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1.
Int J Syst Evol Microbiol ; 70(5): 3379-3390, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32375944

RESUMO

During a survey of fungi in native forests in Chile, several unidentified isolates of Diaporthe were collected from different hosts. The isolates were characterized based on DNA comparisons, morphology, culture characteristics and host affiliation, in accordance with previous descriptions. Phylogenetic analysis of the ITS region, combined with partial tub2 and tef1 genes, showed that the isolates formed three distinct groups representing three new taxa. The three new species of Diaporthe, Diaporthe araucanorum on Araucaria araucana, Diaporthe foikelawen on Drimys winteri and Diaporthe patagonica on Aristotelia chilensis are described and illustrated in the present study.


Assuntos
Florestas , Filogenia , Saccharomycetales/classificação , Chile , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Genes Fúngicos , RNA Ribossômico 16S/genética , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA
2.
BMC Evol Biol ; 20(1): 37, 2020 03 14.
Artigo em Inglês | MEDLINE | ID: mdl-32171235

RESUMO

BACKGROUND: Various ecological groups of earthworms very likely constitute sharply isolated niches that might permit speciation of their symbiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different host groups. The nuclear highly variable ITS1-5.8S-ITS2 region and the hypervariable D1/D2 region of the 28S rRNA gene have proven to be useful tools for the delimitation of species boundaries in closely related free-living ciliate taxa. In the present study, the power of these molecular markers as well as of the secondary structure of the ITS2 molecule were tested for the first time in order to discriminate the species of endosymbiotic ciliates that were isolated from the gastrointestinal tract of three ecologically different groups of lumbricid earthworms. RESULTS: Nineteen new ITS1-5.8S-ITS2 region and D1/D2-28S rRNA gene sequences were obtained from five astome species (Anoplophrya lumbrici, A. vulgaris, Metaradiophrya lumbrici, M. varians, and Subanoplophrya nodulata comb. n.), which were living in the digestive tube of three ecological groups of earthworms. Phylogenetic analyses of the rRNA locus and secondary structure analyses of the ITS2 molecule robustly resolved their phylogenetic relationships and supported the distinctness of all five species, although previous multivariate morphometric analyses were not able to separate congeners in the genera Anoplophrya and Metaradiophrya. The occurrence of all five taxa, as delimited by molecular analyses, was perfectly correlated with the ecological groups of their host earthworms. CONCLUSIONS: The present study indicates that morphology-based taxonomy of astome ciliates needs to be tested in the light of molecular and ecological data as well. The use of morphological identification alone is likely to miss species that are well delimited based on molecular markers and ecological traits and can lead to the underestimation of diversity and overestimation of host range. An integrative approach along with distinctly increased taxon sampling would be helpful to assess the consistency of the eco-evolutionary trend in astome ciliates.


Assuntos
Cilióforos/classificação , Cilióforos/isolamento & purificação , DNA Espaçador Ribossômico/genética , Trato Gastrointestinal/parasitologia , Oligoquetos/parasitologia , RNA Ribossômico 28S/genética , Animais , Cilióforos/genética , DNA Espaçador Ribossômico/análise , Ecologia , Genes de RNAr/genética , Interações Hospedeiro-Parasita/fisiologia , Oligoquetos/classificação , Oligoquetos/genética , Filogenia , RNA Ribossômico , RNA Ribossômico 28S/análise , Análise de Sequência de DNA
3.
Electron. j. biotechnol ; 44: 41-46, Mar. 2020. tab, ilus
Artigo em Inglês | LILACS | ID: biblio-1087698

RESUMO

Background: The main objective of this study was to isolate fungi associated with Anthopleura xanthogrammica and measure their antimicrobial and enzymatic activities. A total of 93 fungal strains associated with A. xanthogrammica were isolated in this study, of which 32 isolates were identified using both morphological characteristics and internal transcribed spacer (ITS) sequence analysis. The antibacterial activities of 32 fungal isolates were tested against Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Edwardsiella tarda, Vibrio harveyi, Fusarium oxysporum, and Pyricularia oryzae by agar diffusion assay. Extracellular hydrolytic enzyme activities of the fungal isolates were determined by agar diffusion assays. Enzyme activities were detected from clear halo size. Results: The isolated fungi belonged to 18 genera within 7 taxonomic orders of 1 phylum. The genera Aspergillaceae were the most diverse and common. The antimicrobial activities of 32 isolates were evaluated, and 19 (59.4%) of fungi isolate displayed unique antimicrobial activities. All fungal strains displayed at least one enzyme activity. The most common enzyme activities in the fungi isolates were amylase and protease, while the least common were pectinase and xylanase. Conclusions: This is first report on the sea anemone-derived fungi with antimicrobial and enzyme activities. Results indicated that sea anemone is a hot spot of fungal diversity and a rich resource of bioactive natural products.


