No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts
... Nuclear DNA was extracted from dried and cleaned basidiomata of ca. 0.2 g of ample amount using 2% CTAB protocol following Gardes and Bruns (1993). Primers used during amplifications were ITS1F 5ʹ-CCT GGT CAT TTA GAG GAA GT A A-3 ʹ and ITS4 5ʹ-TCC TCC GCT CTA TTG ATA TGC-3ʹ for the nrITS region, while LR0R 5ʹ-ACC CGC TGA ACT TAA GC-3ʹ and LR5 5ʹ-TCC TGA GGG AAA CTT CG-3ʹ for the nrLSU region (Gardes and Bruns 1993;White et al. 1990). ...
... 0.2 g of ample amount using 2% CTAB protocol following Gardes and Bruns (1993). Primers used during amplifications were ITS1F 5ʹ-CCT GGT CAT TTA GAG GAA GT A A-3 ʹ and ITS4 5ʹ-TCC TCC GCT CTA TTG ATA TGC-3ʹ for the nrITS region, while LR0R 5ʹ-ACC CGC TGA ACT TAA GC-3ʹ and LR5 5ʹ-TCC TGA GGG AAA CTT CG-3ʹ for the nrLSU region (Gardes and Bruns 1993;White et al. 1990). PCR conditions described by Gardes and Bruns (1993) were followed where the cycling program entailed an initial denaturation step at 94 °C for 2 min, denaturation at 94 °C for 30 s, annealing at 54 °C for 1 min, extension at 71 °C for 2 min, and a final extension at 71 °C for 5 min for 35 cycles . ...
... Primers used during amplifications were ITS1F 5ʹ-CCT GGT CAT TTA GAG GAA GT A A-3 ʹ and ITS4 5ʹ-TCC TCC GCT CTA TTG ATA TGC-3ʹ for the nrITS region, while LR0R 5ʹ-ACC CGC TGA ACT TAA GC-3ʹ and LR5 5ʹ-TCC TGA GGG AAA CTT CG-3ʹ for the nrLSU region (Gardes and Bruns 1993;White et al. 1990). PCR conditions described by Gardes and Bruns (1993) were followed where the cycling program entailed an initial denaturation step at 94 °C for 2 min, denaturation at 94 °C for 30 s, annealing at 54 °C for 1 min, extension at 71 °C for 2 min, and a final extension at 71 °C for 5 min for 35 cycles . Gel electrophoresis was used for total DNA extraction and for PCR amplification of DNA using 1% agarose gel (Voytas 2000). ...
Two new species under the names of Lepiota brunneopileata and L. pakistanensis are described herein based on four collections during mushroom surveys in 2021-2022 from scrubland in district Gujrat, Pakistan. Morpho-anatomy and phylogenetic placement, based on Internal Transcribed Spacer (nrITS) and Larger Subunit (nrLSU), clustered them into Lepiota sect. Lepiota and Stenosporae. Lepiota brunneopileata is characterized by brown to dark brown disk, squamules on light brown pileus surface as well as on stipe, spurred, truncate basidiospores (3.9-7.0 × 2.7-4.1 μm), narrowly clavate to cylindrical and utriform cheilocystidia, with light brown to brown trichodermal pileus covering elements. Lepiota pakistanensis possesses small basidiomata with ochraceous disk, ochraceous to light brown cottony squamules on creamy white pileus surface, fusiform to slightly amygdaliform basidiospores (10.3-11.7 × 4.7-5.8 μm), clavate to broadly clavate cheilocystidia, trichodermal pileus covering with long cylindrical to fusiform terminal elements and spherocystous to clavate basal elements.
... Quality and quantity of the DNA extracts were checked with agarose gel electrophoresis. The amplification and sequencing reactions of the ITS rDNA region were performed with the primer set ITS1F and ITS4 (White et al. 1990, Gardes et Bruns 1993 under the usual ITS PCR conditions. The purified PCR product was sequenced from both directions with the primers mentioned above using BigDye fluorescent chemistry (Applied Biosystems, Foster City, USA) on an ABI PRISM 3130xl genetic analyser (Applied Biosystems). ...
Available as Open Acces in Czech Mycology 76(1): 83–94 (http://www.czechmycology.org/_cmo/CM76106.pdf). A new record of the rare agaric species Gymnopilus stabilis from the Czech Republic is described morphologically and genetically. The basidiomata show good agreement with the recently published epitype and diagnostic characters of the species. While the robustness of the basidiomata, the presence of a pink hue, and a distinct sweetish aromatic smell are typical characters, though not
always present, the predominantly warm orange colour of adult pilei seems to be stable character. The combination of fleshy basidiomata and typical pileus colour distinguishes G. stabilis from
G. penetrans/hybridus and G. decipiens, which are taxa sometimes confused with G. stabilis. Comparison of the nearest ITS rDNA sequences from GenBank confirmed the identity of our record and
showed that the species is distributed not only in Europe and Siberia, but also in Pakistan and India. The ecological characterisation of G. stabilis is updated, showing that it is a saprotrophic species on dead wood of conifers, both Pinus and Picea, but also a facultative anthracophilous fungus able to
grow on burnt wood and ash.
... Molecular sequence data were generated for four loci: the internal transcribed spacers (ITS) of ribosomal DNA (ITS1-5.8S rDNA-ITS2 region) were amplified with primers ITS1F (Gardes et Bruns 1993) and ITS4 (White et al. 1990), the 28S subunit of ribosomal DNA (LSU) with primers LR0R and LR6 (Vilgalys et Hester 1990), the 18S subunit of rDNA (SSU) with primers NS1 and NS6 (White et al. 1990), and translation elongation factor-1alpha (EF1a) with primers EF1-983F and EF1-1567R (Rehner et Buckley 2005). PCR was performed with Kapa polymerase (Kapa Biosystems, Wilmington, USA) following a standard protocol with 37 cycles and an annealing temperature of 54°C. ...
Octospora pulchrispora (Pezizales)-a new bryophilous species on Cynodontium polycarpon.-Czech Mycol. 76(1): 45-62. Octospora pulchrispora Sochorová et Eckstein is described as a new species based on finds from the Czech Republic. It features a remarkable ascospore ornamentation formed by low, branching, cyanophilous ridges. It parasitises the acrocarpous moss Cynodontium polycarpon (Rhabdoweisiaceae) and induces galls on the rhizoids. In the phylogenetic analysis based on the LSU, SSU and EF1a loci, O. pulchrispora formed a highly supported clade with Octospora gyalectoides agg., O. leucoloma, O. gemmicola, O. axillaris, O. excipulata, O. bridei and two undescribed Octospora species.: Octospora pulchrispora (Pezizales)-nový bryofilní druh na Cynodontium polycarpon.-Czech Mycol. 76(1): 45-62. Octospora pulchrispora Sochorová et Eckstein (zemnička krásnovýtrusá) je popsána jako nový druh pro vědu podle nálezů z České republiky. Vyznačuje se zajímavou ornamentikou výtrusů, která je tvořena nízkými, větvenými, cyanofilními hřebínky. Parazituje na akrokarpním mechu psízubci mno-hoplodém-Cynodontium polycarpon (Rhabdoweisiaceae), na jehož rhizoidech indukuje tvorbu hálek. Ve fylogenetické analýze založené na lokusech LSU, SSU a EF1a tvořila O. pulchrispora silně podpořený klad s Octospora gyalectoides agg., O. leucoloma, O. gemmicola, O. axillaris, O. exci-pulata, O. bridei a dvěma nepoposanými druhy rodu Octospora.
... Test DNA was extracted using the Plant Genomic DNA Purification (Thermo Scientific) kit -according to the enclosed instructions. ITS 1/2 rDNA amplification was performed with fungi-specific primers: ITS1-F (5 'CTT GGT CAT TTA GAG GAA GTAA 3') (Gardes and Bruns, 1993) and ITS4 (5 'TCC TCT GCT TAT TGA TAT GC 3') (White et al., 1990) by PCR. The PCR reactive mixture (25 μl) consisted of 12.5 μl of 2xMixPCR (A & A Biotechnology), 0.2 μM of each primer, 1.5 μl of purified and diluted environmental DNA and 10.6 μl of water. ...
... Genomic DNA was directly isolated using a modified 2% CTAB procedure from a section of each specimen's thallus with apothecia (Gardes and Bruns 1993). Extracted DNA was used for PCR amplification of the ITS nrDNA marker using a pair of primers: ITS1F forward primer (5′CTT GGT CAT TTA GAG GAA GTAA3′) and ITS4 reverse primer (5′ TCC TCC GCT TAT TGA TAT GC 3′) (White et al. 1990). ...
