Evolutionary relationships among Ascochyta species infecting wild and cultivated hosts in the legume tribes Cicereae and Vicieae

Evolutionary relationships were inferred among a worldwide sample of Ascochyta fungi from wild and cultivated legume hosts based on phylogenetic analyses of DNA sequences from the ribosomal internal transcribed spacer regions (ITS), as well as portions of three protein-coding genes: glyceraldehyde-3-phosphate-dehydrogenase (G3PD), translation elongation factor 1-alpha (EF) and chitin synthase 1 (CHS). All legume-associated Ascochyta species had nearly identical ITS sequences and clustered with other Ascochyta, Phoma and Didymella species from legume and nonlegume hosts. Ascochyta pinodes (teleomorph: Mycosphaerella pinodes [Berk. & Blox.] Vestergen) clustered with Didymella species and not with well characterized Mycosphaerella species from other hosts and we propose that the name Didymella pinodes (Berk. & Blox.) Petrak (anamorph: Ascochyta pinodes L.K. Jones) be used to describe this fungus. Analysis of G3PD revealed two major clades among legume-associated Ascochyta fungi with members of both clades infecting pea ("Ascochyta complex"). Analysis of the combined CHS, EF and G3PD datasets revealed that isolates from cultivated pea (P. sativum), lentil (Lens culinaris), faba bean (Vicia faba) and chickpea (Cicer arietinum) from diverse geographic locations each had identical or similar sequences at all loci. Isolates from these hosts clustered in well supported clades specific for each host, suggesting a co-evolutionary history between pathogen and cultivated host. A. pisi, A. lentis, A. fabae and A. rabiei represent phylogenetic species infecting pea, lentil, faba bean and chickpea, respectively. Ascochyta spp. from wild relatives of pea and chickpea clustered with isolates from related cultivated hosts. Isolates sampled from big-flower vetch (Vicia grandiflora) were polyphyletic suggesting that either this host is colonized by phylogenetically distinct lineages of Ascochyta or that the hosts are polyphyletic and infected by distinct evolutionary lineages of the pathogen. Phylogenetic species identified among legume-associated Ascochyta spp. were fully concordant with previously described morphological and biological species.     

Biological and Molecular Characterization of Three Isolates of Tomato aspermy virus Infecting Chrysanthemums in India

Severe mosaic, chlorotic ringspots and flower deformation were observed during the winter of November 2006–February 2007 on chrysanthemums ( Chrysanthemum morifolium ) at three locations in India: Lucknow (UP), Dhanbad (MP) and Kolkata (WB). Tomato aspermy virus (TAV) was detected in affected plants by ELISA and by RT-PCR using TAV specific primers. These TAV isolates were mechanically transmitted to test plant species and also by aphids ( Aphis gossypii ) to Lycopersicon esculentum . The complete RNA 3 of each TAV isolate was cloned and sequenced and determined to be 2386 nucleotides (nt) long, and to encode two open reading frames (ORFs): the movement protein (MP) of 741 nt and the coat protein (CP) of 657 nt translating in to 246 and 218 amino acid (aa), respectively. When RNA 3 sequences of the Indian isolates were multiple aligned with seven other strains of TAV occurring worldwide, Indian isolates shared 98–99% identities among themselves and with the KC, V, P, B, I and C strains of TAV. In phylogenetic analysis, the Lucknow and Kolkata isolates of TAV clustered together and showed a close relationship with the KC-TAV strain from South Korea, whereas the Dhanbad isolate formed an independent cluster and showed closeness with the V-TAV strains from Spain and Australia. Recombination events were also observed in the CP region of the Dhanbad isolate, supporting its diverse behaviour. This is the first report of the complete RNA 3 sequence of these three Indian TAV isolates.     