Assuntos
Aspergillus/isolamento & purificação , Anêmonas-do-Mar/microbiologia , Antibacterianos/isolamento & purificação , Peptídeo Hidrolases/metabolismo , Filogenia , Poligalacturonase/metabolismo , Aspergillus/enzimologia , Aspergillus/genética , Bactérias/efeitos dos fármacos , DNA Espaçador Ribossômico , Biodiversidade , Fungos/isolamento & purificação , Fungos/genética , Amilases/metabolismo , Antibacterianos/farmacologia
4.
PLoS Negl Trop Dis ; 14(3): e0008130, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32130209

RESUMO

BACKGROUND: Yellow fever, dengue, chikungunya and Zika viruses are responsible for considerable morbidity and mortality in humans. Aedes aegypti and Aedes albopictus are the most important mosquito vectors involved in their transmission. Accurate identification of these species is essential for the implementation of control programs to limit arbovirus transmission, during suspected detections at ports of first entry, to delimit incursions or during presence/absence surveillance programs in regions vulnerable to invasion. We developed and evaluated simple and rapid colorimetric isothermal tests to detect these two mosquito species based on loop-mediated isothermal amplification (LAMP) targeting the ribosomal RNA internal transcribed spacer 1 (ITS1). METHODOLOGY/PRINCIPAL FINDINGS: Samples were prepared by homogenizing and heating at 99 oC for 10 min before an aliquot was added to the LAMP reaction. After 40 min incubation at 65 oC, a colour change indicated a positive result. The tests were 100% sensitive and species-specific, and demonstrated a limit of detection comparable with PCR-based detection (TaqMan chemistry). The LAMP assays were able to detect target species for various life stages tested (adult, 1st instar larva, 4th instar larva and pupa), and body components, such as legs, wings and pupal exuviae. Importantly, the LAMP assays could detect Ae. aegypti DNA in mosquitoes stored in Biogents Sentinel traps deployed in the field for 14 d. A single 1st instar Ae. aegypti larva could also be detected in a pool of 1,000 non-target 1st instar Aedes notoscriptus, thus expediting processing of ovitrap collections obtained during presence/absence surveys. A simple syringe-sponge protocol facilitated the concentration and collection of larvae from the ovitrap water post-hatch. CONCLUSIONS/SIGNIFICANCE: We describe the development of LAMP assays for species identification and demonstrate their direct application for surveillance in different field contexts. The LAMP assays described herein are useful adjuncts to laboratory diagnostic testing or could be employed as standalone tests. Their speed, ease-of-use, low cost and need for minimal equipment and training make the LAMP assays ideal for adoption in low-resource settings without the need to access diagnostic laboratory services.


Assuntos
Aedes/classificação , Aedes/crescimento & desenvolvimento , Colorimetria/métodos , Entomologia/métodos , Técnicas de Diagnóstico Molecular/métodos , Mosquitos Vetores/classificação , Mosquitos Vetores/crescimento & desenvolvimento , Técnicas de Amplificação de Ácido Nucleico/métodos , Aedes/genética , Animais , DNA Espaçador Ribossômico/genética , Feminino , Mosquitos Vetores/genética , Sensibilidade e Especificidade
5.
PLoS Negl Trop Dis ; 14(3): e0008077, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32214313

