Antagonistic and plant growth promoting activities of endophytic and soil actinomycetes

The objective of this study was the isolation and screening of actinomycete isolates for antagonistic potential and plant growth promoting activities. A total of 321 isolates were recovered from different plants, their rhizospheric soils and non-rhizospheric soils of Punjab and Himachal Pradesh regions. Out of these, 62 were endophytic, 156 were rhizospheric and 103 were non-rhizospheric isolates. In primary screening (dual culture assay), 83 isolates antagonised one or more test phytopathogenic fungi. From these active isolates, 20 were found to be antagonistic in well diffusion assay (secondary screening) and most of them demonstrated broad spectrum inhibitory activity against five to six test fungi. Studies on plant growth promoting activities revealed that 12 showed abilities to produce indole acetic acid, 10 produced siderophores and 12 showed ammonia production. Phosphate solubilisation was observed in five isolates and four fixed atmospheric N₂. In addition, production of hydrolytic enzymes such as chitinase, amylase, cellulase and protease was demonstrated by five, twenty, eleven and eleven isolates, respectively. The results of this study indicate that these isolates may be used as biocontrol and plant growth promoting agents. Morphological and chemotaxonomic studies revealed that all the active isolates belonged to the genus Streptomyces     

Molecular characterization of Mycobacterium tuberculosis isolates from Izmir, Turkey

In recent years, molecular typing methods have been used in epidemiologic studies of Mycobacterium tuberculosis isolates in various areas of the world. However, there have been few data on this issue in Turkey. We describe the molecular characterization of 56 Mycobacterium tuberculosis isolates recovered from individual patients in Izmir and the surrounding area by three different molecular methods. Isolated M. tuberculosis strains were characterized by IS6110 RFLP, spoligotyping and major genetic group designation. In total, 51 RFLP and 35 spoligopatterns were identified. Fourteen (25%) isolates were indicated as low copy number. Based on three genotypic characterization methods together, five clusters with two isolates each were identified. Most of the isolates (98.2%) were assigned as genetic groups 2 or 3. Only one isolate was identified as Beijing family strain (principal genetic group 1). The shared international clades were found to be Beijing-family, var T1 (ST 37), LAM (Latin-American-Mediterranean) 7 (ST 41), LAM 9 (ST 42), Haarlem 1 (ST 47), Haarlem 3 (ST 50) and T1 (ST 53). In this study, IS6110 RFLP, spoligotyping and major genetic group designation were found to be useful methods for molecular epidemiologic studies.     

A comparison of Peronospora parasitica (Downy mildew) isolates from Arabidopsis thaliana and Brassica oleracea using amplified fragment length polymorphism and internal transcribed spacer 1 sequence analyses

Amplified fragment length polymorphism (AFLP) fingerprints and internal transcribed spacer 1 (ITS1) sequences from 27 Peronospora parasitica isolates (collected from Arabidopsis thaliana or Brassica oleracea), 5 Albugo candida isolates (from the same hosts and from Capsella bursa-pastoris), and 1 Bremia lactucae isolate (from Lactuca sativa) were compared. The AFLP analysis divided the isolates into five groups that correlated with taxonomic species and, in most cases, with host origin. The only exception was a group consisting of A. candida isolates from both B. oleracea and C. bursa-pastoris. ITS1 sequence analysis divided the isolates into the same five groups, demonstrated the divergence between P. parasitica isolates from A. thaliana and B. oleracea, and, using previously published ITS1 sequences, clearly showed the relationship between A. candida isolates from different hosts.     

Isolation and identification of crude oil-degrading yeast strains from Khafji oil field,saud Arabia

Twenty five yeasts isolated were isolated from Khurais oil field in Saudi Arabia and assayed to evaluate their biodegradability. Only five isolates (namely, A1, A2, A3, A4 and A5) showed potential use of oil as sole carbon source. During incubation period, highest growth rate were recorded for A1, A2 and A3 isolates. Low growth distinguished A4 isolate; A5 isolate could not degrade oil.Spectrophotometrical analysis for four yeast isolates biodegradation activities indicated that, A1 isolate was superior for oil degradation (61%) comparing with A4 isolate which reflected lowest degradation % (33%). A2 and A3 isolates showed moderate biodegradation activity (56 and 51% respectively).D1/D2 domain of the 26S rRNA gene sequence was used as molecular marker to identify five yeast isolates. After comparing 26S rRNA gene sequences of five yeast isolates with highly similarity isolates, five yeast isolates (A1, A2, A3, A4 and A5)were submitted to database as Candida tropicalis (MW488263), Candida tropicalis (MW488264), Rhodotorula mucilaginosa (MW488265) and Rhodosporidium toruloides (MW488266) respectively. Using OXF1/ACR1 primer, specific lipase gene amplicon with 250 bp were detected with in all four yeast isolates.     