Detection of acylated homoserine lactones produced by Vibrio spp. and related species isolated from water and aquatic organisms

Aims: To assess the diversity in production of acylated homoserine lactones (AHLs) among Vibrio spp and related species. Methods and Results: A total of 106 isolates, with representatives of 28 Vibrio spp and related species, were investigated for the production of AHLs. For this, a rapid method for the screening of AHLs was developed based on the use of bacterial biosensors using a double‐layer microplate assay. At least one bacterial biosensor was activated in 20 species, Agrobacterium tumefaciens being the most frequently activated biosensor. One isolate of Vibrio anguillarum, Vibrio rotiferianus and Vibrio metschnikovii activated the Chromobacterium violaceum biosensor, which is not common among the Vibrionaceae family. For those species with more than one isolate, the biosensor activation profile was the same except for two species, V. anguillarum and V. metschnikovii, which varied among the different isolates. Conclusions: AHL production was observed in the majority of the studied species, with a diverse biosensor activation profile. Significance and Impact of the Study: The high diversity in AHL production is in consistence with the high diversity in ecological niches of the Vibrionaceae family. The absence of AHL detection in eight species warrants further work on their quorum‐sensing systems.     

霍乱弧菌和副溶血弧菌分离株的gyrB基因系统发育分析

依据gyrB基因部分编码序列构建系统发育树以分类和鉴别霍乱弧菌和副溶血弧菌,并探讨其种系发生关系。扩增并测序13株霍乱弧菌、8株副溶血弧菌、2株嗜水气单胞菌及1株类志贺邻单胞菌的gyrB基因(编码DNA促旋酶B亚单位)序列,并采用距离法与最大似然法构建系统发育树。两种方法所构建的树结构完全一致,霍乱弧菌、副溶血弧菌、嗜水气单胞菌及类志贺邻单胞菌各自形成一个独立的簇。其中,霍乱肠毒素基因(ctxA)阳性的霍乱弧菌(8株O139群与2株O1群ElTor型)聚类成一分枝;3株副溶血弧菌临床株(1株2002年流行株,2株2004年分离株)与1日本菌株及2001年1株自环境分离的毒力株聚类。系统发育分析靶分子gyrB基因可以良好区分上述4种常见病原菌。产毒O139群霍乱弧菌与产毒O1群ElTor型霍乱弧菌关系密切。副溶血弧菌环境毒力株与本地区临床主要流行株在系统发育关系上较为接近,可能是潜在的致病菌。     

Arsenic-resistant bacteria isolated from agricultural soils of Bangladesh and characterization of arsenate-reducing strains

Aims:  To analyse the arsenic-resistant bacterial communities of two agricultural soils of Bangladesh, to isolate arsenic-resistant bacteria, to study their potential role in arsenic transformation and to investigate the genetic determinants for arsenic resistance among the isolates.
Methods and Results:  Enrichment cultures were performed in a minimal medium in the presence of As(III) and As(V) to isolate resistant bacteria. Twenty-one arsenic-resistant bacteria belonging to different genera of Gram-positive and Gram-negative bacteria were isolated. The isolates, with the exception of Oceanimonas doudoroffii Dhal Rw, reduced 2 mmol l⁻¹ As(V) completely to As(III) in aerobic conditions. Putative gene fragments for arsenite efflux pumps were amplified in isolates from Dhal soil and a putative arsenate reductase gene fragment was amplified from a Bacillus sp. from Rice soil.
Conclusions:  Phylogenetically diverse arsenic-resistant bacteria present in agricultural soils of Bangladesh are capable of reducing arsenate to arsenite under aerobic conditions apparently for detoxification purpose.
Significance and Impact of the Study:  This study provides results on identification, levels of arsenic resistance and reduction of arsenate by the bacterial isolates which could play an important role in arsenic cycling in the two arsenic-contaminated soils in Bangladesh.     

The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-O1 Vibrio cholerae.

The DNA sequences of the asd genes from 45 isolates of Vibrio cholerae (19 clinical O1 isolates, 2 environmental nontoxigenic O1 isolates, and 24 isolates with different non-O1 antigens) were determined. No differences were found within either sixth- or seventh-pandemic isolates; however, variation was found between the two forms and among the non-O1 isolates. O139 isolates had sequences identical to those of seventh-pandemic isolates. Phylogenetic trees with Vibrio mimicus as the outgroup suggest that the sixth-pandemic, seventh-pandemic, and U.S. Gulf isolates are three clones that have evolved independently from different lineages of environmental, nontoxigenic, non-O1 V. cholerae isolates. There is evidence for horizontal transfer of O antigen, since isolates with nearly identical asd sequences had different O antigens, and isolates with the O1 antigen did not cluster together but were found in different lineages. We also found evidence for recombination events within the asd gene of V. cholerae. V. cholerae may have a higher level of genetic exchange and a lower level of clonality than species such as Salmonella enterica and Escherichia coli.     