Chlorangium ahmadii sp. nov. and Circinaria darelensis sp. nov. are described as new species from Pakistan. A comparative morpho-anatomical, chemical study and ITS-based molecular analyses confirmed the positions of these species within the genera Chlorangium and Circinaria. Chlorangium ahmadii sp. nov. differs from its closely related species, C. alpicola in having light brown to whitish-brown thallus (vs. brownish-grey to greyish-green), flat to concave apothecial disc (vs. concave to convex when young, becoming more flat when old), smaller exciple 20-35 μm (vs. 65-85 μm) and larger ascospores 27-40 × 22-25 μm (vs. 19-24 × 19-23 μm). Circinaria darelensis sp. nov. is distinguished from its closely related species, C. maculata in having crustose-areolate light brown to greyish-brown thallus (vs. areolate, brown, olive brown to dark olive), absence of lobes (vs. presence), taller hymenium 120-190 μm (vs. 100-125 µm) and smaller ascospores 14-17 × 6-10 μm (vs. 22.5-27.5 × 15-20 µm).
... El DNA total fue extraído a partir de especímenes secos de herbario, empleando una modificación del protocolo de MURRAY & THOMPSON (1980). La amplificación por PCR, basada en MULLIS & FALOONA (1987), incluyó 35 ciclos con una temperatura de anillamiento de 54 º C, y fue llevada a cabo con los cebadores ITS1F e ITS4 (WHITE et al., 1990, GARDES & BRUNS, 1993 para la región ITS, así como los cebadores LR0R y LR5 (VILGALYS & HESTER, 1990;CUBETA et al., 1991), para la región 28S; bRPB2-6F2 (reverso de bRPB2-6R2), y bRPB2-7R2 para el gen de la segunda subunidad mayor de la RNA polimerasa II (rpb2) (MATHENY et al., 2007). Los resultados fueron controlados en un gel de agarosa al 1%, y las reacciones positivas fueron purificadas y secuenciadas con uno o ambos cebadores de PCR. ...
Amanita meridioceciliae Illescas sp. nov., a new Mediterranean taxon included in Amanita series Ceciliae. A. meridioceciliae is described and illustrated from collections made in Andalusia, in a Mediterranean environment, associated with Quercus spp. in neutral to decalcified soils. This new species is macro- and microscopically similar to Amanita ceciliae (Berk. & Broome) Bas. Analysis of the ITS, LSU and RPB2 genetic markers of both species clearly support their differentiation from each other and from other species of the genus, which confirms that this is a new species, for which the binomial Amanita meridioceciliae is proposed.
Key words: Amanitaceae, Vaginatae, taxonomy, phylogeny, Andalusia, Spain.
... DNA was extracted using the Genomic Mini AX Plant Kit (A&A Biotechnology, Gdynia, Poland) according to the manufacturer's protocol. The primers used were ITS 1F (Gardes and Bruns 1993) and ITS4 (White et al. 1990) for ITS1-5.8S-ITS2, Bt2a, and Bt2b (Glass and Donaldson 1995) for TUB2, and EF1 and EF2 (O'Donnell et al. 1998) or EF1-728 (Carbone andKohn 1999) andTEF1rev (Kullnig-Gradinger et al. 2002) for TEF1-α. ...
Organic debris accumulated in bird nests creates a unique environment for organisms, including microbes. Built from various plant materials that are typically enriched by animal residues, bird nest favours the development of various fungal groups. The aim of this study was to investigate the chemical properties of the material deposited in the white stork Ciconia ciconia nests and the link between extracellular enzyme activity and the diversity and composition of culturable fungi. Our findings revealed low C/P and N/P ratio values in the nest materials, which indicate a high P availability. Nest material C/N/P ratio ranged from 67/8/1 to 438/33/1. Enzymatic activity strongly correlated with the content of carbon, nitrogen, and pH of the material deposited in the nests. A total of 2726 fungal isolates were obtained from the nests, from which 82 taxa were identified based on morphology and DNA sequence data. The study indicates that white stork nests are microhabitat characterised by diverse chemical and biochemical properties. We found relationship between the fungal richness and diversity and the C/P and N/P ratios of materials from the nests. Our study showed that culturable fungi occurred frequently in materials with high levels of C, N, and P, as well as high concentrations of base alkaline elements (Ca, Mg, and K).
... After pure cultures were obtained, the cetyl trimethylammonium bromide (CTAB) DNA extraction protocol (Blanchette et al., 2016) was used. PCR amplification was targeted for the internal transcribed spacer (ITS) region of rDNA with the primer pair ITS1F/4 (Gardes & Bruns, 1993). PCR amplification reagents included 12.5 μL of GoTaq® Green Master Mix (Promega, Madison, WI, USA), 9.5 μL of sterile water, 1 μL of each primer, 0.5 μL Calbiochem® albumin, bovine serum, fraction V, crystalline (EMD Biosciences, Inc., La Jolla, CA, USA) and 1 μL of template DNA for a final volume of 25.5 μL. ...
The forest pathogen, Heterobasidion irregulare , is a serious threat to conifers in North America including Minnesota. Fungi native to Minnesota were isolated and tested in laboratory and field assays to evaluate their antagonism towards H . irregulare . One management strategy for plant pathogens, and especially H. irregulare , is to use fungi as biological control agents. A successful biological control agent used to manage root rot disease caused by H. irregulare is the fungus Phlebiopsis gigantea . The goal of this research was to screen different native fungi, including P. gigantea , against H. irregulare and examine and quantify their interactions in vitro and ex vitro. A set of four different antagonism assays were conducted. These assays served as a screening process involving both the laboratory and the field. Interactions were first examined with dual inoculation studies on media and wood discs of red pine ( Pinus resinosa ). These assays demonstrated strong inhibition and limited growth of H. irregulare by select fungi, including Phanerochaete livescens and P. gigantea . Another assay involved using soil microcosms and wood wedges of red pine. This allowed for a different examination, as wood wedges were inoculated with a candidate antagonistic fungus and placed in soil microcosms with H. irregulare . The opposite interaction was also examined with wedges inoculated with H. irregulare and then placed in soil microcosms containing different candidate fungi. In the field, large wood discs were placed around stumps and inoculated with candidate fungi in a red pine plantation infected with H. irregulare . Certain fungi performed well in different assays, but across all assays, P. gigantea performed the best. The antagonism of P. gigantea was most noticeable on wood discs and wood wedges used in vitro, as H. irregulare was not able to be reisolated from these substrates. Overall, these results provide more information on the fungi that appear to be acting as antagonists in forests to prevent H. irregulare from colonizing and provide new information on potential candidate fungi that could be used as a new biological control agent.
... The crude DNA was used as a template for PCR amplification. The primer pairs ITS5/ITS4 (Gardes and Bruns 1993;White et al. 1990) and LR0R/LR7 (Vilgalys and Hester 1990) were selected to amplify the ITS and nLSU regions, respectively. The PCR procedures were as follows: for the ITS region, initial denaturation was performed at 95 °C for 3 min, 34 cycles at 94 °C for 40 s, 45 s at 57.2 °C, 1 min at 72 °C, and finally a 10 min extension at 72 °C; for the nLSU region, the initial denaturation was performed at 94 °C for 1 min, followed by 34 cycles at 94 °C for 30 s, 1 min at 47.2 °C, 1.5 min at 72 °C, and finally a 10 min extension at 72 °C. ...
Wood-inhabiting fungi have important economic values as well as playing a major ecological role in forest ecosystem cycles. The Dabie Mountains, at the junction of Henan, Hubei, and Anhui Provinces, Central China, provide an ideal climate and favorable niches for the speciation and diversification of various forms of life including fungi. We studied the species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi that revealed 175 wood-inhabiting basidiomycetous species, of which 20 represented unidentified species, based on morphological and phylogenetic analyses of 575 specimens collected from ten sampling sites. These species belonged to two classes, 11 orders, 42 families, and 106 genera of Basidiomycota, and included 12 edible species, 28 medicinal species, four poisonous species, and seven forest pathogens. Four types of fungal distribution pattern at the genus level were recognized for 65 genera, while another 41 genera could not be placed in any known distribution pattern. The five sampling sites in the eastern part of the Dabie Mountains had significantly higher species diversity and phylogenetic diversity of wood-inhabiting basidiomycetous fungi than those in the western part, and thus deserve priority in terms of conservation. The community of wood-inhabiting basidiomycetous fungi in the Dabie Mountains is generally affected by a combination of habitat filtering and competitive exclusion. This study provides a basis on which to build actions for the comprehensive recognition, utilization, and conservation of wood-inhabiting basidiomycetous fungi in the region.
