Molecular phylogenetic and scanning electron microscopical analyses places the Choanephoraceae and the Gilbertellaceae in a monophyletic group within the Mucorales (Zygomycetes, Fungi)

A multi-gene genealogy based on maximum parsimony and distance analyses of the exonic genes for actin (act) and translation elongation factor 1 alpha (tef), the nuclear genes for the small (18S) and large (28S) subunit ribosomal RNA (comprising 807, 1092, 1863, 389 characters, respectively) of all 50 genera of the Mucorales (Zygomycetes) suggests that the Choanephoraceae is a monophyletic group. The monotypic Gilbertellaceae appears in close phylogenetic relatedness to the Choanephoraceae. The monophyly of the Choanephoraceae has moderate to strong support (bootstrap proportions 67% and 96% in distance and maximum parsimony analyses, respectively), whereas the monophyly of the Choanephoraceae-Gilbertellaceae clade is supported by high bootstrap values (100% and 98%). This suggests that the two families can be joined into one family, which leads to the elimination of the Gilbertellaceae as a separate family. In order to test this hypothesis single-locus neighbor-joining analyses were performed on nuclear genes of the 18S, 5.8S, 28S and internal transcribed spacer (ITS) 1 ribosomal RNA and the translation elongation factor 1 alpha (tef) and beta tubulin (betatub) nucleotide sequences. The common monophyletic origin of the Choanephoraceae-Gilbertellaceae clade could be confirmed in all gene trees and by investigation of their ultrastructure. Sporangia with persistent, sutured walls splitting in half at maturity and ellipsoidal sporangiospores with striated ornamentations and polar ciliate appendages arising from spores in persistent sporangia and dehiscent sporangiola represent synapomorphic characters of this group. We discuss our data in the context of the historical development of their taxonomy and physiology and propose a reduction of the two families to one family, the Choanephoraceae sensu lato comprising species which are facultative plant pathogens and parasites, especially in subtropical to tropical regions.     

Ultrastructure of mucoralean sporangiospores

The fine structure of sporangiospores found in members of the Choanephoraceae, Cunninghamellaceae, Mortierellareae, Mucoraceae, Pilobolaceae, Syncephalastraceae and Thamnidiaceae (Mucorales) is reviewed. Sporangiospore structure in the merosporangiferous Dimargaritaceae (Dimargaritales), Kickxellaceae (Kickxellales) and Piptocephalidaceae (Zoopagales) is also considered briefly for comparison with the merosporangiferous Syncephalastraceae.     

Rhizoferrin: A complexone type siderophore of the mocorales and entomophthorales (Zygomycetes)

The present investigation presents evidence that rhizoferrin, a novel polycarboxylate or complexone-type siderophore, originally isolated from Rhizopus microsporus, represents the common siderophore within the Zygomycetes. Thus, rhizoferrin could be detected by HPLC analysis in various families of the Mucorales, e.g., Rhizopus microsporus var. rhizopodiformis, Mucor mucedo and Phycomyces nitens (Mucoraceae), Chaetostylum fresenii and Cokeromyces recurvatus (Thamnidiaceae), Cunninghamella elegans and Mycotypha africana (Choanephoraceae) and Mortierella vinacea (Mortierellaceae) and in Basidiobolus microsporus (Entomophthorales). The function of rhizoferrin as a siderophore in the fungus R. microsporus var. rhizopodiformis was demonstrated by time- and concentration-dependent uptake of [55Fe]-labelled rhizoferrin, yielding saturation kinetics with values of Km = 8 microM and V(max) = 1.2 nmol min-1 (mg dry wt)-1.     

Taxonomic studies of Choanephoraceae in India

Summary A taxonomic study of the members of the family Choanephoraceae was undertaken. Almost all the species of the family have been isolated from various sources in India. Two genera, viz.,Blakeslea andChoanephora have been recognized and a key to the genera has been given. The genusBlakeslea includes only one speciesB. trispora and the genusChoanephora five species. A key to the species has also been given. A new variety ofChoanephora circinans, viz.,C. circinans var.prolifera Mehrotra andMehrotra based on the proliferating vesicular apices of the sporangiophores has been described.     

Sequence-based differentiation of strains in the Mycobacterium avium complex.