Identification and characterization of Francisella species from natural warm springs in Utah, USA

Aims: To characterize Francisella isolated from two natural warm springs in Utah and compare them to a strain isolated from a patient with probable exposure to one of the springs in 2001. Methods and Results: A total of 39 presumptive Francisella isolates were obtained from two springs, Wasatch Hot Spring and Hobo Warm Spring, just north of Salt Lake City, Utah. All isolates were characterized by a combination of biochemical and molecular analyses, including novel PCR/electrospray ionization‐mass spectrometry (ESI‐MS) typing assays. Thirty‐one were identified as F. philomiragia, while the remaining eight were identified as F. tularensis ssp. novicida. Phylogenetic analysis of the 16S rRNA sequences revealed 27 isolates, which clustered with F. philomiragia, albeit into two distinct clades. The remaining isolates clustered along with other F. tularensis strains including the Utah clinical isolate. Testing with the PCR/ESI‐MS assays confirmed the identities of the isolates, but both yielded DNA signatures distinct from that of the clinical isolate. Conclusion: We were successful in isolating several Francisella strains from natural warm springs; however, none appeared to genetically match the original 2001 clinical isolate. Significance and Impact of the Study: This work highlights the presence of viable, potentially pathogenic Franscisella species living in the unique environmental niche of natural warm springs.     

Identification of vhhP2, a novel genetic marker of Vibrio harveyi, and its application in the quick detection of V. harveyi from animal specimens and environmental samples

Aims:  To investigate the species-specific prevalence of vhhP2 among Vibrio harveyi isolates and the applicability of vhhP2 in the specific detection of V. harveyi from crude samples of animal and environmental origins.
Methods and Results:  A gene ( vhhP2 ) encoding an outer membrane protein of unknown function was identified from a pathogenic V. harveyi isolate. vhhP2 is present in 24  V. harveyi strains isolated from different geographical locations but is absent in 24 strains representing 17 different non- V. harveyi species, including V. parahaemolyticus and V. alginolyticus . A simple polymerase chain reaction method for the identification of V. harveyi was developed based on the conserved sequence of vhhP2 . This method was demonstrated to be applicable to the quick detection of V. harveyi from crude animal specimens and environmental samples. The specificity of this method was tested by applying it to the examination of two strains of V. campbellii , which is most closely related to V. harveyi . One of the V. campbellii strains was falsely identified as V. harveyi .
Conclusions:  vhhP2 is ubiquitously present in the V. harveyi species and is absent in most of the non- V. harveyi species; this feature enables vhhP2 to serve as a genetic marker for the rapid identification of V. harveyi . However, this method can not distinguish some V. campbellii strains from V. harveyi .
Significance and Impact of the Study:  the significance of our study is the identification of a novel gene of V. harveyi and the development of a simple method for the relatively accurate detection of V. harveyi from animal specimens and environmental samples.     

Population Structure and Genetic Diversity within Peach latent mosaic viroid Field Isolates from Peach Showing three Symptoms

To gain insight into the molecular basis of field isolates inducing the symptoms of leaf yellowing, discolouration along leaf sides and leaf mosaic, six isolates from peach showing the three different symptoms in the field were studied by single-strand conformation polymorphism analysis and nucleotide sequence analysis. Results revealed that each Peach latent mosaic viroid (PLMVd) isolate is composed of a population of genetically related variants (haplotypes), one being predominant with frequencies from 32% to 57%, and most of others having a low frequency of 4–5%. Each predominant haplotype was sequenced, as well as some non-predominant haplotypes selected randomly for comparative purposes. In each isolate, sequence alignment among the predominant and non-predominant haplotypes demonstrated that the predominant haplotype had the least variation with others among them, and its sequence was identical to the consensus sequence, which inflected that the predominant haplotype displayed a wide representative of sequence for others in a PLMVd isolate. The similarities and genetic distance between the predominant sequences from peach showing the same symptoms were higher and smaller, respectively, than that with different symptoms; they were more than 98.8% and <1%, respectively, between the predominant sequences with same symptomatic source, and were <98.5% and more than 1%, respectively, between the predominant sequences with different symptomatic source. Some particular variations were indicated for these isolates, and it revealed that the isolates with the symptom of discolouration along leaf sides on their source peach trees had a G or U in position 169 nt, and the isolates with the symptom of leaf yellowing had U and C in 115 and 116 nt, respectively, and the isolates with the symptom of leaf mosaic showed diversity at (3 nt: delete C; 5 nt: A and 54 nt: U).     