Supplementary Information
The online version contains supplementary material available at 10.1186/s43008-023-00130-9.
... genomic DNa was extracted from dried samples using the ezup Column Fungi genomic DNa Purification Kit (Sangon Biotech, Shanghai, China) in accordance with the manufacturer's instructions. For PCR amplification, the primer pairs ITS4/ITS5 and LR5/LR0R were used to amplify the ITS and LSu regions, respectively (Vilgalys & hester 1990;White et al. 1990;gardes & Bruns 1993). The PCR amplification reactions were performed on an eppendorf Mastercycler thermal cycler (eppendorf, Inc., hamburg, germany). ...
A newly discovered fungal species associated with conifers in China, Alloclavaria orientalis, is formally described and illustrated. A molecular phylogenetic analysis of concatenated internal transcribed spacer and nuclear ribosomal RNA large subunit sequences supported the monophyly of A. orientalis as a distinct lineage within the Alloclavaria clade.
... Genomic DNA was extracted from small pieces of dried basidiomata with PhytoSorb (Sintol, Moscow, Russia) according to the manufacturer's instructions. The internal transcribed spacer regions of the nuclear ribosomal DNA (ITS nrDNA) were amplified with the primers pair ITS1F/ITS4B (Gardes, Bruns, 1993). PCR reactions were performed ...
The first findings of recently described polypore fungus Sidera tibetica are revealed in the Caspian lowland forests of the Samursky National Park in the Republic of Dagestan, Russia. Basidiomata collected on Pinus brutia var. eldarica were studied by both light microscopy and molecular methods. Detailed information on new localities and habitats of Sidera tibetica as well as the collection numbers of specimens deposited in the Mycological Herbarium of the Komarov Botanical Institute of RAS (LE) are provided. Two complete sequences of ITS1-5.8S-ITS2 nuclear ribosomal DNA for Caucasian specimens of S. tibetica have been obtained and submitted to the GenBank database. Newly generated sequences are formed a separate well-supported clade in the Maximum Likelihood phylogenetic analysis together with all available ITS nrDNA sequences of S. tibetica originated from Belarussian and Chinese collections including the reference sequence from a holotype.
... DNA extraction was performed with mycelia from pure cultures using a NaOH extraction protocol according to (Osmundson et al. 2013). Fresh fungal material for each collection was also preserved in dimethyl sulfoxide (DMSO) solution and used for DNA extraction (Dawson et al. 1998).The rDNA of the internal transcribed spacer region (ITS), using primers ITS1F and ITS4 (Gardes and Bruns 1993), was amplified via a polymerase chain reaction (PCR) according to previous studies (Blanchette et al. 2016;Held et al. 2021). Gel electrophoresis was done using SYBR green I pre-stain and read with a Dark Reader DR45 to confirm the successful PCR reactions. ...
Background
Xylaria is a diverse and ecologically important genus in the Ascomycota. This paper describes the xylariaceous fungi present in an Ecuadorian Amazon Rainforest and investigates the decay potential of selected Xylaria species. Fungi were collected at Yasuní National Park, Ecuador during two collection trips to a single hectare plot divided into a 10-m by 10-m grid, providing 121 collection points. All Xylaria fruiting bodies found within a 1.2-m radius of each grid point were collected. Dried fruiting bodies were used for culturing and the internal transcribed spacer region was sequenced to identify Xylaria samples to species level. Agar microcosms were used to assess the decay potential of three selected species, two unknown species referred to as Xylaria 1 and Xylaria 2 and Xylaria curta , on four different types of wood from trees growing in Ecuador including balsa ( Ochroma pyramidale ), melina ( Gmelina arborea ), saman ( Samanea saman ), and moral ( Chlorophora tinctoria ). ANOVA and post-hoc comparisons were used to test for differences in biomass lost between wood blocks inoculated with Xylaria and uninoculated control blocks. Scanning electron micrographs of transverse sections of each wood and assay fungus were used to assess the type of degradation present.
Results
210 Xylaria collections were sequenced, with 106 collections belonging to 60 taxa that were unknown species, all with less than 97% match to NCBI reference sequences. Xylaria with sequence matches of 97% or greater included X . aff. comosa (28 isolates), X. cuneata (9 isolates) X. curta and X . oligotoma (7 isolates), and X . apiculta (6 isolates)., All Xylaria species tested were able to cause type 1 or type 2 soft rot degradation in the four wood types and significant biomass loss was observed compared to the uninoculated controls. Balsa and melina woods had the greatest amount of biomass loss, with as much as 60% and 25% lost, respectively, compared to the controls.
Conclusions
X ylaria species were found in extraordinary abundance in the Ecuadorian rainforest studied. Our study demonstrated that the Xylaria species tested can cause a soft rot type of wood decay and with the significant amount of biomass loss that occurred within a short incubation time, it indicates these fungi likely play a significant role in nutrient cycling in the Amazonian rainforest.
... rDNA) RNA genes were performed with total 50 μl standard reaction volume for each sample. Optimum amplification conditions were obtained with 25 μl 2 × Taq PCR MasterMix in each tube with 19 μl of distilled water, 2 μl of DNA extracts and 2 μl of the primers ITS1F and ITS4 (Gardes andBruns 1993, White et al. 1990). The thermal cycling conditions included an initial denaturation step of 95°C for 5 min., followed by 35 cycles of 95°C for 45 sec. ...
Lichens are most dominant elements of Antarctic terrestrial vegetation, however, they are still not well known. In this paper, Lendemerialla vaczii is described as a new lichen species to science from the James Ross Island and Horseshoe Island, Antarctic Peninsula, based on morphology and phylogenetic analysis. The new species is characterized by brownish cream or buff-colored areolate thallus lacking vegetative propagules, black and lecideine apothecia and very thin (up to 1 µm) septa in ascospores. Phylogenetic analysis of nrITS sequence data shows that new species clusters in the genus Lendemeriella with a high bootstrap support. The new species is compared with other Lendemeriella species and other related crustose Teloschistaceae species without anthraquinones and a comprehensive description is provided. An identification key to 10 species of Lendemeriella is also provided.
... El DNA total fue extraído a partir de especímenes secos de herbario empleando una modificación del protocolo de MURRAY & THOMPSON (1980). La amplificación por PCR, basada en MULLIS & FA-LOONA (1987), fue llevada a cabo con los primers ITS1F e ITS4 (WHITE & al., 1990;GARDES & BRUNS, 1993) para la región ITS rDNA. Las reacciones de PCR incluyeron 35 ciclos con una temperatura de anillamiento de 54º C. Los resultados fueron comprobados en un gel de agarosa al 1%, y las reacciones positivas fueron purificadas y secuenciadas con uno o ambos primers de PCR. ...
... DNA from each isolate was extracted by placing a small amount of fungal tissue in an alkaline-Tris solution and incubating at 95°C for 10 min to lyse the cells (41). The supernatant was used for PCR amplification with the primers ITS1f and LR3 (42,43). PCR products cleaned with Exonuclease and Antarctic Phosphatase enzymes (Sigma-Aldrich, St. Louis, MO, USA) were sent to Michigan State University Research Technology Support Facility Genomics Core (East Lansing, MI, USA) for Sanger sequencing. ...
Terpenes are among the oldest and largest class of plant-specialized bioproducts that are known to affect plant development, adaptation, and biological interactions. While their biosynthesis, evolution, and function in aboveground interactions with insects and individual microbial species are well studied, how different terpenes impact plant microbiomes belowground is much less understood. Here we designed an experiment to assess how belowground exogenous applications of monoterpenes (1,8-cineole and linalool) and a sesquiterpene (nerolidol) delivered through an artificial root system impacted its belowground bacterial and fungal microbiome. We found that the terpene applications had significant and variable impacts on bacterial and fungal communities, depending on terpene class and concentration; however, these impacts were localized to the artificial root system and the fungal rhizosphere. We complemented this experiment with pure culture bioassays on responsive bacteria and fungi isolated from the sorghum rhizobiome. Overall, higher concentrations (200 µM) of nerolidol were inhibitory to Ferrovibrium and tested Firmicutes. While fungal isolates of Penicillium and Periconia were also more inhibited by higher concentrations (200 µM) of nerolidol, Clonostachys was enhanced at this higher level and together with Humicola was inhibited by the lower concentration tested (100 µM). On the other hand, 1,8-cineole had an inhibitory effect on Orbilia at both tested concentrations but had a promotive effect at 100 µM on Penicillium and Periconia . Similarly, linalool at 100 µM had significant growth promotion in Mortierella , but an inhibitory effect for Orbilia . Together, these results highlight the variable direct effects of terpenes on single microbial isolates and demonstrate the complexity of microbe-terpene interactions in the rhizobiome.