The complete 16S-23S rDNA internal transcribed spacer (ITS) was sequenced in 35 reference strains of the Mycobacterium avium complex. Twelve distinct ITS sequences were obtained, each of which defined a "sequevar"; a sequevar consists of the strain or strains which have a particular sequence. ITS sequences were identified which corresponded to M. avium (16 strains, four ITS sequevars) and Mycobacterium intracellulare (12 strains, one ITS sequevars). The other seven M. avium complex strains had ITS sequences which varied greatly from those of M. avium and M. intracellulare and from each other. The 16S-23S rDNA ITS was much more variable than 16S rDNA, which is widely used for genus and species identification. Phylogenetic trees based on the ITS were compatible with those based on 16S rDNA but were more detailed and had longer branches. The results of ITS sequencing were consistent with the results of hybridization with M. avium and M. intracellulare probes (Gen-Probe) for 30 of 31 strains tested. Serologic testing correlated poorly with ITS sequencing. Strains with the same sequence were different serovars, and those of the same serovar had different sequences. Sequencing of the 16S-23S rDNA ITS should be useful for species and strain differentiation for a wide variety of bacteria and should be applicable to studies of epidemiology, diagnosis, virulence, and taxonomy.     

Genetic diversity of Rhizoctonia solani associated with potato tubers in France

The soilborne fungus Rhizoctonia solani is a pathogen of many plants and causes severe damage in crops around the world. Strains of R. solani from the anastomosis group (AG) 3 attack potatoes, leading to great yield losses and to the downgrading of production. The study of the genetic diversity of the strains of R. solani in France allows the structure of the populations to be determined and adapted control strategies against this pathogen to be established. The diversity of 73 French strains isolated from tubers grown in the main potato seed production areas and 31 strains isolated in nine other countries was assessed by phylogenetic analyses of (i) the internal transcribed spacer sequences (ITS1 and ITS2) of ribosomal RNA (rRNA), (ii) a part of the gene tef-1α and (iii) the total DNA fingerprints of each strain established by amplified fragment length polymorphism (AFLP). The determination of the AGs of R. solani based on the sequencing of the ITS region showed three different AGs among our collection (60 AG 3 PT, 8 AG 2-1 and 5 AG 5). Grouping of the strains belonging to the same AG was confirmed by sequencing of the gene tef-1α used for the first time to study the genetic diversity of R. solani. About 42% of ITS sequences and 72% of tef-1α sequences contained polymorphic sites, suggesting that the cells of R. solani strains contain several copies of ITS and the tef-1α gene within the same nucleus or between different nuclei. Phylogenetic trees showed a greater genetic diversity within AGs in tef-1α sequences than in ITS sequences. The AFLP analyses showed an even greater diversity among the strains demonstrating that the French strains of R. solani isolated from potatoes were not a clonal population. Moreover there was no relationship between the geographical origins of the strains or the variety from which they were isolated and their genetic diversity.     

阴道分离因肯毛孢子菌的分子鉴定和种内分型

分别采用rRNA基因内转录间隔区(ITS)和基因间隔区(IGS1)测序,ITS和IGS1区PCR限制性片段长度多态性分析(PCR-RFLP)和基因组DNA的随机扩增多态性DNA(RAPD)等方法,对三株因肯毛孢子菌Trichosporon inkin进行分子特征及种内分型研究。结果显示,不同菌株的rRNA基因ITS区和IGS1区的序列相似性均高达100%,RFLP酶切图谱具有较理想的种内一致性,而不同菌株的RAPD图谱不尽相同。研究表明:rRNA基因IGS1区测序及RFLP酶切可考虑用于因肯毛孢子菌的菌种分子鉴定,而基因组DNA的RAPD则较适合于菌种的种内分型。     

Molecular divergence of the soil yeasts Williopsis sensu stricto

Fifty-three strains of saturn-spored yeasts were analyzed by means of restriction analysis of the amplified fragment of rDNA which comprised the 5.8S rRNA gene and the internal transcribed spacers ITS1 and ITS2. The use of endonucleases HaeIII and MspI enabled clear differentiation of yeast species Williopsis mucosa, W. salicorniae, Zygowilliopsis californica, Komagataea pratensis, and the Williopsis sensu stricto complex. Minisatellite primer M13 was proposed for the differentiation between twin species of Williopsis sensu stricto, which have identical restriction profiles. PCR with primer M13 enabled reidentification of a number of collection strains, species identification of saturn-spored isolates from the Far East, and detection of three strains affiliated to novel taxa. The latter have unique PCR profiles and differ in the nucleotide sequences of ITS1 and ITS2 fragments of rDNA. Possible variations in the results obtained with different molecular methods are discussed.     

