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PubMed1998

Sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6, and V9 domains reveal highly species-specific variations within the genus Agrocybe.

A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included A. aegerita, A. chaxingu, and A. erebia; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included A. pediades; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included A. paludosa, A. firma, A. alnetorum, and A. praecox; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included A. vervacti and A. dura. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The conservation of the sequences of the V4, V6, and V9 domains of the mitochondrial SSU rRNA within species and the high degree of interspecific variation found in the Agrocybe species studied open the way for these sequences to be used as specific molecular markers of the Basidiomycota.

Base Sequence↗

PubMed2000

PCR primers that amplify fungal rRNA genes from environmental samples.

Two PCR primer pairs were designed to amplify rRNA genes (rDNA) from all four major phyla of fungi: Ascomycota, Basidiomycota, Chytridomycota, and Zygomycota. PCRs performed with these primers showed that both pairs amplify DNA from organisms representing the major taxonomic groups of fungi but not from nonfungal sources. To test the ability of the primers to amplify fungal rDNA from environment samples, clone libraries from two avocado grove soils were constructed and analyzed. These soils possess different abilities to inhibit avocado root rot caused by Phythophthora cinnamomi. Analysis of the two rDNA clone libraries revealed differences in the two fungal communities. It also revealed a markedly different depiction of the soil fungal community than that generated by a culture-based analysis, confirming the value of rDNA-based approaches for identifying organisms that may not readily grow on agar media. Additional evidence of the usefulness of the primers was obtained by identifying fungi associated with avocado leaves. In both the soil and leaf analyses, no nonfungal rDNA sequences were identified, illustrating the selectivity of these PCR primers. This work demonstrates the ability of two newly developed PCR primer sets to amplify fungal rDNA from soil and plant tissue, thereby providing unique tools to examine this vast and mostly undescribed community of organisms.

Ascomycota↗

PubMed2005

Phylum- and class-specific PCR primers for general microbial community analysis.

Amplification of a particular DNA fragment from a mixture of organisms by PCR is a common first step in methods of examining microbial community structure. The use of group-specific primers in community DNA profiling applications can provide enhanced sensitivity and phylogenetic detail compared to domain-specific primers. Other uses for group-specific primers include quantitative PCR and library screening. The purpose of the present study was to develop several primer sets targeting commonly occurring and important groups. Primers specific for the 16S ribosomal sequences of Alphaproteobacteria, Betaproteobacteria, Bacilli, Actinobacteria, and Planctomycetes and for parts of both the 18S ribosomal sequence and the internal transcribed spacer region of Basidiomycota were examined. Primers were tested by comparison to sequences in the ARB 2003 database, and chosen primers were further tested by cloning and sequencing from soil community DNA. Eighty-five to 100% of the sequences obtained from clone libraries were found to be placed with the groups intended as targets, demonstrating the specificity of the primers under field conditions. It will be important to reevaluate primers over time because of the continual growth of sequence databases and revision of microbial taxonomy.

Bacteria↗

PubMed2006

Evolution of the P-type II ATPase gene family in the fungi and presence of structural genomic changes among isolates of Glomus intraradices.