IMPORTANCE
Terpenes represent one of the largest and oldest classes of plant-specialized metabolism, but their role in the belowground microbiome is poorly understood. Here, we used a “rhizobox” mesocosm experimental set-up to supply different concentrations and classes of terpenes into the soil compartment with growing sorghum for 1 month to assess how these terpenes affect sorghum bacterial and fungal rhizobiome communities. Changes in bacterial and fungal communities between treatments belowground were characterized, followed by bioassays screening on bacterial and fungal isolates from the sorghum rhizosphere against terpenes to validate direct microbial responses. We found that microbial growth stimulatory and inhibitory effects were localized, terpene specific, dose dependent, and transient in time. This work paves the way for engineering terpene metabolisms in plant microbiomes for improved sustainable agriculture and bioenergy crop production.
... Genomic DNA was extracted from lichen apothecia or lobes tips (30-40 per sample) using a modified CTAB method (Doyle and Doyle 1990). PCR was performed using universal the primers ITS1F and ITS4 for fungi and ITS1 and ITS4 for algae (White et al. 1990;Gardes and Bruns 1993). The yield of the PCRs was verified by running the products on a 1% agarose gel stained with ethidium bromide. ...
A new species, Xanthoria tendraensis (Teloschistales, Lecanoromycetes), is described from species-poor lichen communities on shell dunes of the Tendra Spit (northern Black Sea coast, Ukraine), based both on morphological and molecular data. This lichen is similar to X. ectaneoides but differs in having longer ascospores with thicker walls at the poles. A new lichen association, Xanthorietum tendraensis, is described from stable grey dunes. Its characteristic species are Lecania sylvestris s. lat., Polyozosia perpruinosa, Scythioria phlogina and X. tendraensis. The species composition of the new association is similar to communities of Aspicilion contortae (Verrucarietea nigrescentis). Six new sequences of nrITS region were obtained for Xanthoria tendraensis, Xanthocarpia fulva s. lat. and Trebouxia crenulata, which was identified as a photobiont of X. tendraensis.
... For PCR amplification, we combined general fungal primers with others specifically designed to amplify DNA from the tremellalean fungi (Millanes et al. 2011;Freire-Rallo et al. 2023). To perform the PCRs, we used the primers ITS1F (Gardes & Bruns 1993), BasidLSU3-3 (Millanes et al. 2011) and TRMcal_R2 (Freire-Rallo et al. 2023 to amplify the internal transcribed spacer I, the 5.8S rDNA gene and the internal transcribed spacer II gene. PCR reactions were carried out using Illustra TM Hot Star PCR beads, according to the manufacturer's instructions. ...
Tremella caloplacae (Zahlbr.) Diederich is a species complex including at least nine different species. Here, we formally describe the new species Tremella elegantis , T. nimisiana , T. parietinae , T. pusillae and T. sorediatae . Tremella elegantis induces galls in the hymenium of Rusavskia elegans and forms 2-celled basidia, where cells rarely elongate and sometimes give the appearance of two immature, independent basidia. Tremella nimisiana has small basidiomata (less than 1 mm diam.), narrowly ellipsoid to pyriform 2-celled, occasionally clavate to subcylindrical 3-celled basidia, and grows in the hymenium of Xanthocarpia species. Tremella parietinae is characterized by the exclusive growth in the hymenium of Xanthoria parietina , the broadly fusiform to ellipsoid probasidia, and the subspherical, pyriform or ellipsoid 2(–3)-celled basidia. Tremella pusillae has ellipsoidal probasidia, 2(–3)-celled pyriform or ellipsoidal basidia that sometimes are constricted at the septum, and grows only on Calogaya pusilla . Tremella sorediatae is characterized by inducing galls on the thallus of Rusavskia sorediata and by pyriform to ellipsoid basidia that sometimes are constricted at the septum. Three species are not formally described and are left unnamed as Tremella sp. 13 on Calogaya biatorina , Tremella sp. 14 on Calogaya decipiens and Tremella sp. 15 on Polycauliona sp. Tremella caloplacae in the strict sense is re-circumscribed as a species confined to Variospora species.
Microbial necromass is increasingly recognized as an important fast‐cycling component of the long‐term carbon present in soils. To better understand how fungi and bacteria individually contribute to the decomposition of fungal necromass, three particle sizes (>500, 250–500, and <250 μm) of Hyaloscypha bicolor necromass were incubated in laboratory microcosms inoculated with individual strains of two fungi and two bacteria. Decomposition was assessed after 15 and 28 days via necromass loss, microbial respiration, and changes in necromass pH, water content, and chemistry. To examine how fungal–bacterial interactions impact microbial growth on necromass, single and paired cultures of bacteria and fungi were grown in microplates containing necromass‐infused media. Microbial growth was measured after 5 days through quantitative PCR. Regardless of particle size, necromass colonized by fungi had higher mass loss and respiration than both bacteria and uninoculated controls. Fungal colonization increased necromass pH, water content, and altered chemistry, while necromass colonized by bacteria remained mostly unaltered. Bacteria grew significantly more when co‐cultured with a fungus, while fungal growth was not significantly affected by bacteria. Collectively, our results suggest that fungi act as key early decomposers of fungal necromass and that bacteria may require the presence of fungi to actively participate in necromass decomposition.
The mining industry strives to reduce its water footprint by recycling water in ore processing. This leads to build‐up of ions, flotation chemicals and microbial biomass, which may affect the process. The Boliden Kevitsa mine in Northern Finland is exposed to seasonal change and recycles up to 90% of the process water. We studied the variation in size, composition and putative functions of microbial communities in summer and winter in the ore processing plant. The raw water, Cu and Ni thickener overflow waters had statistically significantly higher bacterial numbers in winter compared to summer, and specific summer and winter communities were identified. Metagenomic analysis indicated that Cu and Hg resistance genes, sulphate/thiosulphate, molybdate, iron(III) and zinc ABC transporters, nitrate reduction, denitrification, thiosulphate oxidation and methylotrophy were more common in winter than in summer. Raw water drawn from the nearby river did not affect the microbial communities in the process samples, indicating that the microbial communities and metabolic capacities develop within the process over time in response to the conditions in the processing plant, water chemistry, used chemicals, ore properties and seasonal variation. We propose that the microbial community structures are unique to the Boliden Kevitsa mine and processing plant.
Leaf decomposition varies widely across temperate forests, shaped by factors like litter quality, climate, soil properties, and decomposers, but forest heterogeneity may mask local tree influences on decomposition and litter‐associated microbiomes. We used a 24‐yr‐old common garden forest to quantify local soil conditioning impacts on decomposition and litter microbiology.
We introduced leaf litter bags from 10 tree species (5 arbuscular mycorrhizal; 5 ectomycorrhizal) to soil plots conditioned by all 10 species in a full‐factorial design. After 6 months, we assessed litter mass loss, C/N content, and bacterial and fungal composition. We hypothesized that (1) decomposition and litter‐associated microbiome composition would be primarily shaped by the mycorrhizal type of litter‐producing trees, but (2) modified significantly by underlying soil, based on mycorrhizal type of the conditioning trees.
Decomposition and, to a lesser extent, litter‐associated microbiome composition, were primarily influenced by the mycorrhizal type of litter‐producing trees. Interestingly, however, underlying soils had a significant secondary influence, driven mainly by tree species, not mycorrhizal type. This secondary influence was strongest under trees from the Pinaceae.
Temperate trees can locally influence underlying soil to alter decomposition and litter‐associated microbiology. Understanding the strength of this effect will help predict biogeochemical responses to forest compositional change.
The root nodules of actinorhizal plants are home to nitrogen‐fixing bacterial symbionts, known as Frankia, along with a small percentage of other microorganisms. These include fungal endophytes and non‐Frankia bacteria. The taxonomic and functional diversity of the microbial consortia within these root nodules is not well understood. In this study, we surveyed and analyzed the cultivable, non‐Frankia fungal and bacterial endophytes of root nodules from red and Sitka alder trees that grow together. We examined their taxonomic diversity, co‐occurrence, differences between hosts, and potential functional roles. For the first time, we are reporting numerous fungal endophytes of alder root nodules. These include Sporothrix guttuliformis, Fontanospora sp., Cadophora melinii, an unclassified Cadophora, Ilyonectria destructans, an unclassified Gibberella, Nectria ramulariae, an unclassified Trichoderma, Mycosphaerella tassiana, an unclassified Talaromyces, Coniochaeta sp., and Sistotrema brinkmanii. We are also reporting several bacterial genera for the first time: Collimonas, Psychrobacillus, and Phyllobacterium. Additionally, we are reporting the genus Serratia for the second time, with the first report having been recently published in 2023. Pseudomonas was the most frequently isolated bacterial genus and was found to co‐inhabit individual nodules with both fungi and bacteria. We found that the communities of fungal endophytes differed by host species, while the communities of bacterial endophytes did not.