Laboratory evaluation of the virulence of Beauveria bassiana isolates to the sorghum shoot borer Chilo partellus Swinhoe (Lepidoptera: Pyralidae) and their characterization by RAPD-PCR

Beauveria bassiana has long been used as a mycopesticide. It has a wide host range; isolates have been reported to differ in host range and virulence to a given insect species. Identification of a molecular marker linked to a virulent phenotype to a target pest would be useful in screening for isolates effective against it. Twenty B. bassiana isolates were tested for their virulence to the second instar larvae of Chilo partellus Swinhoe in laboratory bioassays and their DNA fingerprints were generated by RAPD-PCR. Three arbitrary categories of aggressiveness were chosen; isolates that caused >70%, between 70 and 40% and <40% larval mortality were grouped as highly, medium and less aggressive types, respectively. In the random amplified polymorphic DNA (RAPD) analysis a 30% variability was observed among the isolates; which clustered into three major groups. The groups based on virulence rating did not match with the RAPD clusters. One of the highly aggressive isolates clustered with less aggressive isolates in one cluster and the other grouped along with the medium aggressive isolates in a different cluster. The B. bassiana isolates were classified phenotypically based on the taxonomic order of the original insect host and the climatic zone (tropical/temperate) from which they were isolated. No correlation between the aggressiveness of the isolate and the relatedness of the original insect host to the tested insect was observed; both the highly aggressive isolates were from coleopteran insects. A correlation was found between the RAPD grouping and the phenotypic classification of the isolates. All the lepidopteran isolates grouped into one major cluster, most sub clusters were constituted by isolates from the same climatic zone.     

Random Amplified Polymorphic DNA and Polymerase Chain Reaction Markers for the Differentiation and Detection of Stenocarpella maydis in Maize Seeds

The genetic relationship of 34 isolates of Stenocarpella maydis from different geographic regions in South Africa was analysed by random amplified polymorphic DNA (RAPD) and ribosomal DNA markers. Two genetic groups were differentiated by using three RAPD primers and correlated to the cultural morphology of the isolates. Of all the isolates tested, 79.4% were clustered into RAPD group I (RG I), which did not sporulate when cultured on potato dextrose agar (PDA) at 25°C for 10 days. The rest of the isolates designated as RG II sporulated on PDA medium and showed a higher genetic variation. Ribosomal DNA (rDNA) was amplified using polymerase chain reaction (PCR) with the universal primers, internal transcribed spacer (ITS) 1 and ITS 4. Restriction digestion of PCR products displayed three types (RF A, RF B and RF C) of profiles. RF A was in accordance with RG I. RF B was consistent with RG II except for one isolate, U5. However, U5 displayed a unique profile and had no restriction sites for Hpa II and Hae III. The results indicate that two distinct genetic groups exist among S. maydis isolates from maize in S. Africa. The ITS1 and ITS2 regions of rDNA were sequenced and primers were designed. The designed primer pair P1/P2 permitted a sensitive and specific detection of S. maydis .     

Effects of ants on the reproductive success of Euphorbia cyparissias and associated pathogenic rust fungi

Ants are common visitors to the flowers of Euphorbia cyparissias , and also often forage on E. cyparissias stems that are infected by rust fungi of the species complex Uromyces pisi . These fungi sterilise their host, produce nectar and require insects for their sexual reproduction. Our objective was to determine whether ant visits enhance the sexual reproduction of either E. cyparissias or the rust fungi. Uromyces pisi is known to be obligately outcrossing, whereas a breeding system experiment established that E. cyparissias can self, but sets more seeds when outcrossed. We used insect exclusion experiments to test whether ants fertilise the rust fungi and to determine whether ants are pollinators of E. cyparissias . These experiments showed that insect pollination is necessary for seed set and that ants can pollinate the flowers. However, ants do not fertilise the rust fungi.     