RESUMO

BACKGROUND: Phlebotomus (Larroussius) perniciosus and Canis familiaris are respectively the only confirmed vector and reservoir for the transmission of Leishmania (L.) infantum MON-1 in Tunisia. However, the vector and reservoir hosts of the two other zymodemes, MON-24 and MON-80, are still unknown. The aim of this study was to analyze the L. infantum life cycle in a Tunisian leishmaniasis focus. For this purpose, we have focused on: i) the detection, quantification and identification of Leishmania among this sand fly population, and ii) the analysis of the blood meal preferences of Larroussius (Lar.) subgenus sand flies to identify the potential reservoirs. METHODOLOGY AND FINDINGS: A total of 3,831 sand flies were collected in seven locations from the center of Tunisia affected by human visceral leishmaniasis. The collected sand flies belonged to two genus Phlebotomus (Ph.) (five species) and Sergentomyia (four species). From the collected 1,029 Lar. subgenus female sand flies, 8.26% was positive to Leishmania by ITS1 nested PCR. Three Leishmania spp. were identified: L. infantum 28% (24/85), L. killicki 13% (11/85), and L. major 22% (19/85). To identify the blood meal sources in Ph. Lar. subgenus sand flies, engorged females were analyzed by PCR-sequencing targeting the vertebrate cytochrome b gene. Among the 177 analyzed blood-fed females, 169 samples were positive. Sequencing results showed seven blood sources: cattle, human, sheep, chicken, goat, donkey, and turkey. In addition, mixed blood meals were detected in twelve cases. Leishmania DNA was found in 21 engorged females, with a wide range of blood meal sources: cattle, chicken, goat, chicken/cattle, chicken/sheep, chicken/turkey and human/cattle. The parasite load was quantified in fed and unfed infected sand flies using a real time PCR targeting kinetoplast DNA. The average parasite load was 1,174 parasites/reaction and 90 parasites/reaction in unfed and fed flies, respectively. CONCLUSION: Our results support the role of Ph. longicuspis, Ph. perfiliewi, and Ph. perniciosus in L. infantum transmission. Furthermore, these species could be involved in L. major and L. killicki life cycles. The combination of the parasite detection and the blood meal analysis in this study highlights the incrimination of the identified vertebrate in Leishmania transmission. In addition, we quantify for the first time the parasite load in naturally infected sand flies caught in Tunisia. These findings are relevant for a better understanding of L. infantum transmission cycle in the country. Further investigations and control measures are needed to manage L. infantum transmission and its spreading.


Assuntos
DNA/análise , Comportamento Alimentar , Conteúdo Gastrointestinal/química , Conteúdo Gastrointestinal/parasitologia , Especificidade de Hospedeiro , Leishmania infantum/isolamento & purificação , Phlebotomus/fisiologia , Animais , DNA/genética , Impressões Digitais de DNA , DNA Espaçador Ribossômico/genética , Transmissão de Doença Infecciosa , Feminino , Humanos , Leishmania infantum/genética , Masculino , Phlebotomus/parasitologia , Reação em Cadeia da Polimerase , Análise de Sequência de DNA , Tunísia
6.
Artigo em Inglês | MEDLINE | ID: mdl-32049260

RESUMO

Candidemia is a significant cause of bloodstream infections (BSI) in nosocomial settings. The identification of species can potentially improve the quality of care and decrease human mortality. Quantitative PCR (qPCR) was evaluated for Candida albicans detection using culture suspensions containing C. albicans , spiked human blood, the cloned qPCR target fragment (ITS2 region) and the results of these assays were compared. The assays showed a good detection limit: C. albicans DNA extracted from yeast (sensitivity 0.2 CFU/µL), spiked human blood (sensitivity 10 CFU/mL), and cloned fragment of ITS2 region (sensitivity 20 target copies/µL). The efficiency of ITS2 fragment-qPCR ranged from 89.67 to 97.07, and the linearity (R2) of the standard curve ranged from 0.992 to 0.999. The results showed that this ITS2-qPCR has a great potential as a molecular prototype model for the development of a test to be applied in clinical practice, greatly reducing the time of candidemia diagnosis, which is extremely important in this clinical setting.


Assuntos
Candida albicans/genética , Candidemia/microbiologia , Candida albicans/isolamento & purificação , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Humanos , Reação em Cadeia da Polimerase em Tempo Real , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
7.
Microbes Environ ; 35(1)2020.
Artigo em Inglês | MEDLINE | ID: mdl-32074549

RESUMO

Microcystis aeruginosa was quantitatively surveyed in 88 freshwater environments across Japan within 3| |weeks in 2011. In order to clarify the distribution pattern of M. aeruginosa at the intra-species level, three major genotypes, which were defined by 16S-23S rRNA inter-transcribed-spacer (ITS) regions, were selectively detected using quantitative real-time PCR assays. Of the 68 sites at which the Microcystis intergenic-spacer region of the phycocyanin (IGS-PC) gene was detected, the M. aeruginosa morphotype-related genotype (MG1) dominated in 41 sites, followed by the non-toxic M. wesenbergii-related genotype (MG3). A correlation analysis showed that total nitrogen and phosphate positively correlated with the abundance of IGS-PC, which positively correlated with microcystin synthetase gene abundance. A redundancy analysis of genotype compositions showed that pH positively correlated with the dominance of MG3 and negatively correlated with MG1, i.e., both toxic and non-toxic genotypes. Our survey of Microcystis populations over a wide area revealed that MG1 is a dominant genotype in Japan.