Dead trees are vital structural elements in forests playing key roles in the carbon and nutrient cycle. Stem traits and fungal community composition are both important drivers of stem decay, and thereby affect ecosystem functioning, but their relative importance for stem decomposition over time remains unclear.
To address this issue, we used a common garden decomposition experiment in a Dutch larch forest hosting fresh logs from 13 common temperate tree species. In total, 25 fresh wood and bark traits were measured as indicators of wood accessibility for decomposers, nutritional quality and chemical or physical defence mechanisms. After 1 and 4 years of decay, we assessed the richness and composition of wood‐inhabiting fungi using amplicon sequencing and determined the proportional wood density loss.
Average proportional wood density loss for the first year was 18.5%, with further decomposition occurring at a rate of 4.3% year⁻¹ for the subsequent 3 years across tree species. Proportional wood density loss varied widely across tree species in the first year (8.7–24.8% year⁻¹) and subsequent years (0–11.3% year⁻¹). The variation was directly driven by initial wood traits during the first decay year, then later directly driven by bark traits and fungal community composition. Moreover, bark traits affected the composition of wood‐inhabiting fungi and thereby indirectly affected decomposition rates. Specifically, traits promoting resource acquisition of the living tree, such as wide conduits that increase accessibility and high nutrient concentration, increased initial wood decomposition rates. Fungal community composition, but not fungal richness explained differences in wood decomposition after 4 years of exposure in the field, where fungal communities dominated by brown‐rot and white‐rot Basidiomycetes were linked to higher wood decomposition rate.
Synthesis: Understanding what drives deadwood decomposition through time is important to understand the dynamics of carbon stocks. Here, using a tailor‐made experimental design in a temperate forest setting, we have shown that stem trait variation is key to understanding the roles of these drivers; initially, wood traits explained decomposition rates while subsequently, bark traits and fungal decomposer composition drove decomposition rates. These findings inform forest management with a view to selecting tree species to promote carbon storage.
BACKGROUND
Microstegium vimineum (Trin.) A. Camus, commonly called stiltgrass, is a dominant weed in the United States and China. Although a lot of control approaches have been attempted, an economic, effective and practical measure has not been available to control the weed so far.
RESULTS
A serious rust disease of Microstegium vimineum was observed in three regions of Wenzhou city in China, from 2019 to 2021, with a disease incidence ranging from 82% to 97%. Typical rust disease symptoms on Microstegium vimineum were prominently visible during the early monsoon season (June–July), with chlorotic spots on the leaf surfaces. The morphological characterization of the strain WZ‐1 which was isolated from the diseased leaves was consistent with Puccinia polliniicola. The virulence tests showed that the average disease index of Microstegium vimineum plants could reach 35% at 10 days post‐inoculation. The host specificity of Puccinia polliniicola was tested on 64 plant species from 12 families and it did not cause any diseased symptoms on 24 major crops and 36 weeds, but slightly infected four gramineous weeds, Arthraxon hispidus, Polypogon fugax, Cynodon dactylon, and Microstegium ciliatum. However, newly‐produced urediniospores were not observed on the slightly infected plants. The urediniospores of strain WZ‐1 infected the Microstegium vimineum leaves by two main approaches: mycelium or appressorium invaded the stoma; and mycelium or appressorium directly invaded intercellular spaces. Field experiments showed that the rust disease naturally prevailed among Microstegium vimineum populations, causing severe rust disease symptoms on the leaf surface. The rust epidemic effectively controlled all of the target plants in the closed plot where the rust was released.
CONCLUSION
Puccinia polliniicola strain WZ‐1 has great potential to be used as a classical biological control agent against Microstegium vimineum. © 2024 Society of Chemical Industry.
Lecidea varians is among the most common and abundant bark-dwelling crustose lichens in temperate eastern North America. As presently delimited, it is highly variable, including chemical and morphological diversity well beyond that currently accepted for most lichen species. The generic placement of L. varians has also been questioned for decades. It has long been recognized as aberrant in Lecidea and Pyrrhospora, excluded from Lecidella, and more recently transferred to Traponora. Drawing from the results of extensive chemical, molecular phylogenetic and morphological studies, we show that L. varians and its relatives represent a previously unrecognized lineage within the speciose lichen family Lecanoraceae. The lineage appears to occupy an isolated position, distinct from the aforementioned genera, and is newly described as the genus Xanthosyne (typified by L. varians). The chemical and morphological variation within L. varians is mirrored by, but not entirely correlated with, considerable molecular diversity. A new taxonomy is proposed for L. varians and its relatives to serve as a framework for future studies. Three species are recognized: X. varians (≡ Lecidea varians), common and widespread in parts of North America; X. granularis, a new species from the Atlantic Coast of eastern North America that differs morphologically from X. varians in having a leprose thallus; and X. sharnoffiorum, a new species also found mainly along the Atlantic Coast of eastern North America, which has a coarsely granular, non-leprose thallus and produces a unique, unidentified xanthone. Multiple well-supported lineages were recovered within X. varians that correlate to varying degrees with chemical and morphological variability, as well as geographic distribution. Eight subspecies are recognized to accommodate the variation within X. varians: X. varians subsp. exigua comb. nov. (≡ Lecidea exigua) characterized by the presence of atranorin and a consistent set of three xanthones, is widespread in southern Europe and western North America (coastal California); X. varians subsp. varians (≡ Lecidea varians) is distributed mainly in northeastern North America and produces thuringione and arthothelin; X. varians subsp. morsei subsp. nov. is morphologically and chemically variable, with one chemotype (thiophanic acid) with a northeastern distribution, and the other with a unique and unidentified xanthone, found mainly in the interior U.S.A.; X. varians subsp. obscura subsp. nov. occurs mainly in the central U.S.A. and North Temperate regions, produces a unique, unidentified xanthone and generally has black apothecia with green epihymenial pigments; X. varians subsp. pseudomorsei subsp. nov. and X. varians subsp. submorsei subsp. nov. resemble X. varians subsp. morsei but differ in molecular sequence characters; X. varians subsp. subtilis comb. nov. (≡ Lecidea subtilis) and X. varians subsp. subexigua subsp. nov. occur in the Appalachian Mountains, the former producing atranorin and the latter lacking atranorin, both with thiophanic acid with or without other xanthones. In an addendum, Lecidella subviridis is discussed with respect to the genus Xanthosyne. An identification key is provided for all species and their subspecies within Xanthosyne.
Climate warming is severely affecting high‐latitude regions. In the Arctic tundra, it may lead to enhanced soil nutrient availability and interact with simultaneous changes in grazing pressure. It is presently unknown how these concurrently occurring global change drivers affect the root‐associated fungal communities, particularly mycorrhizal fungi, and whether changes coincide with shifts in plant mycorrhizal types.
We investigated changes in root‐associated fungal communities and mycorrhizal types of the plant community in a 10‐yr factorial experiment with warming, fertilisation and grazing exclusion in a Finnish tundra grassland.
The strongest determinant of the root‐associated fungal community was fertilisation, which consistently increased potential plant pathogen abundance and had contrasting effects on the different mycorrhizal fungal types, contingent on other treatments. Plant mycorrhizal types went through pronounced shifts, with warming favouring ecto‐ and ericoid mycorrhiza but not under fertilisation and grazing exclusion. Combination of all treatments resulted in dominance by arbuscular mycorrhizal plants. However, shifts in plant mycorrhizal types vs fungi were mostly but not always aligned in their magnitude and direction.
Our results show that our ability to predict shifts in symbiotic and antagonistic fungal communities depend on simultaneous consideration of multiple global change factors that jointly alter plant and fungal communities.
Altering plant carbon allocation from leaves to stems is key to improve biomass for forage, fuel, and renewable chemicals. The sorghum dry stalk (D) locus controls a quantitative trait for sugar accumulation, with enhanced carbon allocation in the stems of juicy green (dd) sorghum but reduced carbon allocation in that of dry white (DD) sorghum. However, it remains unclear whether altering sorghum sugar accumulation in stem affects below‐ground microbiome. Here we investigated sorghum rhizosphere soil microbiome in near isogenic lines with different magnitude of carbon allocations and accumulation in the stems. Results showed that enhanced carbon accumulation in stems of juicy green sorghum results in stronger selection in rhizosphere microbiome assembly. The rhizosphere soil microbial communities selected in juicy green sorghum tended to be fast‐growing microbial taxa which possessed potential functions that would promote higher potential capacity to use chemically labile carbon sources and potentially result in higher potential decomposition rates. We found the rhizosphere microbes selected by juicy green sorghum form weaker interactions than dry white sorghum. This is the first comprehensive study revealing how the different magnitude of carbon allocations to stems regulates microbial community assembly, microbial interaction, and microbial functions. This study indicates that future plant modification for bioenergy crops should also consider the impacts on belowground microbial community without compromising the sustainability.