Advantage of using PSIRB over PSRB and IRB to improve plant health of tomato

Twenty-one isolates of phosphate solubilizing-indole acetic acid producing rhizobacteria (PSIRB), 20 isolates of phosphate solubilizing rhizobacteria (PSRB) and 42 isolates of indole acetic acid producing rhizobacteria (IRB) were isolated from 49 rhizospheric soil samples of tomato (Lycopersicon esculentum Mill.) collected from tomato growing regions of Karnataka. A method combining Pikovskaya’s and Bric’s technique was developed to isolate PSRIB, PSRB and IRB’s. The selected isolates were further analyzed for their ability to solubilize calcium phytate. Based on the root colonization assays and the abilities of bacterial isolates to increase the seed germination and seedling vigor under laboratory conditions, five isolates were selected from each group for further studies. Under greenhouse conditions, all the selected rhizobacteria isolates significantly increased root length, shoot length, fresh weight, dry weight and total phosphorus content of 30-day-old-seedlings with respect to control. Isolate PSIRB1 and IRB36 significantly reduced the Fusarium wilt incidence over other isolates of same and other group, and the control. On the basis of results from laboratory and greenhouse studies, one bacterial isolate from each group was selected for plant growth and yield analysis studies. Isolate PSIRB2 showed increased plant height, fresh weight, number of fruits per plant and average weight of fruit over PSRB9, IRB36 and untreated controls. Studies on the nature of protection offered by these bacterial isolates following split-root technique revealed that the isolates PSIRB2 and PSRB9 had the ability to induce systemic resistance. One isolate, IRB36 appeared to protect the tomato seedlings through direct antagonism.     

Salicylates and reversible hearing loss

Skin and soft tissue infections were studied in 21 seriously ill narcotic addicts who had been admitted to hospital. Subcutaneous abscesses were present in 14 patients; cellulitis was noted in 3, pyomyositis in 2 and necrotizing fasciitis in 2. In four patients there was septicemia. Infections in 14 patients (66.6 percent) were associated with anaerobic bacteria, which were the exclusive isolates in 6 patients. In seven patients (33.3 percent) isolates were exclusively aerobic bacteria and in eight both aerobes and anaerobes were present. The anaerobic isolates were clostridia (six), peptostreptococci (five), bacteroides (five), peptococci (three), and one of each of Veillonella, Propionibacterium, Eubacterium, Fusobacterium and Actinomyces. Staphylococcus aureus, generally thought to be the most common cause of subcutaneous infections in addicts, was found only in four (19 percent) patients. The other aerobic isolates were Klebsiella (five) and Enterobacter (four) species. When clinical features or the Gram stain of pus suggest that anaerobic bacteria may be present, antibiotic therapy should be directed against both aerobic and anaerobic bacteria until culture results are available.     

Pulsed-field gel electrophoresis for sub-specific differentiation of Serpulina pilosicoli (formerly 'Anguillina coli')

Abstract Pulsed-field gel electrophoresis (PFGE) was developed for subspecific differentiation of Serpulina pilosicoli , and was applied to 52 isolates recovered from cases of intestinal spirochaetosis (IS) in pigs, dogs, human beings and various avian species. The technique was highly sensitive, differentiating the isolates into 40 groupings. Only six groups contained more than one isolate; in five of these groups isolates with the same banding pattern were either from pigs in the same herds (four groups), or from humans in the same community: the sixth group contained two identical Australian porcine isolates from unrelated herds in different states. Overall S. pilosicoli isolates were genetically diverse, but in some cases isolates cultured from the same or different animal species were closely related. This suggested the likelihood of cross-species transmission, including zoonotic spread. PFGE was a powerful tool for epidemiological studies of S. pilosicoli and also allowed examination of genetic relationships between isolates.     

Multiple gene genealogies and species recognition in the ectomycorrhizal fungus Paxillus involutus

Paxillus involutus (basidiomycetes, Boletales) is a common ectomycorrhizal fungus in the Northern Hemisphere. The fungus displays significant variation in phenotypic characters related to morphology, physiology, and ecology. Previous studies have shown that P. involutus contains several intersterility groups and morphological species. In this study, we have used concordance of multiple gene genealogies to identify genetically isolated species of P. involutus. Fragments from five protein coding genes in 50 isolates of P. involutus collected from different hosts and environments in Europe and one location in Canada were analysed using phylogenetic methods. Concordance of the five gene genealogies showed that P. involutus comprises at least four distinct phylogenetic lineages: phylogenetic species I (with nine isolates), II (33 isolates), III (three isolates), and IV (five isolates). The branches separating the four species were long and well supported compared with the species internodes. A low level of shared polymorphisms was observed among the four lineages indicating a long time since the genetic isolation began. Three of the phylospecies corresponded to earlier identified morphological species: I to P. obscurosporus, II to P. involutus s. str., and III to P. validus. The phylogenetic species had an overlapping geographical distribution. Species I and II differed partly in habitat and host preferences.     