BACKGROUND: The P-type II ATPase gene family encodes proteins with an important role in adaptation of the cell to variation in external K+, Ca2+ and Na2+ concentrations. The presence of P-type II gene subfamilies that are specific for certain kingdoms has been reported but was sometimes contradicted by discovery of previously unknown homologous sequences in newly sequenced genomes. Members of this gene family have been sampled in all of the fungal phyla except the arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota), which are known to play a key-role in terrestrial ecosystems and to be genetically highly variable within populations. Here we used highly degenerate primers on AMF genomic DNA to increase the sampling of fungal P-Type II ATPases and to test previous predictions about their evolution. In parallel, homologous sequences of the P-type II ATPases have been used to determine the nature and amount of polymorphism that is present at these loci among isolates of Glomus intraradices harvested from the same field. RESULTS: In this study, four P-type II ATPase sub-families have been isolated from three AMF species. We show that, contrary to previous predictions, P-type IIC ATPases are present in all basal fungal taxa. Additionally, P-Type IIE ATPases should no longer be considered as exclusive to the Ascomycota and the Basidiomycota, since we also demonstrate their presence in the Zygomycota. Finally, a comparison of homologous sequences encoding P-type IID ATPases showed unexpectedly that indel mutations among coding regions, as well as specific gene duplications occur among AMF individuals within the same field. CONCLUSION: On the basis of these results we suggest that the diversification of P-Type IIC and E ATPases followed the diversification of the extant fungal phyla with independent events of gene gains and losses. Consistent with recent findings on the human genome, but at a much smaller geographic scale, we provided evidence that structural genomic changes, such as exonic indel mutations and gene duplications are less rare than previously thought and that these also occur within fungal populations.

Base Sequence↗

PubMedDate not supplied

Spore dispersal of a resupinate ectomycorrhizal fungus, Tomentella sublilacina, via soil food webs.

Patterns of fungal spore dispersal affect gene flow, population structure and fungal community structure. Many Basidiomycota produce resupinate (crust-like) basidiocarps buried in the soil. Although spores are actively discharged, they often do not appear to be well positioned for aerial dispersal. We investigated the potential spore dispersal mechanisms of one exemplar of this growth form, Tomentella sublilacina. It is a widespread ectomycorrhizal fungus that sporulates in the soil organic horizon, can establish from the spore bank shortly after disturbance, but also can be a dominant species in mature forest stands. We investigated whether its spores could be dispersed via spore-based food webs. We examined external surfaces, gut contents and feces from arthropod fungivores (mites, springtails, millipedes, beetles, fly larvae) and arthropod and vertebrate predators (centipedes, salamanders) from on and around T. sublilacina sporocarps. Spore densities were high in the guts of many individuals from all fungivore groups. Centipede gut contents, centipede feces and salamander feces contained undigested invertebrate exoskeletons and many apparently intact spores. DAPI staining of spores from feces of fungivores indicated that 7-73% of spores contained intact nuclei, whereas spores from predators had lower percentages of intact nuclei. The spiny spores often were lodged on invertebrate exoskeletons. To test the viability of spores that had passed through invertebrate guts we used fecal droppings of the millipede Harpaphe haydeniana to successfully inoculate seedlings of Pinus muricata (Bishop pine). These results indicate the potential for T. sublilacina spore dispersal via invertebrates and their predators in soil food webs and might help to explain the widespread distribution of this species. It is likely that this is a general mechanism of dispersal for fungi producing resupinate sporocarps, indicating a need to develop a fuller understanding of the linkages of soil food webs and spore dispersal.

Animals↗

PubMedDate not supplied

Phylogenetic analysis of Tilletia and allied genera in order Tilletiales (Ustilaginomycetes; Exobasidiomycetidae) based on large subunit nuclear rDNA sequences.

The order Tilletiales (Ustilaginomycetes, Basidiomycota) includes six genera (Conidiosporomyces, Erratomyces, Ingoldiomyces, Neovossia, Oberwinkleria and Tilletia) and approximately 150 species. All members of Tilletiales infect hosts in the grass family Poaceae with the exception of Erratomyces spp., which occur on hosts in the Fabaceae. Morphological features including teliospore ornamentation, number and nuclear condition of primary basidiospores and ability of primary basidiospores to conjugate and form an infective dikaryon were studied in conjunction with sequence analysis of the large subunit nuclear rDNA gene (nLSU). Analysis based on nLSU data shows that taxa infecting hosts in the grass subfamily Pooideae form one well supported lineage. This lineage comprises most of the reticulate-spored species that germinate to form a small number of rapidly conjugating basidiospores and includes the type species Tilletia tritici. Two tuberculate-spored species with a large number of nonconjugating basidiospores, T. indica and T. walkeri, and Ingoldiomyces hyalosporus are also included in this lineage. Most of the species included in the analysis with echinulate, verrucose or tuberculate teliospores that germinate to form a large number (>30) of nonconjugating basidiospores infect hosts in the subfamilies Panicoideae, Chloridoideae, Arundinoideae and Ehrhartoideae. This group of species is more diverse than the pooid-infecting taxa and in general do not form well supported clades corresponding to host subfamily. The results of this work suggest that morphological characters used to segregate Neovossia, Conidiosporomyces and Ingoldiomyces from Tilletia are not useful generic level characters and that all included species can be accommodated in the genus Tilletia.