Presence of a novel 16S-23S rRNA gene intergenic spacer insert in Bradyrhizobium canariense strains

Seven slow-growing bacterial strains isolated from root nodules of yellow serradella (Ornithopus compressus) that originated from Asinara Island on North Western Sardinia in Italy were characterized by partial 16S rRNA gene and intergenic spacer (ITS) sequencing as well as amplified fragment length polymorphism (AFLP) genomic fingerprinting. The results indicated that the O. compressus isolates belong to the Bradyrhizobium canariense species. The analysis of ITS sequences divided the branch of B. canariense strains into two statistically separated groups (ITS clusters I and II). All the strains in ITS cluster I showed the presence of unique oligonucleotide insert TTAGAGACTTAGGTTTCTK. This insert was neither found in other described species of the family Rhizobiaceae nor in any other bacterial families and can be used as a natural and high selective genetic marker for ITS cluster I of B. canariense strains. ITS grouping of O. compressus isolates was supported by the unweighted pair group method with arithmetic averages cluster analysis of their AFLP patterns, suggesting that the strains of ITS cluster II were genetically closer to each other than to isolates from the ITS cluster I. A taxonomic importance is supposed of the revealed 19 bp ITS insert for an intraspecific division within high heterogeneous B. canariense species.     

Systematic study of basidiomycetous yeasts - evaluation of the ITS regions of rDNA to delimit species of the genus Rhodosporidium

Nucleotide sequences of internal transcribed spacer (ITS) regions were determined to establish the guidelines for species identification in the genus Rhodosporidium. Forty-two strains of nine species of the genus Rhodosporidium were used for ITS (ITS1 and ITS2) analysis. Intraspecific length polymorphisms and sequence variations were observed within R. azoricum, R. diobovatum, R. paludigenum, R. sphaerocarpum and R. toruloides, while no variation was observed within R. babjevae and R. kratochvilovae. Based on comparison of the levels of intraspecific and interspecific sequence similarity, strains with identical sequences were considered to represent a single species and strains with 92% or lower similarity of ITS sequences were considered to be distinct species in the genus Rhodosporidium.     

rDNA ITS sequence of Rhizopus oryzae: its application to classification and identification of lactic acid producers

Rhizopus oryzae is an important organism for its production of organic acids such as lactic acid, fumaric acid, etc. To date, there were no easy methods to classify strains according to their acid production. The sequences of the ribosomal RNA-encoding DNA (rDNA) internal transcribed spacer (ITS) region of 64 strains of R. oryzae were analyzed and found to conserve mutations correspond to acid production. We have devised a way to use these mutations for a novel method to identify lactic-acid-producing Rhizopus oryzae, by designing specific polymerase chain reaction (PCR) primers on them. Touch down PCR using these primers amplified the ITS DNA of lactic acid producers specifically. By this method, we could isolate lactic acid producing strains from Indonesian fermented foods.     

Analysis of 16S-23S rRNA internal transcribed spacer regions in Pasteurellaceae isolated from laboratory rodents

The internal transcribed spacer (ITS) regions of members of Pasteurellaceae isolated from rodents, including the [Pasteurella] pneumotropica biotypes Jawetz and Heyl, [Actinobacillus] muris, "Hemophilus influenzaemurium" and Bisgaard taxon 17 were studied and their feasibility to discriminate these species was analyzed. The reference strains of all species analyzed showed unique species-specific ITS patterns which were further present in 49 clinical isolates of [P.] pneumotropica biotypes Jawetz and Heyl and [A.] muris allowing their identification by comparison to the reference strains pattern. Sequence analysis of the amplified fragments revealed in all species, with exception of "H. influenzaemurium", a larger ITS(ile+ala) which contained the genes for tRNA(Ile(GAU)) and tRNA(Ala(UGC)) and a smaller ITS(glu) with the tRNA(Glu(UUC)) gene. "H. influenzaemurium" revealed two each of the larger and respectively the smaller ITS fragments. Both the length and the sequence of each ITS type were highly conserved within the [P.] pneumotropica biotypes Jawetz and Heyl and [A.] muris strains tested. On the contrary, ITS sequences revealed significant interspecies variations with identity levels ranging from 61.2 to 89.5% for ITS(ile+ala) and 56.5 to 86.8% for ITS(glu). Sequences regions with significant interspecies variation but highly conserved within the species were identified and might be used to design probes for the identification of rodent Pasteurellaceae to the species level.     