Understanding the complex interactions between trees and fungi is crucial for forest ecosystem management, yet the influence of tree mycorrhizal types, species identity, and diversity on tree‐tree interactions and their root‐associated fungal communities remains poorly understood.
Our study addresses this gap by investigating root‐associated fungal communities of different arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) tree species pairs (TSPs) in a subtropical tree diversity experiment, spanning monospecific, two‐species, and multi‐species mixtures, utilizing Illumina sequencing of the ITS2 region.
The study reveals that tree mycorrhizal type significantly impacts the alpha diversity of root‐associated fungi in monospecific stands. Meanwhile, tree species identity's influence is modulated by overall tree diversity. Tree‐related variables and spatial distance emerged as major drivers of variations in fungal community composition. Notably, in multi‐species mixtures, compositional differences between root fungal communities of AM and EcM trees diminish, indicating a convergence of fungal communities irrespective of mycorrhizal type. Interestingly, dual mycorrhizal fungal communities were observed in these multi‐species mixtures.
This research underscores the pivotal role of mycorrhizal partnerships and the interplay of biotic and abiotic factors in shaping root fungal communities, particularly in varied tree diversity settings, and its implications for effective forest management and biodiversity conservation.
We provide the first North American report of the lichenicolous fungus Pronectria fragmospora. Based on multigene phylogenetic analyses we found this species to be nested within the genus Trichonectria and the new combination Trichonectria fragmospora is proposed. We provide a description and photos of the North American material on Evernia prunastri and a phylogenetic tree showing its placement within the genus. We also compare this species to related species of Trichonectria and similar species of Pronectria.
The Giant Elm Bracket ( Rigidoporus ulmarius ) is a widely-distributed necrotrophic polypore species that causes white heart rot in deciduous trees. Despite its recognition as one of the largest species known for forming basidiomata, this perennial polypore had not been documented in Hungary. However, in recent years, two specimens macroscopically resembling this species were collected on old horse chestnut ( Aesculus hippocastanum ) trees from two different places in Hungary by amateur mycologists. In this study, subsequent morphological and molecular-genetic analyses of these fungal samples confirmed their identity as R . ulmarius . This study represents the first documented occurrence of this plant pathogenic polypore species in Hungary.
Psilocybe zapotecorum is a strongly blue-bruising psilocybin mushroom used by indigenous groups in southeastern Mexico and beyond. While this species has a rich history of ceremonial use, research into its chemistry and genetics has been limited. Herein, we report on mushroom morphology, cultivation parameters, chemical profile, and the full genome sequence of P. zapotecorum. First, we detail growth and cloning methods that are simple, and reproducible. In combination with high resolution microscopic analysis, the strain was identified by DNA barcoding, confirming the field identification. Full genome sequencing reveals the architecture of the psilocybin gene cluster in P. zapotecorum, and can serve as a reference genome for Psilocybe clade I. Characterization of the tryptamine profile revealed a psilocybin concentration of 17.9 ± 1.7 mg/g, with a range of 10.6–25.7 mg/g (n = 7), and similar tryptamines (psilocin, baeocystin, norbaeocystin, norpsilocin, aeruginascin, and 4-HO-tryptamine) in lesser concentrations for a combined tryptamine concentration of 22.5 ± 3.2 mg/g. These results show P. zapotecorum to be a potent and chemically variable Psilocybe mushroom. Chemical profiling, genetic analysis, and cultivation assist in demystifying these mushrooms. As clinical studies with psilocybin gain traction, understanding the diversity of Psilocybe expands the conversation beyond the molecule.
Due to signifcant health risks associated with chemical antifungal agents in food storage, safe and natural sources are now
one of the most frequently demanded ingredient for food preservation. Byproducts from olive trees provide an afordable
and sustainable source of bioactive chemicals. This study will examine the mycelial growth and germination-inhibitory
properties of Olea europaea var. rougette leaves and characterize their phytochemical makeup.The phytochemical screening
revealed the presence of polyphenolics compounds mainly tanins.The chemical composition was analyzed by gas chromatog-
raphy mass spectrometry (GCMS). Total polyphenolic content (TPC), hydrolysable tannins content (HTC) and condensed
tannin content (CTC) were assessed using Foilin ciocalteu, potassium iodide and vanilline methods, respectively. The
mycelial growth and germination inhibition properties were examined on soft wheat based solid and liquid media. Tannic
extract (ethyl acetate extract) revealed highest amounts in polyphenols, hydrolysable tanins and condensed. GC–MS profle
of tannic extract showed the presence of 26 bioactive molecules known for their antifungal potential, mainly: Guaiacol
(0.12%), 2-methoxy-4-vinylphenol (1.52%), Syringol (0.18%), p-tyrosol (4.70%), homovanillyl alcohol (1.32%), 4-propyl-
resorcinol (1.07%), β-camphor (0.17%), β-turmerone (1.57%) and 4-phenyl-quinolin-2-ol (6.58%). The tannic extract (ethyl
acetate fraction) showed signifcant mycelial growth and germination inhibition activities in contrast to hydro-acetonic and
dichloromethanic extracts. Furthermore, myelial growth inhibition showed more efectiveness in comparison to germination
inhibition technique.The results suggested that byproducts of Olea europaea var. rougette leaves are a substantial natural
source of bioactive compounds, especially tannins with potent antifungal characteristics in vitro which make it interesting
to investigate its efectiveness in vivo.
The use of compounds produced by hosts or symbionts for defence against antagonists has been identified in many organisms, including in fungus-farming termites (Macrotermitinae). The obligate mutualistic fungus Termitomyces plays a central role in the symbiosis through plant biomass decomposition and as the main food source for these termites. Several specialised (secondary) metabolites have been isolated from different Termitomyces species, suggesting that they may also aid in antimicrobial defence. Yet, we have a fragmented understanding of Termitomyces’ natural product repertoire. To determine the biochemical potential encoded by diverse Termitomyces species, we comparatively analysed 22 published and 17 newly generated genomes, spanning 21 of 52 described Termitomyces species and five of the 11 termite host genera. After extensive assembly and annotation optimisation, we employed fungiSMASH to detect 754 biosynthetic gene clusters (BGCs) coding for specialised metabolites. BiG-SCAPE analysis and manual curation allowed us to assign 660 of these BGCs to 61 distinct biosynthetic gene cluster families (GCFs), spanning five compound classes. Seven GCFs were shared by all 21 Termitomyces species, 21 GCFs were present in all genomes of several subsets of species, while the remaining 33 GCFs were inconsistently distributed across species. The 25 most abundant GCFs were subjected to codon-based evolutionary constraint analyses to evaluate their evolutionary histories and revealed two GCFs with consistent positive selection in the same gene across the phylogeny and seventeen genes with Termitomyces species-specific episodic positive selection. These patterns of selection indicate that millions of years of termite-fungus symbiosis have led to distinct evolutionary trajectories of biosynthetic gene clusters, ample putative chemical novelties, and uncover a vast non-random and largely unknown chemical potential of Termitomyces.
Two new species of the genus Lecidella, one with a North American-maritime Antarctic distribution and one with a so far exclusively southern South American-maritime Antarctic distribution, are described using molecular and morphological tools. Lecidella ayazii is a species growing on soil and also on mosses and has so far been found on the Antarctic Peninsula, as well as in the alpine areas of the La Sal Mountains, Utah, USA and in the Kivalliq Region (Nunavut) in the north of Canada, whereas L. drakensis occurs mainly on siliceous rocks, rarely on mosses, and has been recorded on both sides of the Drake Passage in southern Patagonia and the Antarctic Peninsula. Phylogenetic analysis of the nrITS sequence data shows that both species belong in the L. elaeochroma clade, each forming a highly supported and distinct group. Furthermore, they also differ in morphological and chemical characters from the species described so far in this clade. In addition, five further accessions were recorded from the maritime Antarctic, which were placed in the cosmopolitan and heterogeneous L. stigmatea clade, of which one could be assigned to the bipolar species L. siplei.