Basidiomycota↗

PubMed2004

[Ecological function of wood-inhabiting fungi in forest ecosystem].

Wood-inhabiting fungi are one of the most important parts of forest ecosystem, and play an important role in degrading the wood in forest ecosystem. The major species of these fungi include the groups of Aphyllophorales (Basidiomycota), Discomycetes (Ascomycota) and some imperfect fungi. They have the ability to degrade cellulose, hemicelluloses and lignin of wood. Three type of wood decaying have been found, i.e., white rot, brown rot and soft rot. Many other organisms of forest ecosystem have symbiosis relationship with wood-decaying fungi. Wood-inhabiting fungi could offer the nutrition for many insects and birds, and spores of many wood-rotting species are spread by some insects. The high biodiversity of wood-decaying fungi is one of the important factors for the health of forest ecosystem.

Ascomycota↗

PubMed2026

Metagenomic Insights Into Microbial Diversity of Tea Rhizosphere of the Kangra Valley.

This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.

Rhizosphere↗

PubMed2001

Detection and taxonomic placement of endophytic fungi within frond tissues of Livistona chinensis based on rDNA sequences.

The 5.8S gene and flanking internal transcribed spacers (ITS1 and ITS2) of the rDNA were amplified from total DNA extracted from frond tissues of Livistona chinensis with universal and fungal-specific primers. These amplified fragments were cloned and sequenced. Phylogenetic analysis based on the 5.8S gene sequences indicated that the six clone sequences obtained were of different origins. Five sequences, P1-9, P2-6, P4-4, P4-5, and P4-7, belonged to the fungi and one sequence, P3-2, belonged to the plants. P1-9 was inferred to belong to the Basidiomycota based on the phylogenetic analysis of the 5.8S gene sequences but could not be identified to lower taxonomic levels. Further identification of the other four fungal clones to lower taxonomic levels was attempted based on phylogenetic analysis and sequence comparison of both the conserved 5.8S gene and the variable ITS regions. The origin of P2-6 was identified to be Glomerella and its anamorph Colletotrichum, the origins of P4-5 and P4-7 were Mycosphaerella and its anamorph Cladosporium, and the origin of P4-4 was the Herpotrichiellaceae. The direct approach to detection and taxonomic placement of endophytic fungi within host tissue without the need for conventional in vitro culturing is discussed.

DNA, Fungal↗

PubMed2002

Group I introns from Zygomycota: evolutionary implications for the fungal IC1 intron subgroup.

The origins of fungal group I introns within nuclear small-subunit (nSSU) rDNA are enigmatic. This is partly because they have never been reported in basal fungal phyla (Zygomycota and Chytridiomycota), which are hypothesized to be ancestral to derived phyla (Ascomycota and Basidiomycota). Here we report group I introns from the nSSU rDNA of two zygomycete fungi, Zoophagus insidians (Zoopagales) and Coemansia mojavensis (Kickxellales). Secondary structure analyses predicted that both introns belong to the IC1 subgroup and that they are distantly related to each other, which is also suggested by different insertion sites. Molecular phylogenetic analyses indicated that the IC1 intron of Z. insidians is closely related to the IC1 intron inserted in the LSU rDNA of the basidiomycete fungus Clavicorona taxophila, which strongly suggests interphylum horizontal transfer. The IC1 intron of C. mojavensis has a low phylogenetic affinity to other fungal IC1 introns inserted into site 943 of nSSU rDNA (relative to E. coli 16S rDNA). It is noteworthy that this intron contains a putative ORF containing a His-Cys box motif in the antisense strand, a hallmark for nuclear-encoded homing endonucleases. Overall, molecular phylogenetic analyses do not support the placement of these two introns in basal fungal IC1 intron lineages. This result leads to the suggestion that fungal IC1 introns might have invaded or been transferred laterally after the divergence of the four major fungal phyla.