Protein variability in Meloidogyne spp. (Nematoda:Meloidogynidae) revealed by two-dimensional gel electrophoresis and mass spectrometry

Total protein variation as revealed by two-dimensional electrophoresis (2D-E) was studied in 18 isolates from populations of Meloidogyne arenaria (six isolates), Meloidogyne incognita (10 isolates), and Meloidogyne javanica (one isolate) plus an unclassified isolate. Gels (80 x 60 x 0.75 mm) were silverstained and digitized in order to compare their protein patterns. Optical density and position of protein patterns were measured using statistical cluster analysis and computer-assisted image analysis software. Only those protein stains or positions that were clearly defined (i.e., without background) were considered. The number of positions in gels ranged from 86 to 203. Each of these positions had 95 clearly expressed proteins that were present in at least two replicates for each isolate. Spot position was considered a taxonomical character with two different states: presence (1) and absence (0). Accordingly, genetic distance was estimated among isolates and species, and a phylogenetic tree was constructed following the cladistic approach based on maximum parsimony analysis. Isolates of M. arenaria--M. javanica--Meloidogyne sp. and of M. incognita formed two separate monophyletic groups. Both groups were clearly defined on the basis of two sets of protein positions that can be considered as diagnostic characters. An attempt to identify these proteins by mass spectrometry was made. Group diagnostic proteins for M. incognita and M. arenaria (and for other proteins common to all isolates) were distinguished by protonated mass signals in the MALDI fingerprinting spectrum.     

Plasma Membrane H+-ATPase Activity in Spores, Germ Tubes, and Haustoria of the Rust Fungus Uromyces viciae-fabae

Using plasma membrane-enriched vesicles, the properties of the H+-ATPase (EC 3.6.1.35) from the rust fungus Uromyces viciae-fabae were studied. The enzyme is strictly Mg2+-dependent and is inhibited by vanadate. The pH-optimum is at 6.7. By Western blot analysis using a monoclonal antibody against corn plasma membrane H+-ATPase a polypeptide of approximately 104 kDa could be detected. The vanadate-sensitive H+-ATPase activity of microsomal vesicles obtained from different stages of rust development was determined. Uredospores had only a very low enzyme activity (1.9 μmol Pi x mg-1 protein x h-1). In germ tubes the ATPase activity was about twofold higher (4.0 μmol Pi x mg-1 protein x h-1). An eightfold higher ATPase activity (16.1 μmol Pi x mg-1 protein x h-1) was found in microsomal vesicles from haustoria which had been isolated from rust-infected Vicia faba leaves. These results suggest, that the electrochemical gradient generated by the H+-ATPase of haustoria plays an important role for their function, possibly by promoting nutrient uptake from host cells.     

Identification of RAPD markers linked to the Uvf-1 gene conferring hypersensitive resistance against rust (<Emphasis Type="Italic">Uromyces viciae-fabae</Emphasis>) in <Emphasis Type="Italic">Vicia faba</Emphasis> L.

Bulk segregant analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to a gene determining hypersensitive resistance in Vicia faba line 2N52 against race 1 of the rust fungus Uromyces viciae-fabae. The monogenic nature of the resistance was determined by analyzing the F(2) population from a cross between resistant line 2N52 and susceptible line VF-176, and further confirmed in the F(2:3)-derived families. Linkage of the RAPD markers was confirmed by screening 55 F(2) plants segregating for resistance. Three RAPD markers (OPD13(736), OPL18(1032) and OPI20(900)) were mapped in coupling phase to the resistance gene for race 1 ( Uvf-1). No recombinants between OPI20(900) and Uvf-1 were detected. Two additional markers (OPP02(1172) and OPR07(930)) were linked to the gene in repulsion phase at a distance of 9.9 and 11.5 cM, respectively. The application of marker-assisted selection to develop new faba bean varieties with rust resistance genes is discussed.     