Molecular sequence data have transformed research on cryptogams (e.g., lichens, microalgae, fungi, and symbionts thereof) but methods are still strongly hampered by the small size and intermingled growth of the target organisms, poor cultivability and detrimental effects of their secondary metabolites. Here, we aim to showcase examples on which a modified direct PCR approach for diverse aspects of molecular work on environmental samples concerning biocrusts, biofilms, and cryptogams gives new options for the research community. Unlike traditional approaches, this methodology only requires biomass equivalent to colonies and fragments of 0.2 mm in diameter, which can be picked directly from the environmental sample, and includes a quick DNA lysis followed by a standardized PCR cycle that allows co-cycling of various organisms/target regions in the same run. We demonstrate that this modified method can (i) amplify the most widely used taxonomic gene regions and those used for applied and environmental sciences from single colonies and filaments of free-living cyanobacteria, bryophytes, fungi, and lichens, including their mycobionts, chlorobionts, and cyanobionts from both isolates and in situ material during co-cycling; (ii) act as a tool to confirm that the dominant lichen photobiont was isolated from the original sample; and (iii) optionally remove inhibitory secondary lichen substances. Our results represent examples which highlight the method’s potential for future applications covering mycology, phycology, biocrusts, and lichenology, in particular.
IMPORTANCE
Cyanobacteria, green algae, lichens, and other cryptogams play crucial roles in complex microbial systems such as biological soil crusts of arid biomes or biofilms in caves. Molecular investigations on environmental samples or isolates of these microorganisms are often hampered by their dense aggregation, small size, or metabolism products which complicate DNA extraction and subsequent PCRs. Our work presents various examples of how a direct DNA extraction and PCR method relying on low biomass inserts can overcome these common problems and discusses additional applications of the workflow including adaptations.
Riassunto Viene descritto ed illustrato Agaricus gemlii, raccolto nella regione Sardegna, che costituisce la prima segnalazione per l'Italia. Viene inoltre proposto un albero filogenetico relativo alle specie di Agaricus sez. Minores, clado I sec. He et al. (2017). Abstract Agaricus gemlii, found in Sardinia, which constitutes the first report in Italy, is described and illustrated. Is also proposed a phylogenetic tree relating to the species of Agaricus sect. Minores, clade I, according to He et al. (2017). Introduzione Fino a qualche decennio fa lo studio delle specie del genere Agaricus si effettuava esclusivamente tramite descrizioni macroscopiche, studi microscopici e osservazione delle reazioni chimiche, molto spesso era difficile separare specie molto simili tra loro, soprattutto quelle inserite in A. sez. Minores, tra le quali la similitudine interspecifica era ed è particolarmente accentuata. L'intervento della biologia molecolare ha dato un sostanziale contributo all'individuazione di specie "nascoste" e ha reso più chiara la filogenesi che, a sua volta, ha permesso una nuova classificazione del genere Agaricus apportando delle sostanziali modifiche. Ciò è soprattutto dovuto ai lavori di vari studiosi europei ed extraeuropei (Zhao et al.
Riassunto Gli autori documentano il ritrovamento inedito per il territorio nazionale di Entoloma calceus, specie recentemente descritta e segnalata solo in Norvegia, Francia e Danimarca. I rinvenimenti, avvenuti in una torbiera a sfagni in Val di Non (TN) nella regione Trentino-Alto Adige, hanno permesso da un lato di approfondire e consolidare la conoscenza di tale entità evidenziandone la variabilità cromatica, dall'altro di confermare la presenza di tale specie in ecosistemi particolari e con flora specializzata come quelli appunto delle torbiere alpine. La presentazione della specie in oggetto è supportata anche dalla ricerca di sequenze omologhe nel database molecolare pubblico NCBI e dall'indagine filogenetica sul marcatore ITS. A tale scopo viene fornito, come completamento al presente lavoro, un albero filogenetico che illustra le relazioni tra Entoloma calceus e le specie geneticamente più vicine all'interno del sottogenere Cyanula di Entoloma. Abstract Entoloma calceus, a recently described species thus far reported only from Norway, France and Denmark, is firstly recorded for the Italian territory. The presented material, collected in a sphagnum peatbog in Val di Non (TN), in Trentino-Alto Adige, allowed both to gain a better understanding of the species phenotypic plasticity, by documenting its chromatic variability, and to confirm its occurrence in particular ecosystems having a specialized flora such as those of alpine peatbogs. The morphological delimitation of the species is supported by a research for homologous ITS sequences present in public molecular database like NCBI and a phylogenetic analysis based on the ITS marker illustrating the relationships between Entoloma calceus and its genetically closest species within Entoloma subgenus Cyanula.
The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.
IMPORTANCE
The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.
The stability of microbial communities, especially among core taxa, is essential for supporting plant health. However, the impacts of disease infection on the stability of rhizosphere fungal core microbiome remain largely unexplored. In this study, we delved into the effects of root rot infestation on the community structure, function, network complexity, and stability of Sanqi fungal core microbiomes, employing amplicon sequencing combined with co-occurrence network and cohesion analyses. Our investigation revealed that root rot disease led to a decrease in the α-diversity but an increase in the β-diversity of the Sanqi fungal core microbiomes in the rhizosphere. Notably, Ilyonectria, Plectosphaerella, and Fusarium emerged as indicator species in the rhizosphere core microbiome of root rot-infected Sanqi plants, while Mortierella predominated as the dominant biomarker taxa in healthy soils. Additionally, root rot diminished the complexity and modularity of the rhizosphere networks by reducing the metrics associated with nodes, edges, degrees, and modularity. Furthermore, root rot resulted in a reduction in the proportion of negative connections in the network and the negative/positive cohesion of the entire core fungal microbiome. Particularly noteworthy was the observation that root rot infection destabilized the rhizosphere core fungal microbiome by weakening the negative connectivity associated with beneficial agents. Collectively, these results highlight the significance of the negative connectivity of beneficial agents in ensuring the stability of core microbial community.
IMPORTANCE
Root rot disease has been reported as the most devastating disease in the production process of artificial cultivated Sanqi ginseng, which seriously threatens the Sanqi industry. This study provides valuable insights into how root rot influences microbial relationships within the community. These findings open up opportunities for disease prevention and the promotion of plant health by regulating microbial interactions. In summary, the research sheds light on the ecological consequences of root rot on rhizosphere fungal microbiomes and offers potential strategies for managing soil-borne diseases and enhancing plant health.
REYES, J.D., T. ILLESCAS & M. BECERRA (2023). Cortinarius persimilis, novelty for the iberian mycobiota, Bol. Soc. Micol Madrid 47: 69-72. The first collections of this recently described taxon from the Iberian Peninsula are illustrated and described.
Symbioses with fungi are important and ubiquitous on dry land but underexplored in the sea. As yet only one seagrass has been shown to form a specific root-fungus symbiosis that resembles those occurring in terrestrial plants, namely the Mediterranean Posidonia oceanica (Alismatales: Posidoniaceae) forming a dark septate (DS) endophytic association with Posidoniomyces atricolor (Pleosporales: Aigialaceae). Using stereomicroscopy, light and scanning electron microscopy, and DNA cloning, here we describe a novel root-fungus symbiosis in the Indo-Pacific seagrass Thalassodendron ciliatum (Alismatales: Cymodoceaceae). Similarly to P. oceanica , the mycobiont of T. ciliatum occurs more frequently in thinner roots that engage in nutrient uptake from the seabed and forms extensive hyphal mantles composed of DS hyphae on the root surface. Contrary to P. oceanica , the mycobiont occurs on the roots with root hairs and does not penetrate its host intraradically. While the cloning revealed a relatively rich spectrum of fungi, they were mostly parasites or saprobes and the identity of the mycobiont remains unknown. Symbioses of seagrasses with fungi are probably more frequent than previously thought, but their functioning and significance are unknown. Melanin present in DS hyphae slows down their decomposition and so is true for the colonized roots. Root symbioses with DS fungi may in this way contribute to blue carbon sequestration in seagrass meadows.
Interactions between organisms are determined by life‐history traits. Ecological strategies regarding species specialisation range from generalist to highly specialised relationships. Although it is expected that habitat fragmentation's effect on species abundance and survival depends on their degree of specialisation and life‐history traits, few studies have delved into the interplay between interaction specialisation, life‐history traits and habitat fragmentation.
Here, we investigate the combined effect of habitat fragmentation, forest structure and life‐history traits (growth form and reproductive mode) on the specialisation of lichen‐forming fungi (mycobionts) toward their photosynthetic partners (photobionts) in lichen symbioses.