Shade tolerance plasticity in response to neutral vs green shade cues in Polygonum species of contrasting ecological breadth

Here we examined species differences in perception and response to two distinct types of shade cue, reduced photosynthetically active radiation (PAR) with and without reduced red : far red ratio (R : FR), in Polygonum persicaria and Polygonum hydropiper, two closely related annuals of contrasting ecological breadth. We compared plasticity data for light-gathering traits from glasshouse experiments at equivalently reduced PAR under neutral shade (R : FR 1.03) and green shade (R : FR 0.702). Species shared the ability to distinguish between the two types of shade, as shown by the ability of each to respond differently to neutral vs green shade for one or more traits. However, the species' responses to these cues differed significantly. Polygonum persicaria expressed stronger shade-tolerance responses (increased leaf allocation and leaf area ratio) to reduced PAR alone than to green shade. By contrast, P. hydropiper expressed slightly less plasticity for these traits in neutral than in green shade. The pronounced plastic response of P. persicaria to neutral shade may contribute to the range of habitats this widespread species can occupy, which includes neutral-shade environments such as urban settings.     

Phylogeny of Mycobacterium tuberculosis Beijing strains constructed from polymorphisms in genes involved in DNA replication, recombination and repair

Background

The Beijing family is a successful group of M. tuberculosis strains, often associated with drug resistance and widely distributed throughout the world. Polymorphic genetic markers have been used to type particular M. tuberculosis strains. We recently identified a group of polymorphic DNA repair replication and recombination (3R) genes. It was shown that evolution of M. tuberculosis complex strains can be studied using 3R SNPs and a high-resolution tool for strain discrimination was developed. Here we investigated the genetic diversity and propose a phylogeny for Beijing strains by analyzing polymorphisms in 3R genes.

Methodology/Principal Findings

A group of 3R genes was sequenced in a collection of Beijing strains from different geographic origins. Sequence analysis and comparison with the ones of non-Beijing strains identified several SNPs. These SNPs were used to type a larger collection of Beijing strains and allowed identification of 26 different sequence types for which a phylogeny was constructed. Phylogenetic relationships established by sequence types were in agreement with evolutionary pathways suggested by other genetic markers, such as Large Sequence Polymorphisms (LSPs). A recent Beijing genotype (Bmyc10), which included 60% of strains from distinct parts of the world, appeared to be predominant.

Conclusions/Significance

We found SNPs in 3R genes associated with the Beijing family, which enabled discrimination of different groups and the proposal of a phylogeny. The Beijing family can be divided into different groups characterized by particular genetic polymorphisms that may reflect pathogenic features. These SNPs are new, potential genetic markers that may contribute to better understand the success of the Beijing family.     

IGS基因及RAPD标记分析在加特隐球酵母基因分类中的应用

根据ITS1-5.8S-ITS2区域的特异核酸序列变化,加特隐球酵母Cryptococcus gattii(≡新型隐球酵母加特变种Cryptococcu neoformans var.gattii)可分为6种基因型。本研究通过检测加特隐球酵母的IGS基因,发现其IGS序列有着更丰富的变异和信息位点。通过结合加特隐球酵母RAPD(随机扩增的多态性DNA)图谱比较研究,与IGS和ITS的序列分析结果大体一致,说明新近发现的加特隐球酵母ITS8型确实有别于以前报道过的其他加特隐球酵母ITS基因型。研究证明IGS1及IGS2基因片段分析可以作为加特隐球酵母基因分类鉴定中有效的辅助鉴别的分子生物学方法,联合多种基因分类鉴定的方法可以更有效地揭示新型隐球酵母加特变种种内不同基因亚型间的遗传进化关系。     

Artocarpus (Moraceae)-gall midge pollination mutualism mediated by a male-flower parasitic fungus

A previously undescribed pollination system involving a monoecious tree species, Artocarpus integer (Moraceae), pollinator gall midges, and fungi is reported from a mixed dipterocarp forest in Sarawak, Borneo. The fungus Choanephora sp. (Choanephoraceae, Mucorales, Zygomycetes) infects male inflorescences of A. integer, and gall midges (Contarinia spp., Cecidomyiinae, Diptera) feed on the fungal mycelia and oviposit on the inflorescence. Their larvae also feed on the mycelia and pupate in the inflorescence. The gall midges are also attracted by female inflorescences lacking mycelia, probably due to a floral fragrance similar to that of male inflorescences. Because of the sticky pollen, dominance of Contarinia spp. in flower visitors, and pollen load observed on Contarinia spp. collected on both male and female inflorescences, Artocarpus integer is thought to be pollinated by the gall midges. Although several pathogenic fungi have been reported to have interactions with pollinators, this is the first report on a pollination mutualism in which a fungus plays an indispensable role. The pollination system described here suggests that we should be more aware of the roles fungi can play in pollinations.     