Assuntos
Microbiologia Ambiental , Água Doce/microbiologia , Proliferação Nociva de Algas , Microcystis/genética , Proteínas de Bactérias/genética , DNA Espaçador Ribossômico/genética , Água Doce/química , Genótipo , Concentração de Íons de Hidrogênio , Japão , Microcystis/classificação , Nitrogênio/análise , Peptídeo Sintases/genética , Fosfatos/análise , Ficocianina/genética
8.
PLoS One ; 15(1): e0227860, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31978185

RESUMO

Adventitious roots in canopy soils associated with silver beech (Nothofagus menziesii Hook.f. (Nothofagaceae)) form ectomycorrhizal associations. We investigated the extent to which canopy ectomycorrhizal communities contribute to overall diversity of ectomycorrhizal fungi associated with silver beech. Hyphal ingrowth bags were buried for 12 months in canopy and terrestrial soils of five trees at one site. We used amplicon sequencing of the nuclear ribosomal internal transcribed spacer 2 region (ITS2) to assess diversity of both ectomycorrhizal and non-ectomycorrhizal OTUs in hyphal ingrowth bags. There was a significant difference in ectomycorrhizal fungal community diversity between the terrestrial and canopy hyphal ingrowth bag communities. Ectomycorrhizal community composition of the terrestrial and canopy environments was also significantly different. Some ectomycorrhizal taxa were significantly differentially represented in either the terrestrial or canopy environment. The hyphal ingrowth bags also accumulated non-ectomycorrhizal species. The non-ectomycorrhizal fungi also had significantly different diversity and community composition between the canopy and terrestrial environments. Like the ectomycorrhizal community, some non-ectomycorrhizal taxa were significantly differentially represented in either the terrestrial or canopy environment. The canopy soil microhabitat provides a novel environment for growth of ectomycorrhizal adventitious roots and enables the spatial partitioning of ectomycorrhizal and non-ectomycorrhizal fungal diversity in the forest.


Assuntos
DNA Espaçador Ribossômico/genética , Ecossistema , Micobioma/genética , Micorrizas/genética , Raízes de Plantas/genética , Biodiversidade , DNA Fúngico/genética , Fagus/microbiologia , Hifas/genética , Hifas/crescimento & desenvolvimento , Raízes de Plantas/microbiologia , Microbiologia do Solo
9.
BMC Evol Biol ; 20(1): 2, 2020 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-31906844

RESUMO

BACKGROUND: Regions within the nuclear ribosomal operon are a major tool for inferring evolutionary relationships and investigating diversity in fungi. In spite of the prevalent use of ribosomal markers in fungal research, central features of nuclear ribosomal DNA (nrDNA) evolution are poorly characterized for fungi in general, including lichenized fungi. The internal transcribed spacer (ITS) region of the nrDNA has been adopted as the primary DNA barcode identification marker for fungi. However, little is known about intragenomic variation in the nrDNA in symbiotic fungi. In order to better understand evolution of nrDNA and the utility of the ITS region for barcode identification of lichen-forming fungal species, we generated nearly complete nuclear ribosomal operon sequences from nine species in the Rhizoplaca melanophthalma species complex using short reads from high-throughput sequencing. RESULTS: We estimated copy numbers for the nrDNA operon, ranging from nine to 48 copies for members of this complex, and found low levels of intragenomic variation in the standard barcode region (ITS). Monophyly of currently described species in this complex was supported in phylogenetic inferences based on the ITS, 28S, intergenic spacer region, and some intronic regions, independently; however, a phylogenetic inference based on the 18S provided much lower resolution. Phylogenetic analysis of concatenated ITS and intergenic spacer sequence data generated from 496 specimens collected worldwide revealed previously unrecognized lineages in the nrDNA phylogeny. CONCLUSIONS: The results from our study support the general assumption that the ITS region of the nrDNA is an effective barcoding marker for fungi. For the R. melanophthalma group, the limited amount of potential intragenomic variability in the ITS region did not correspond to fixed diagnostic nucleotide position characters separating taxa within this species complex. Previously unrecognized lineages inferred from ITS sequence data may represent undescribed species-level lineages or reflect uncharacterized aspects of nrDNA evolution in the R. melanophthalma species complex.