Amino Acid Motifs↗

PubMed2007

Soil fungal communities underneath willow canopies on a primary successional glacier forefront: rDNA sequence results can be affected by primer selection and chimeric data.

Soil fungal communities underneath willow canopies that had established on the forefront of a receding glacier were analyzed by cloning the polymerase chain reaction (PCR)-amplified partial small subunit (18S) of the ribosomal (rRNA) genes. Congruence between two sets of fungus-specific primers targeting the same gene region was analyzed by comparisons of inferred neighbor-joining topologies. The importance of chimeric sequences was evaluated by Chimera Check (Ribosomal Database Project) and by data reanalyses after omission of potentially chimeric regions at the 5'- and 3'-ends of the cloned amplicons. Diverse communities of fungi representing Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota were detected. Ectomycorrhizal fungi comprised a major component in the early plant communities in primary successional ecosystems, as both primer sets frequently detected basidiomycetes (Russulaceae and Thelephoraceae) forming mycorrhizal symbioses. Various ascomycetes (Ophiostomatales, Pezizales, and Sordariales) of uncertain function dominated the clone libraries amplified from the willow canopy soil with one set of primers, whereas the clone libraries of the amplicons generated with the second primer set were dominated by basidiomycetes. Accordingly, primer bias is an important factor in fungal community analyses using DNA extracted from environmental samples. A large proportion (>30%) of the cloned sequences were concluded to be chimeric based on their changing positions in inferred phylogenies after omission of possibly chimeric data. Many chimeric sequences were positioned basal to existing classes of fungi, suggesting that PCR artifacts may cause frequent discovery of new, higher level taxa (order, class) in direct PCR analyses. Longer extension times during the PCR amplification and a smaller number of PCR cycles are necessary precautions to allow collection of reliable environmental sequence data.

Artifacts↗

PubMed2005

Occurrence and diversity of yeasts in the mid-atlantic ridge hydrothermal fields near the Azores Archipelago.

The yeast community associated with deep-sea hydrothermal systems of the Mid-Atlantic Rift was surveyed for the first time. This study relied on a culture-based approach using two different growth media: a conventional culture medium for yeasts supplemented with sea salts (MYPss) and the same medium additionally supplemented with sulfur (MYPssS). For the evaluation of species diversity, a molecular approach involving minisatellite-primed polymerase chain reaction (MSP-PCR) strain typing and sequence analysis of the D1/D2 domains of the 26S rDNA was followed. In the seven water samples that were studied, the number of colony-forming units per liter (cfu/L) ranged from 0 to 5940. The nonpigmented yeasts were much more abundant than the pink-pigmented ones. This disproportion was not observed in studies of other marine systems and may be due to the unique conditions of hydrothermal vents, characterized by a rich animal and microbial diversity and therefore by the availability of organic compounds utilizable by yeasts. Higher counts of nonpigmented yeast were obtained using MYPss, whereas for pink yeasts, higher counts were obtained using MYPssS. Moreover, among pink yeasts, some of the MSP-PCR classes obtained were composed of isolates obtained only on MYPssS, which might be an indication that these isolates are adapted to the ecosystems of the hydrothermal vents. Twelve phylotypes belonged to the Ascomycota and seven phylotypes belonged to the Basidiomycota. The nonpigmented yeasts were identified as Candida atlantica, C. atmosphaerica, C. lodderae, C. parapsilosis, Exophiala dermatitidis, Pichia guilliermondii, and Trichosporon dermatis, whereas the pigmented yeasts were identified as Rhodosporidium diobovatum, R. sphaerocarpum, R. toruloides, and Rhodotorula mucilaginosa. Some of the yeasts that were found belong to phylogenetic groups that include species reported from other marine environments, and eight phylotypes represent undescribed species. The new phylotypes found at Mid-Atlantic Ridge hydrothermal fields represent 33% of the total number of yeast taxa that were found.