Secreted proteins of Uromyces fabae: similarities and stage specificity

Uromyces fabae on Vicia faba is a model system for obligate biotrophic interactions. Searching for potential effector proteins we investigated the haustorial secretome of U. fabae (biotrophic stage) and compared it with the secretome of in vitro grown infection structures, which represent the pre-biotrophic stage. Using the yeast signal sequence trap method we identified 62 genes encoding proteins secreted from haustoria and 42 genes encoding proteins secreted from in vitro grown infection structures. Four of these genes were identical in both libraries, giving a total of 100 genes coding for secreted proteins. This finding indicates a strong stage-specific regulation of protein secretion. Similarity with previously identified proteins was found for 39 of the sequences analysed, 28 of which showed similarity to proteins identified among members of the order Uredinales only. This might be taken as an indication for possible roles in virulence and host specificity unique to the Uredinales.     

Molecular and genetic analyses of geographic variation in isolates of Phoma macrostoma used for biological weed control

Molecular and genetic approaches were used to evaluate the genetic relatedness among isolates of the fungus Phoma macrostoma Montagne originating from Canada and Europe and to other species in the genus Phoma. Distinct differences were observed in genetic variation among nine species of the genus Phoma. Randomly amplified polymorphic DNA (RAPD) revealed the presence of intraspecific genetic variation among the isolates of P. macrostoma, with the isolates being used for biological weed control being distributed in a distinct phylogenetic cluster. Additional variation within the biocontrol isolate cluster in P. macrostoma was revealed by pulsed field gel electrophoresis (PFGE), which showed that biocontrol isolates generated two different chromosomal profiles, however the profiles did not relate to their Canadian ecozone origin. Mating studies showed that biocontrol isolates of P. macrostoma from Canada did not produce sexual reproductive structures and were incapable of crossing. These studies also confirmed that no obvious differentiation exists among the biocontrol isolates of P. macrostoma from Canadian Ecozones 3 and 4.     

Global survey of diversity among environmental saltwater Bacteriovoracaceae

Halophilic Bacteriovorax (Bx), formerly known as the marine Bdellovibrio, are Gram-negative, predatory bacteria found in saltwater systems. To assess their genetic diversity and geographical occurrence, the small subunit rRNA (ssu-rRNA) gene sequences were analysed from 111 marine, salt lake and estuarine isolates recovered from 27 locations around the world. Phylogenetic analysis of these isolates using Geobacter as the outgroup revealed eight distinct ribotype clusters each with at least two isolates. Each cluster was composed of isolates with >or= 96.5% similarity in ssu-rRNA sequences. Three single isolate outliers were observed. Many of the Bx ribotypes were widely dispersed among different types of ecosystems (e.g. cluster III was recovered from the Great Salt Lake, the Atlantic Ocean, Pacific Ocean, Chesapeake Bay and gills of aquarium fish). However, cluster V was only recovered from a single ecosystem, estuaries. Cluster V was originally detected in the Chesapeake Bay and subsequently in the Pamlico Sound/Neuse River system. Principal coordinate analysis revealed that the sequences of the isolates from different environments were distinct from each other. The results of this study reveal the saltwater Bx to be phylogenetically and environmentally more diverse than was previously known.     

Characterization of novel bovine gastrointestinal tract Treponema isolates and comparison with bovine digital dermatitis treponemes

This study aimed to isolate and characterize treponemes present in the bovine gastrointestinal (GI) tract and compare them with bovine digital dermatitis (BDD) treponemes. Seven spirochete isolates were obtained from the bovine GI tract, which, on the basis of 16S rRNA gene comparisons, clustered within the genus Treponema as four novel phylotypes. One phylotype was isolated from several different GI tract regions, including the omasum, colon, rumen, and rectum. These four phylotypes could be divided into two phylotype pairs that clustered closest with each other and then with different, previously reported rumen treponemes. The treponemes displayed great genotypic and phenotypic diversity between phylotypes and differed considerably from named treponeme species and those recently reported by metagenomic studies of the bovine GI tract. Phylogenetic inference, based on comparisons of 16S rRNA sequences from only bovine treponemes, suggested a marked divergence between two important groups. The dendrogram formed two major clusters, with one cluster containing GI tract treponemes and the other containing BDD treponemes. This division among the bovine treponemes is likely the result of adaptation to different niches. To further differentiate the bovine GI and BDD strains, we designed a degenerate PCR for a gene encoding a putative virulence factor, tlyC, which gave a positive reaction only for treponemes from the BDD cluster.