Assuntos
Ascomicetos/genética , Código de Barras de DNA Taxonômico , Líquens/genética , Ascomicetos/classificação , Núcleo Celular/genética , Código de Barras de DNA Taxonômico/métodos , DNA Fúngico/genética , DNA Intergênico , DNA Ribossômico , DNA Espaçador Ribossômico/genética , Sequenciamento de Nucleotídeos em Larga Escala , Líquens/classificação , Filogenia , Simbiose , Sequências de Repetição em Tandem
10.
Rev Soc Bras Med Trop ; 53: e20190364, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31994667

RESUMO

The present report describes the first case of postpartum disseminated histoplasmosis in a 24-year-old HIV-negative woman. On the tenth day after vaginal delivery, the patient presented with dyspnea, fever, hypotension, tachycardia, and painful hepatomegaly. Yeast-like Histoplasma capsulatum features were isolated in the buffy coat. The phylogenetic analysis demonstrated that the fungal isolate was similar to other H. capsulatum isolates identified in HIV patients from Ceará and Latin America. Thus, histoplasmosis development in individuals with transitory immunosuppression or during the period of immunological recovery should be carefully examined.


Assuntos
DNA Fúngico/análise , DNA Espaçador Ribossômico/genética , Histoplasma/genética , Histoplasmose/diagnóstico , Período Pós-Parto , Adulto , Feminino , Histoplasma/isolamento & purificação , Histoplasmose/microbiologia , Humanos , Filogenia , Reação em Cadeia da Polimerase
11.
PLoS One ; 15(1): e0227625, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31914145

RESUMO

Natural hybridization plays important roles in plant evolution and speciation. In this study, we sequenced ribosomal internal transcribed spacer (nrITS), four low-copy nuclear genes (Dbr1, SOS4a, SOS4b and PCRF1) and the chloroplast intergenic spacer trnV-trnM to test the hypothesis of hybridization between two species of Phyllagathis and Sporoxeia (Sonerileae/Dissochaeteae, Melastomataceae). Our results provided compelling evidence for the hybridization hypothesis. All hybrid individuals sampled were first-generation hybrids. The failure of flower production in the F1 hybrid individuals may work as the barrier preventing later-generation hybridization or backcross. Analysis of the chloroplast trnV-trnM sequences showed that the hybridization is bidirectional with S. petelotii as the major maternal parent. Several factors, such as sympatry, similar habitat preference, overlapping flowering season and shared pollinators, might have contributed to this hybridization event. The "intergeneric" hybridization reported in this study suggests close relationship between P. longicalcarata and S. petelotii.


Assuntos
Quimera , Melastomataceae/genética , Proteínas de Plantas/genética , China , Cloroplastos/genética , DNA Espaçador Ribossômico/genética , Flores/genética , Melastomataceae/anatomia & histologia , Melastomataceae/fisiologia
12.
Parasitol Res ; 119(1): 115-122, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31836920

RESUMO

Within livestock production, enteric diseases play an important role, since they cause severe economic losses due to mortality, growth depression, and reduction in the conversion rate. Coccidiosis caused by Eimeria spp. is a parasitic disease of high morbidity that affects various animal species, including sheep. In sheep, eleven species of Eimeria have been identified mainly through microscopical identification of the oocysts; however, this technique has certain limitations that make it difficult to identify the different Eimeria species. The objective of the present study was to morphologically identify the eleven species of Eimeria that infect sheep in the southeastern region of the State of Mexico, as well as obtain the partial sequence of the ITS-1 rRNA region of each species and analyze it phylogenetically. A total of 412 samples were collected from the 13 municipalities that comprise the region I of the State of Mexico, out of which, 40 had approximately 80% of a single Eimeria species. Among these, the eleven Eimeria species reported in sheep were identified. The phylogenetic analysis showed that the species reported in this study are associated with those reported in rabbits, bovines, and birds. It is suggested that the phylogenetic division of sheep in two clades may be associated with the presence or absence of the residual body. It is proposed that the present methodology can be used effectively for diagnosis and to obtain information about the epidemiology of ovine coccidial infection. The results obtained in this study constitute the first report of the ITS-1 region of the eleven Eimeria species that infect sheep worldwide.