Azores↗

PubMed2006

Microbial colonization of beech and spruce litter--influence of decomposition site and plant litter species on the diversity of microbial community.

The present study was conducted to investigate the effect of decomposition site and plant litter species on the colonizing microbial communities. For this, litter bag technique using beech and spruce litter was combined with RNA-based fingerprinting and cloning. Litter bags were incubated for 2 and 8 weeks in the Ah horizon of beech and beech-spruce mixed forest sites. Although sugars and starch were rapidly lost, lignin content increased by more than 40% for beech and more than doubled for spruce litter at both soil sites at the end of the experiment. Denaturing gradient gel electrophoresis analysis of 16S and 18S rRNA RT-PCR products was used for screening of differences between bacterial and fungal communities colonizing the two litter types. Development of the microbial community over time was observed to be specific for each litter type and decomposition site. RT-PCR products from both litter types incubated in beech-spruce mixed forest site were also cloned to identify the bacterial and fungal colonizers. The 16S rRNA clone libraries of beech litter were dominated by gamma-proteobacterial members, whereas spruce libraries were mainly composed of alpha-, beta-, and gamma-proteobacterial members. Ascomycota members dominated the 18S rRNA clone libraries. Clones similar to Zygomycota were absent from spruce, whereas those similar to Basidiomycota and Glomeromycota were absent from beech libraries. Selective effects of litter quality were observed after 8 weeks. The study provides an insight into the bacterial and fungal communities colonizing beech and spruce litter, and the importance of litter quality and decomposition site as key factors in their development and succession.

Bacteria↗

PubMed2004

beta-Glucan synthase induction in mushrooms grown on olive mill wastewaters.

beta-1-3-Glucan synthase activity and its induction by olive mill wastewaters (OMW) was studied in ten fungal strains (Auricularia auricula-judae, Lentinula edodes, Pleurotus eryngii, Stropharia aeruginosa, Agrocybe aegerita, P. pulmonarius, Armillaria mellea, P. ferulae, P. ostreatus, P. nebrodensis). A microtiter-based enzymatic assay on beta-1-3-glucan synthase activity was carried out on all mycelia growth both on the control medium and on OMW. Among the fungi assayed, L. edodes beta-1-3-glucan synthase was highly enhanced in OMW. The main components of OMW, i.e. phenols and lipids, were added separately to the control medium, to highlight the mechanism of L. edodes beta-1-3-glucan synthase induction. A Southern blot analysis and PCR with degenerated primers were carried out to detect the presence of fks1-like genes in these Basidiomycetes. The sequences obtained from the ten Basidiomycota were remarkably similar to fks1 from Filobasidiella neoformans. Spectrofluorimetric and RT-PCR analyses of beta-1-3-glucan synthase were performed on the mycelia of L. edodes. In this fungus, a strong stimulation of beta-1-3-glucan synthase mRNA and protein was recorded in the presence of OMW and phenols.

Agaricales↗

PubMed2001

Biotransformation of benzaldehyde into (R)-phenylacetylcarbinol by filamentous fungi or their extracts.