We studied mycobiont specialisation in epiphytic lichen communities present in 10 fragments of Quercus rotundifolia forest embedded in an agricultural matrix. Both mycobionts and photobionts were identified DNA barcoding and mycobiont specialisation was measured through interaction parameters calculating the relative number of interactions (normalised degree; ND) and the specialisation of each species based on its discrimination from a random selection of partners (d'). Phylogenetic generalised linear mixed models were used to analyse the effect of patch size as well as the life history traits growth form (crustose, foliose, fruticose) and reproduction mode (sexual vs. asexual) on mycobiont specialisation.
Both mycobiont and photobiont richness along the patch size gradient followed a hump‐back pattern, which was more pronounced in photobionts. Mycobionts forming crustose thalli established the largest number of interactions. Mycobiont specialisation (d') was larger for fruticose and foliose forms and species with vegetative reproduction. Along the gradient of fragment size, the relative number of interactions decreased and the specialisation of mycobionts with vegetative reproduction increased.
Synthesis. The study of mycobiont specialisation towards their photobionts in epiphytic lichen communities in a fragmented Mediterranean forest revealed a complex interaction between species' life history traits and habitat fragmentation. In particular, this interplay had a significant impact on the specialisation of mycobionts. The results show the ability of some species to modulate their specialisation according to habitat conditions, suggesting that some species may be more resilient to abiotic changes than expected.
Soil and plant roots are colonized by highly complex and diverse communities of microbes. It has been proposed that bacteria and fungi have synergistic effects on litter decomposition, but experimental evidence supporting this claim is weak. In this study, we manipulated the composition of two microbial kingdoms (Bacteria and Fungi) in experimental microcosms. In microcosms that were inoculated with fungi, litter loss was 47% higher than in microcosms that were not inoculated or only inoculated with bacteria. Combined inoculation with both bacteria and fungi did not significantly enhance decomposition compared with the fungi‐only treatments, and, as such, we found no evidence for complementary effects using our experimental setup. Inoculation with fungi also had a positive impact on plant growth after 4 and 8 weeks (480% and 710% growth stimulation, respectively). After 16 weeks, plant biomass was highest in microcosms where both bacteria and fungi were present pointing to fungal‐bacterial complementarity in stimulating plant growth. Overall, this study suggests that fungi are the main decomposers of plant litter and that the inoculated fungi contribute to plant growth in our experimental system.
In recent years, the genus Bryoria ( Parmeliaceae , Lecanoromycetes ) has been the subject of considerable phylogenetic scrutiny. Here we used information on six gene regions, three nuclear protein-coding markers ( Mcm 7, GAPDH and Tsr 1), two nuclear ribosomal markers (ITS and IGS) and a partial mitochondrial small subunit (mtSSU), to examine infrageneric relationships in the genus and to assess species delimitation in the Bryoria bicolor / B . tenuis group in section Divaricatae . For this purpose, phylogenetic analyses and several of the available algorithms for species delimitation (ASAP, GMYC single, GMYC multiple and bPTP) were employed. We also estimated divergence times for the genus using *BEAST. Our phylogenetic analyses based on the combined data set of six gene loci support the monophyly of sections Americanae , Divaricatae and Implexae , while section Bryoria is polyphyletic and groups in two clades. Species from Bryoria clade 1 are placed in an emended section Americanae . Our study reveals that section Divaricatae is young ( c . 5 My) and is undergoing diversification, especially in South-East Asia and western North America. Separate phylogenetic analyses of section Divaricatae using ITS produced a topology congruent with the current species concepts. However, the remaining gene regions produced poorly resolved phylogenetic trees and the different species delimitation methods also generated highly inconsistent results, congruent with other studies that highlight the difficulty of species delimitation in groups with recent and rapid radiation. Based on our results, we describe the new species B . ahtiana sp. nov., characterized by its bicolorous, caespitose, widely divergent thallus, conspicuously thickening main stems, well-developed secondary branches, and rather sparse third-order branchlets. Another new lineage, referred to here as B . tenuis s. lat., is restricted to western North America and may represent a new species recently diverged from B . tenuis s. str., though further work is needed.
The production of anthraquinones is a major characteristic of most species in the Teloschistaceae . Other secondary metabolites are quite rare in this family, but some species are known to produce depsides, depsidones, xanthones and usnic acid. A new monotypic genus, Neoplaca , with a new species N. mirabilis, is described from the subfamily Caloplacoideae of the family Teloschistaceae , lacking anthraquinones but containing the naphthopyrans simonyellin and consimonyellin. This is the first time this class of organic compounds has been found in the family Teloschistaceae and the second in the order Teloschistales , where simonyellin has been detected in Brigantiaeaceae . Simonyellin and consimonyellin have also previously been reported in the family Roccellaceae . Neoplaca mirabilis is currently known from the two nearby localities in Yakutia, Russia, where it is common and grows on base-rich soil on exposed south-facing siliceous outcrops. The thallus consists of scattered whitish to greyish, or rarely with pale yellow tinge, squamules 1–4.5 mm diam. and 0.3–1 mm thick with citrine to orange-yellow blastidia produced from their margin; apothecia and pycnidia are unknown. In addition to naphthopyrans, N. mirabilis contains an unidentified brown pigment similar in some features to melanin. The new species is also interesting in that the pigments are apparently located inside the cells of the cortex, not on their surface, where anthraquinones are found in Teloschistaceae .
Los microorganismos presentes en su entorno influyen en el crecimiento de las plantas y pueden ser mutualistas, como los hongos formadores de micorrizas, o no mutualistas, como los hongos endófitos. En este estudio se aislaron especies fúngicas de la raíz y suelo rizosférico de arándano (Vaccinium corymbosum L.) cultivado en el estado de Michoacán, México con la finalidad de analizar su potencial como promotores de desarrollo vegetal. Seis cepas fúngicas fueron identificadas molecularmente mediante las regiones del espaciador transcrito interno (ITS) del ADN ribosomal. Se evaluó su capacidad de modificar el desarrollo de plántulas de Arabidopsis thaliana (Col 0) mediante dos configuraciones experimentales (cajas Petri compartimentadas y no compartimentadas), para investigar la influencia de compuestos difusibles y volátiles sobre el fenotipo de la planta. Phialocephala fortinii y Mortierella alpina promovieron el crecimiento de Arabidopsis thaliana, sobre todo en cajas compartimentadas, donde se observó un incremento de la longitud de raíz principal (≥ 2 cm) y en el número de raíces laterales (≥ 34), sugiriendo que los compuestos volátiles son los responsables de estos incrementos. Las especies promotoras de desarrollo vegetal seleccionadas se evaluaron mediante líneas reporteras ARR5::GUS y DR5::GUS para estimar la respuesta de genes a la acumulación de citocininas y auxinas en los tejidos vegetales. Los resultados indican que Phialocephala fortinii y Mortierella alpina actúan diferencialmente sobre el crecimiento de las plantas y representan un recurso biológico con gran potencial para su uso como bioestimulantes en la agricultura actual.
Three twig-growing lichen species belonging to the family Teloschistaceae from southern Patagonia are described as new to science: Marchantiana pyramus sp. nov., with minute apothecia, orange due to dominant content of emodin, M. ramulicola sp. nov., with minute olive apothecia with dominant parietin and Austroplaca thisbe sp. nov., with clear yellow apothecia also with dominant parietin. Marchantiana subpyracea , M. epibrya and M. queenslandica are new combinations for species which, so far, are known only from New Zealand and Australia. Blastenia circumpolaris is shown to be very common in Patagonia and Marchantiana asserigena is documented for the first time from the Southern Hemisphere, viz. the Falkland Islands. The genus Marchantiana is analyzed here using three genes and is shown to be closely related to Yoshimuria ; although appearing as paraphyletic, a monophyletic origin cannot be ruled out. Morphology, ecology and distribution support a monophyletic treatment and Marchantiana is therefore treated as such.
Oxneriaria immersa H.S.Asghar, R.Zulfiqar & Khalid, sp. nov. and O. insignis R.Zulfiqar & Khalid,
sp. nov. (Megasporaceae) are described here as new to science, both characterized by their elongating/spreading marginal areoles. The distinguishing features of O. immersa H.S.Asghar, R.Zulfiqar &
Khalid, sp. nov. are poriform-aspicilioid apothecial discs, a smaller hymenium and hypothecium
(90-100 and 50-70 µm, respectively) and larger ascospores (20-25×10-15 µm). The key characters of
O. insignis R.Zulfiqar & Khalid, sp. nov. are distinctly lecanorine apothecial discs, a taller hymenium
and hypothecium (190-230 and 100-160 µm, respectively) and smaller ascospores (15-21×9-13 µm).
Detailed morpho-anatomical descriptions and a nrITS phylogeny of both species along with a worldwide key to the genus Oxneriaria S.Y.Kondr. & Lőkös are provided
ResearchGate has not been able to resolve any references for this publication.