Assuntos
Coccidiose/veterinária , Eimeria/classificação , Eimeria/genética , Doenças dos Ovinos/parasitologia , Animais , Bovinos , DNA Espaçador Ribossômico/genética , Eimeria/isolamento & purificação , Fezes/parasitologia , Gado/parasitologia , México , Oocistos , Filogenia , RNA Ribossômico/genética , Coelhos , Ovinos/parasitologia
13.
Int J Syst Evol Microbiol ; 70(2): 1158-1165, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31833830

RESUMO

Two yeast strains isolated from soil collected in Hokkaido, Japan, were found to secrete two extracellular lipases that exhibited activities at both 25 and 4 °C. Both strains could utilize olive oil, rapeseed oil, lard and fish oil as sole carbon sources. The similarity of the D1/D2 domain of the large subunit ribosomal RNA (LSU rRNA) sequence of these yeast strains to that of other yeasts in the GenBank database was very low (<96 %). The phylogenetic trees based on the LSU rRNA sequences and translation elongation factor-1-α (tef1-α) sequences indicated that both strains represented a member of the Wickerhamomyces /Candida clade. Sexual reproduction was not observed. The name Wickerhamomyces psychrolipolyticus f.a., sp. nov is proposed for this newly described yeast species producing cold-active lipases. This novel species is distinguishable from the type strains of other related species, Wickerhamomyces alni, Candida ulmi and Candida quercuum due to their abilities to grow at 4 to 30 °C, to produce lipase that is active also at 4 °C and to assimilate soluble starch.


Assuntos
Filogenia , Saccharomycetales/classificação , Microbiologia do Solo , Composição de Bases , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Japão , Lipase , Técnicas de Tipagem Micológica , Fator 1 de Elongação de Peptídeos/genética , Subunidades Ribossômicas Maiores/genética , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA , Temperatura
14.
Int J Syst Evol Microbiol ; 70(1): 199-203, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31596197

RESUMO

Two yeast strains, DMKU-WBL1-3 and DMKU GT3-16, were obtained from grease samples collected from grease traps at the Kasetsart University canteen, Thailand. Pairwise sequence analysis indicated that the strains were closely related to Candida cylindracea NRRL Y-17506T, but differed by 11 and 35 nucleotide substitutions in the D1/D2 domain of the large subunit (LSU) rRNA gene and the ITS region, respectively. Based on sequence divergences, the novel species was distinguished from C. cylindracea. The results of phylogenetic analysis based on the concatenated sequences from small subunit rRNA, ITS region and LSU rRNA genes showed that the two strains and C. cylindracea NRRL Y-17506T formed a distinct lineage related to the genus Babjeviella. A novel genus, Limtongozyma, is proposed to accommodate these clade members. Hence, Candida cylindracea NRRL Y-17506T is transferred to this genus and assigned as the type species of the genus. The holotype of Limtongozyma siamensis is DMKU-WBL1-3.


Assuntos
Filogenia , Saccharomycetales/classificação , Candida/classificação , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Técnicas de Tipagem Micológica , RNA Ribossômico/genética , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA , Tailândia
15.
Int J Syst Evol Microbiol ; 70(2): 1112-1116, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31778349

RESUMO

Two strains (YSP-384 and YSP-399), representing a novel Torulaspora species, were isolated from two nipa inflorescence sap samples collected in Trang province in the southern part of Thailand. The two strains had identical sequences of the D1/D2 domains of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) regions. The two strains were closest to Torulaspora maleeae CBS 10694T, but with 1.1 % nucleotide substitutions in the D1/D2 domains of the LSU rRNA gene and 5.2 % nucleotide substitutions in the ITS regions. Phylogenetic analysis based on the concatenated sequences of the ITS regions and the D1/D2 domains of the LSU rRNA gene supported that the two strains represented a distinct species in the genus Torulaspora. Some phenotypic characteristics of the two strains differed from T. maleeae including the two strains have ability to assimilate d-xylose, d-glucono-δ-lactone and melizitose, and inability to ferment maltose and raffinose, whereas T. maleeae has opposite results. Therefore, the two strains are described as representing a novel species, for which the name Torulaspora nypae sp. nov. was proposed.