Sequence conservation in the internal transcribed spacers and 5.8S ribosomal RNA of parasitic scuticociliates Miamiensis avidus (Ciliophora, Scuticociliatia)

The scuticociliate Miamiensis avidus is a histophagous parasite that causes high mortality in cultured marine fishes, with clinical signs of severe ulcers and hemorrhages in the skeletal muscle. The internal transcribed spacer (ITS) region, which is widely used in taxonomy and molecular phylogeny because of a high degree of variation, was compared for 21 cloned strains of M. avidus (Ciliophora, Scuticociliatia). These strains were isolated from olive flounder Paralichthys olivaceus, ridged-eye flounder Pleuronichthys cornutus and spotted knifejaw Oplegnathus fasciatus in Korea and Japan. The ITS1 (140 bp), ITS2 (236 bp) and 5.8S (119 bp) regions from 21 strains were identical, indicating that these regions are highly conserved in M. avidus. Phylogenic analysis of ITS2 shows that the ciliate should be included in the Philasterida with a close relationship to Pseudocohnilembus hargisi. This study exhibits the first detailed analysis of the ITS1, 5.8 S and ITS2 rRNA regions of M. avidus.     

多聚酶链反应技术鉴别肾综合征出血热病毒血清型的初步研究

肾综合征出血热(HFRS)为一组抗原性密切相关的布尼亚科汉坦病毒引起的急性传染病。在我国存在至少两种临床表现、动物宿主及流行特征截然不同的血清型别,即血清Ⅰ型(汉坦型)和血清Ⅱ型(汉城型)。这两型病毒间的血清学定型已有报道。近年来,除啮齿类动物外,从临床病人以及非啮齿类动物体内也分离到了HFRS病毒。同时出现两类型别毒株共存,以及从家鼠体内分离到野鼠型毒株或从野鼠体内分离到家鼠型毒株的复杂情形。为此,准确检定并鉴别不同来源毒株型别,将为深入了解其病原学、流行病学以及制定疫苗生产策略提供重要信息。     

First Report of a New Isolate of <Emphasis Type="Italic">Metarhizium rileyi</Emphasis> from Maize Fields of Quivicán,Cuba

Metarhizium rileyi (Farlow) Samson is an important entomopathogenic fungus of more than 30 species of Lepidoptera larvae. The aim of this research was to characterize isolate of M. rileyi from Quivicán, Cuba on the basis of morphological and molecular approaches. The fungus was isolated from samples of S. frugiperda larvae collected from maize fields of Quivicán municipality, Mayabeque province, Cuba, and it was cultured on PDA?+?Ampicillin solid media for morphological characterization. The DNA was isolated using CTAB method and internal transcribed spacer (ITS1, ITS4) were used as the primers for the amplification. The amplified products of 1335 bp were purified and sequenced at CINVESTAV-IPN in both the directions using the above primers. A consensus sequence was obtained by alignment of the forward and reverse sequences for this region and deposited in GenBank (MG637450). The fungus produced slightly cottony colony of pale green color and dispersed conidia and septal mycelium were observed under the optical microscope. A BLAST search of the sequence in GenBank revealed a 99% of identity with several strains of N. rileyi (e.g., AF368501.1, AB268359.1 and EU553337.1) and M. rileyi (e.g., KY436756.1). This is the first report of M. rileyi isolate from maize fields of Quivicán in Cuba and this is important for biodiversity studies and is another possibility for Integrated Pest Management.     

Molecular divergence of the soil yeasts <Emphasis Type="Italic">Williopsis</Emphasis> sensu stricto

Fifty-three strains of Saturn-spored yeasts were analyzed by means of restriction analysis of the amplified fragment of rDNA comprising the 5.8S rRNA gene and the internal transcribed spacers ITS1 and ITS2. The use of endonucleases HaeIII and MspI enabled clear differentiation of yeast species Williopsis mucosa, W. salicorniae, Zygowilliopsis californica, and Komagataea pratensis and the Williopsis sensu stricto complex. The minisatellite primer M13 was proposed for differentiation between sibling species of Williopsis sensu stricto, which have identical restriction profiles. PCR with primer M13 enabled reidentification of a number of collection strains, species identification of Saturn-spored isolates from the Far East, and detection of three strains affiliated to novel taxa. The latter have unique PCR profiles and differ in the nucleotide sequences of ITS1 and ITS2 fragments of rDNA. Possible variations in the results obtained with different molecular methods are discussed.Translated from Mikrobiologiya, Vol. 73, No. 6, 2004, pp. 768–776.Original Russian Text Copyright © 2004 by Naumova, Gazdiev, Naumov.