Extracts of 14 filamentous fungi were examined regarding their potential for production of (R)-phenylacetylcarbinol [(R)-PAC], which is the chiral precursor in the manufacture of the pharmaceuticals ephedrine and pseudoephedrine. Benzaldehyde and pyruvate were transformed at a scale of 1.2 ml into PAC by cell-free extracts of all selected strains, covering the broad taxonomic spectrum of Ascomycota, Zygomycota and Basidiomycota. Highest final PAC concentrations were obtained with the extracts of Rhizopus javanicus and Fusarium sp. [78-84 mM (11.7-12.6 g/l) PAC within 20 h from initial substrate concentrations of 100 mM benzaldehyde and 150 mM pyruvate]. (R)-PAC was in about 90-93% enantiomeric excess. Rhizopus javanicus had the advantage of faster growth than Fusarium sp. Rhizopus javanicus mycelia were used as an example in a biotransformation process based on whole cells and benzaldehyde and glucose as substrates. The substrate pyruvate was generated through the fungal fermentation of glucose. Only 19 mM PAC (2.9 g/l) were produced within 8 h from 80 mM benzaldehyde. with evidence of significant benzyl alcohol production.

Acetone↗

PubMed2000

The ribosomal DNA of the Zygomycete Mucor miehei.

The ribosomal DNA-from the Zygomycete Mucor miehei has been characterised. The complete rDNA unit was cloned by heterologous PCR using primers whose sequence matched conserved regions of the rDNA from related fungal species. The sequence of the overlapping PCR products revealed the existence of a repeated unit of 9574 bp. The genes encoding the different rRNA species were identified by their homology to the corresponding sequences from other fungi. We estimate that the rDNA unit is present in the genome of M. miehei in about 100 copies. This estimation was made by comparing the intensity of its hybridisation signal in a Southern blot with that of the mmp gene coding for aspartyl protease, which was assumed to be contained in single copy. The size and structure of the M. miehei rDNA unit was similar to that of other fungi. The genes encoding the 25S, 18S and 5.8S RNAs are closely linked within the repeated unit which also contains the 5S gene. This latter gene appears to be transcribed in the opposite direction. The 25S, 18S and 5.8S genes showed 70-80% homology to the corresponding genes from other fungi, whereas the degree of homology for the 5S gene was much lower. The highest homology (about 80%) corresponded to the few available sequences from other Mucor species. Homology to genes from other Zygomycota was no higher than that observed for genes from the Ascomycota or Basidiomycota fungi.

Base Sequence↗

PubMed2005

Contrasting root associated fungi of three common oak-woodland plant species based on molecular identification: host specificity or non-specific amplification?

An increasingly popular approach used to identify arbuscular mycorrhizal (AM) fungi in planta is to amplify a portion of AM fungal small subunit ribosomal DNA (SSU-rDNA) from whole root DNA extractions using the primer pair AM1-NS31, followed by cloning and sequencing. We used this approach to study the AM fungal community composition of three common oak-woodland plant species: a grass (Cynosurus echinatus), blue oak (Quercus douglasii), and a forb (Torilis arvensis). Significant diversity of AM fungi were found in the roots of C. echinatus, which is consistent with previous studies demonstrating a high degree of AM fungal diversity from the roots of various hosts. In contrast, clones from Q. douglasii and T. arvensis were primarily from non-AM fungi of diverse origins within the Ascomycota and Basidiomycota. This work demonstrates that caution must be taken when using this molecular approach to determine in planta AM fungal diversity if non-sequence based methods such as terminal restriction fragment length polymorphisms, denaturing gradient gel electrophoresis, or temperature gradient gel electrophoresis are used.

Apiaceae↗

PubMed1989

Phylogenetic association of Pneumocystis carinii with the 'Rhizopoda/Myxomycota/Zygomycota group' indicated by comparison of 5S ribosomal RNA sequences.

The cytoplasmic 5S ribosomal RNA (5S rRNA) sequence from Pneumocystis carinii was determined. A sequence comparison matrix of 382 eukaryote 5S rRNA sequences and an evolutionary tree were constructed to establish the phylogenetic position of Pneumocystis. The data suggest that Pneumocystis is associated with the Rhizopoda/Myxomycota/Zygomycota group (= 'Protista fungi') but not with common fungi, such as Ascomycota or Basidiomycota, nor with other protozoa.

Animals↗