Assuntos
Arecaceae/microbiologia , Inflorescência/microbiologia , Filogenia , Torulaspora/classificação , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Técnicas de Tipagem Micológica , Análise de Sequência de DNA , Tailândia , Torulaspora/isolamento & purificação
16.
Int J Syst Evol Microbiol ; 70(2): 1059-1063, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31746728

RESUMO

A total of 21 yeast isolates were recovered as part of a research project on biodiversity of yeasts in traditional dairy products in Alborz province, Iran. Standard protocols were used to carry out phenotypic, biochemical, physiological characterization and the phylogenetic analysis of combined the D1/D2 domain of the large ribosomal subunit (26S or LSU) and ITS region sequences. Five strains represented a potential new ascomycetous yeast species. Ascospore formation was not observed in these strains, and they did not ferment the examined carbon sources. Phylogenetic analysis placed these isolates in a well-supported sub-clade in the genus Saccharomycopsis. Here, we describe this novel yeast as Saccharomycopsis oxydans sp. nov.


Assuntos
Laticínios/microbiologia , Microbiologia de Alimentos , Filogenia , Saccharomycopsis/classificação , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Irã (Geográfico) , Técnicas de Tipagem Micológica , Subunidades Ribossômicas Maiores/genética , Saccharomycopsis/isolamento & purificação , Análise de Sequência de DNA
17.
RNA ; 26(2): 209-217, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31748405

RESUMO

Compensatory mutations are crucial for functional RNA because they maintain RNA configuration and thus function. Compensatory mutation has traditionally been considered to be a two-step substitution through the GU-base-pair intermediate. We tested for an alternative AC-mediated compensatory mutation (ACCM). We investigated ACCMs by using a comprehensive sampling of ribosomal internal transcribed spacer 2 (ITS2) from 3934 angiosperm species in 80 genera and 55 families. We predicted ITS2 consensus secondary structures by using LocARNA for structure-based alignment and partitioning paired and unpaired regions. We examined and compared the substitution rates and frequencies among base pairs by using RNA-specific models. Base-pair states of ACCMs were mapped onto the inferred phylogenetic trees to infer their evolution. All types of compensatory mutations involving the AC intermediate were observed, but the most frequent substitutions were with AU or GC pairs, which are part of the AU-AC-GC pathway. Compared with the GU intermediate, AC had a lower frequency and higher mutability. Within the AU-AC-GC pathway, the AU-AC substitution rate was much slower than the AC-GC substitution rate. No consistently higher overall rate was identified for either pathway among all 80 sampled lineages, though compensatory mutations through the AC intermediate averaged about half that through the GU intermediate. These results demonstrate an alternative compensatory mutation between AU and GC that helps address the controversial inference of inferred simultaneous double substitutions.


Assuntos
DNA Espaçador Ribossômico/genética , Magnoliopsida/genética , Conformação de Ácido Nucleico , Adenina , Pareamento de Bases , Citosina , Mutação , Filogenia , RNA de Plantas/genética
18.
Microbiol Res ; 231: 126371, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31734584

RESUMO

Eleven soil samples were collected from different plantations at the Forestry Model Base, Northeast Forestry University, China (45°43'10″N, 126°37'15″E), and 122 Trichoderma strains (T1-T122) were isolated. Nine Trichoderma species were identified based on morphological and molecular classification methods. The diversity of woody fungi was analyzed based on the type and quantity of Trichoderma spp. in the soil samples isolated from each plantation. Subdominant T. pseudoharzianum T17 (TpsT17) was screened and its biocontrol potential against Fusarium oxysporum CFCC86068 (Fox68) and growth promotion of Populus davidiana × P. alba var. pyramidalis (PdPap) seedlings were investigated. Compared with PdPap + Fox68 treatment, PdPap + TpsT17 + Fox68 treatment had an obvious antagonistic effect on Fox68 based on the status of roots and stomata of the poplar seedlings. In addition, pretreatment with TpsT17 increased catalase activity 14-fold and decreased hydrogen peroxide and malondialdehyde concentrations 2.57- and 7-fold, respectively, in the PdPap + TpsT17 + Fox68 treatment compared with the PdPap + Fox68 treatment. The transcription levels of PR1, JAZ6751, MYC2, MP, and JAR1 in PdPap + TpsT17+Fox68-treated plants were upregulated 5.75-, 5.63-, 14.88-, 8.24-, and 10.45-fold, respectively, at 3 d, while LAX2 exhibited little change in comparison with the level in PdPap + Fox-treated plants. TpsT17 was detected in the roots and stems of PdPap + TpsT17- and PdPap + TpsT17+Fox68-treated PdPap 28 d after inoculation, which demonstrated the endogenous capacity of TpsT17.


