Sakhalin in 2017 (see details under Taxonomy). ...
... Thallus fragments were removed to minimize the risk of contamination by, for example, lichenicolous fungi. PCR amplification, purification and sequencing were performed as described in Gerasimova et al. (2018). Cycling conditions included initial denaturation at 95°C for 2 min, 5 cycles of 95°C for 40 s, 54°C for 60 s, 72°C for 90 s, 33 cycles of 95°C for 40 s, 54°C for 60 s, 72°C for 90 s, and a final extension step at 72°C for 7 min. ...
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.
... Five to eight apothecia were used from fresh material not older than 5 years and thallus fragments were removed in order to minimize the risk of contamination by, for example, lichenicolous fungi. PCR amplification, purification and sequencing were performed as described in Gerasimova et al. (2018). Cycling conditions included initial denaturation at 95°C for 2 min, 5 cycles of 95°C for 40 s, 54°C for 60 s and 72°C for 90 s, 33 cycles of 95°C for 40 s, 54°C for 60 s and 72°C for 90 s, and a final extension step at 72°C for 7 min. ...
In recent years, several species that have long been considered to belong in Bacidia s. lat. have been transferred to other genera such as Bellicidia , Bibbya , Scutula , and also to Toniniopsis , accommodating species previously placed in Bacidia and Toninia . One of its widespread species, Toniniopsis subincompta , can be recognized by its thinly granular thallus, dark brown to black apothecia, green epithecium, red-brown hypothecium, and bacilliform ascospores. However, it shows considerable variation in thallus structure, and coloration of apothecia, hypothecium and exciple. We sequenced 20 specimens of T. subincompta to investigate whether there is phylogenetic support for the delimitation of species in accordance with the variability of the observed characters. For phylogenetic analyses, we used newly generated sequence data from the nuclear internal transcribed spacer (nrITS), mitochondrial small subunit (mtSSU) and DNA-directed RNA polymerase II subunit ( RPB 2). Maximum likelihood and Bayesian inference analyses, as well as three species delimitation programs, provided consistent evidence that T. subincompta forms two separate lineages, to be recognized at the species level. The complex nomenclature of T. subincompta (basionym Lecidea subincompta ) shows it to be a synonym of Bellicidia incompta . For the most common taxon previously called Bacidia ( Toniniopsis ) subincompta , the new combination T. separabilis is made, rather than proposing a conserved type for Lecidea subincompta . Toniniopsis dissimilis is newly described to accommodate the less common taxon. Toniniopsis dissimilis is characterized by a predominantly wrinkled to warted to subsquamulose thallus; generally grey-brown to dark brown apothecia, often with a lighter margin; a dark brown hypothecium, frequently gradually merging into the coloration of the exciple below and the lateral part of the exciple attached to the hymenium; a mostly colourless rim and lateral part of the exciple. The closely related T. separabilis is characterized by a thallus of mostly single or contiguous ±loose granules, often forming short, coralloid, isidium-like bulges; darker apothecia, with a margin mostly of the same colour or darker than the disc; a comparatively thinner hypothecium easily separated from the exciple below. The rim and lateral part of the exciple often contain either a blue, brown or mixed blue-brown colour in the upper part or along the whole margin. Lectotypes of Bacidia vegeta , Lecidea bacillifera f. melanotica and Secoliga atrosanguinea var. affinis (the synonyms of T. separabilis ) are selected. Cyanotrophy and the occurrence of albino morphs in T. separabilis are discussed.
The paper presents data on six lichen species new to Sakhalin Island. Two of them, namely Physconia subpulverulenta and Bacidia elongata, are recorded for the Sakhalin Region for the first time. Mycobilimbia carneoalbida, Mycobilimbia tetramera, Chaenotheca xyloxena, and Pseudoschismatomma rufescens are noted for Sakhalin Island for the first time. Brief information on distribution, ecology, distinctive characters and illustrations are provided for the species.
Four species of Bacidina (Ramalinaceae, Lecanorales, Ascomycota) are described as new to science from northern Europe (mainly Swedish material): Bacidina ferax S.Ekman, Bacidina lignicola S.Ekman, Bacidina maculans S.Ekman and Bacidina populnea S.Ekman. Another two species are resurrected from synonymy: Bacidina caerulea (Körb.) S.Ekman (based on Bacidia caerulea Körb.) and Bacidina circumpallens (Nyl.) S.Ekman (based on Lecidea circumpallens Nyl.). An additional four combinations are made: Bacidina friesiana (Hepp) S.Ekman (based on Biatora friesiana Hepp), Bacidina subfuscula (Nyl.) S.Ekman (based on Lecidea subfuscula Nyl.), Bacidina tarandina (Nyl.) S.Ekman (based on Lecidea tarandina Nyl.) and Bacidina tenella (Kullh.) S.Ekman (based on Bacidia tenella Kullh.). The morphology, distribution and nomenclature of all 28 species of Bacidina currently known from Scandinavia (Sweden, Norway, Denmark) are treated and an identification key is provided. In addition, Bacidina friesiana is discussed (for comparison with B. caerulea ) even if it is not currently known from Scandinavia. Two of the treated species ( B. epithallina ined., B. parasitica ined.) are parasites on cyanolichens but are not formally introduced here because of the scarcity of available material. Bilimbia arceutinoides Anzi is reduced to synonymy with Bilimbia sabuletorum (Schreb.) Arnold and Lecidea luteola var. chlorotica Ach. is reduced to synonymy with Bacidia rubella (Hoffm.) A.Massal. It is concluded that despite the present work, the diversity of the genus Bacidina remains insufficiently understood, at least in Scandinavia.
As a result of expeditionary investigations on Iturup Island (southern group of islands of the Kuril archipelago), 61 species of lichens were identified as new to the island, including Porpidia contraponenda and Xylographa rubescens – new to the Russian Far East, and Amandinea coniops and Arthonia dispuncta – new to the South of the Russian Far East. Six species are new to the Sakhalin Region. The difference in species composition of the Sea of Okhotsk coast and the Pacific coast of Iturup Island is briefly discussed.
Micarea xanthonica and Trapelia elacista are reported as new to Asia and Russia, Lecania coreana and Lepraria pseudoarbuscula are reported new to Russia, Micarea globulosella is reported for the first time for the Russian Far East, Rinodina herreri is reported for the second time for Asia and Russia from Khabarovsk Territory, and Coenogonium isidiatum is reported for the second time for Russia from Primorye Territory. A comparison of known isidiate Coenogonium species is made. Lichenomphalia umbellifera is reported as new to the Kuril Islands and Sakhalin Region. Ramalina thrausta is newly reported from Sakhalin Island. The characteristic features of the specimens from the Russian Far East and comparisons with similar species are given.