Assuntos
Endófitos/isolamento & purificação , Fusarium/crescimento & desenvolvimento , Populus , Trichoderma , Antibiose , Antifúngicos , Agentes de Controle Biológico , Catalase/metabolismo , DNA Espaçador Ribossômico , Endófitos/genética , Endófitos/metabolismo , Agricultura Florestal , Genes Fúngicos , Micoses/microbiologia , Filogenia , Doenças das Plantas/microbiologia , Imunidade Vegetal , Populus/enzimologia , Populus/microbiologia , Plântula/metabolismo , Microbiologia do Solo , Trichoderma/genética , Trichoderma/isolamento & purificação , Trichoderma/metabolismo
19.
Int J Syst Evol Microbiol ; 70(2): 1086-1092, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31751201

RESUMO

Six polymorphic yeast strains with strong antifungal activities isolated from dicot plants in an alkaline-lake desert region were subjected to taxonomic examination. The phylogenetic trees reconstructed by using neighbour-joining, maximum-likelihood and Bayesian methods from concatenated D1/D2 and ITS-5.8S-ITS2 sequences revealed phylogenetic affinity to Ustilaginaceae, but the large phylogenetic distance separating the isolates from the most closely related groups of species indicates that they represent a separate species. The sequences of the genes coding for the LSU rDNA, act1, rpb2 and a protein of unknown function corroborate this position. The isolates can easily be distinguished from their closest relatives by physiological tests (utilisation of carbon and nitrogen sources). Based on these results, a new species, Mycosarcoma aegyptiacum sp. nov., is proposed to accommodate the isolates. All isolates are polymorphic. Transitions between budding-yeast and pseudohyphal morphologies which take place during colony formation result in morphologically different colony sectors and invasive growth into the medium. Neither sexual mating nor sporulation was observed in cultures growing on laboratory media.


Assuntos
Filogenia , Rudbeckia/microbiologia , Ustilaginales/classificação , Teorema de Bayes , DNA Fúngico/genética , DNA Ribossômico/genética , DNA Espaçador Ribossômico/genética , Egito , Lagos , Técnicas de Tipagem Micológica , Folhas de Planta/microbiologia , Análise de Sequência de DNA , Ustilaginales/isolamento & purificação , Leveduras/classificação , Leveduras/isolamento & purificação
20.
Int J Syst Evol Microbiol ; 70(2): 977-981, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31724935

RESUMO

Strain SY-07 was isolated from decaying leaves of Avicennia marina collected from Syhat mangroves, Dammam city, Arabian Gulf, Saudi Arabia. Phylogenetic analyses of three genes [D1/D2 region of the LSU and SSU rRNA genes and internal transcribed spacer (ITS) region] showed that strain SY-07 represents a novel species of the genus Saturnispora distinct from closely related species. Saturnispora mendoncae was the most closely related species with an LSU gene sequence similarity of 89.3 % (58 nucleotide substitutions and four indels out of 578 nt), 97 % similarity for the SSU gene (42 nucleotide substitutions and 10 indels out of 1614 nt) and 88 % similarity for the ITS region (15 nucleotide substitutions and eight indels out of 430 nt). In addition, strain SY-07 differed from S. mendoncae by its ability to assimilate d-galactose (weak), d-xylose (weak), meso-erythritol (delayed), glucono-δ-lactone, citrate (delayed) and ethylamine. S. mendoncae produced persistent asci that contain two to four spherical ascospores and lacked pseudohyphae, while sexual reproduction was not observed in strain SY-07 and extensive and pseudohyphae were present. Strain SY-07 was able to grow at between 25 and 40 °C, while S. mendoncae did not grow at 37 °C. The name Saturnispora mangrovi f.a., sp. nov. is proposed for strain SY-07. The holotype is CBS 15874, with the ex-type culture AUMC 12005. The MycoBank number for Saturnispora mangrovi f.a., sp. nov. is MB 827036.


Assuntos
Avicennia/microbiologia , Filogenia , Folhas de Planta/microbiologia , Saccharomycetales/classificação , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Técnicas de Tipagem Micológica , Saccharomycetales/isolamento & purificação , Arábia Saudita , Análise de Sequência de DNA , Esporos Fúngicos
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