The effect of inbreeding on aggregation of complex diseases in genetic isolates

We have studied the effect of genetic processes in ethnically and demographically diverse isolates on the epidemiology of complex diseases. Our long-term studies of five indigenous Dagestan ethnic groups have revealed ten genetic isolates with aggregation of schizophrenia-related diseases. According to Neel’s classification (1992), these isolates belong to primary and secondary depending on the duration of demographic process. We have found that the average demographic ages of the examined primary and secondary isolates were about 4000 and 700 years, respectively. The inbreeding level F was studied using two methods: analysis of marriage structure in three generations, which is traditional in population-genetic studies, and analysis of the same structure in extensive pedigrees (up to 11–13 generations). We have shown that with the second method, the F value increases two- to threefold in various isolates. The accumulated inbreeding in the primary isolates proved to be twofold higher than that in the secondary ones. Primary isolates have revealed relatively higher genetic and clinical homogeneity in combination with higher aggregation of population-specific complex disease pathology compared to secondary isolates. A decrease in observed recombinations and the number of genomic loci linked with the disease in primary isolates have been also demonstrated. Thus, our studies showed that complex diseases can be less expensive and mapping of genes for time-consuming if conducted in primary rather than in secondary isolates, in particular when dealing with genetically heterogeneous outbred human populations.     

Efficacy of flagellin gene typing for epidemiological studies of Campylobacter jejuni in poultry estimated by comparison with macrorestriction profiling

Thirty isolates of Campylobacter jejuni isolated from 29 different Danish broiler flocks were chosen for the evaluation of PCR-Fla typing as a genotyping tool. Except for two isolates that originated from the same broiler flock, the isolates were clearly distinguishable on basis of their macrorestriction profiles using the restriction endonucleases SmaI and KpnI. PCR-Fla typing of the 30 isolates yielded 16 distinct genotypes, whereas one isolate was untypeable by this method. The dominant PCR-Fla type (1/1) was shared by eight isolates, and five additional Fla groups containing two or three isolates were obtained. The PCR-Fla type of one isolate changed spontaneously after five subcultures, illustrating the relative plasticity of the gene locus. Comparison of MRPs within and between Fla-types support the view that some PCR-Fla types may be conserved within clonal lines. It is concluded that PCR-Fla typing is useful as a genotyping tool in large-scale epidemiological studies but that additional analyses with other methods are required to properly define interstrain relationships.     

Selection and characterization of feather-degrading bacteria from canola meal compost

Canola meal that contains a high level of protein (40% crude protein) was used as compost material for the isolation of feather-degrading bacteria. After 7 and 14 days, bacteria were isolated from compost amended and unamended with soil. Eighty bacterial isolates from canola meal compost were then grown on milk-agar and isolates that produced proteolytic enzymes were identified by the formation of clear haloes around the colonies. A feather medium was chosen for a secondary selection of feather-degrading isolates. Of the eight isolates that hydrolyzed milk protein, five isolates hydrolyzed feathers. Their keratinolytic activities were subsequently confirmed by an assay using azo-keratin as substrate. Seven of the eight bacteria that hydrolyzed milk protein were Bacillus spp, and all five isolates that hydrolyzed feathers were strains of Bacillus licheniformis. Protease inhibition studies indicated that serine proteases are the predominant proteolytic enzymes produced by these feather-degrading isolates. Received 02 April 1999/ Accepted in revised form 17 June 1999     

Determination of the most closely related bacillus isolates to Bacillus anthracis by multilocus sequence typing

There have been many efforts to develop Bacillus anthracis detection assays, but the problem of false-positive results has often been encountered. Therefore, to validate an assay for B. anthracis detection, it is critical to examine its specificity with the most closely related Bacillus isolates that are available. To define the most closely related Bacillus isolates to B. anthracis in our Bacillus collections, we analyzed by multilocus sequence typing (MLST) the phylogeny of 77 closely related Bacillus isolates selected from 264 Bacillus isolates. The selection includes all the Bacillus isolates that have been shown in our previous studies to produce false-positive results by some anthrax-detection assays. The MLST phylogenetic analyses revealed that 27 of the non-B. anthracis isolates clustered within the B. anthracis clade, and four of them (three sequence types, STs) had the highest degree of genetic relatedness with B. anthracis, 18 (11 STs) had the second highest, and five (five STs) had the third highest. We anticipate that the inclusion of the 19 ST isolates when analyzing B. anthracis detection assays will prove to be useful for screening for their specificity to detect B. anthracis.     

Occurrence of Bacillus sporothermodurans and other aerobic spore-forming species in feed concentrate for dairy cattle

AIMS: To determine the aerobic spore composition and presence of Bacillus sporothermodurans spores in feed concentrate for dairy cattle. METHODS AND RESULTS: Six feed concentrate samples from five different farms were analysed. High levels of spores (up to 10(6) spores g(-1)) were found. Identification of 100 selected isolates was obtained by a combination of fatty acid methyl esters analysis, amplified ribosomal DNA restriction analysis and 16S rDNA sequencing. Ninety-seven isolates could be identified to the species level or assigned to a phylogenetic species group. Most of the isolates obtained after a heat treatment of 10 min at 80 degrees C were identified as members of the B. subtilis group (32 isolates), B. pumilus (25 isolates), B. clausii (eight isolates) and B. licheniformis (eight isolates). The isolates with very heat-resistant spores, obtained after a heat treatment of 30 min at 100 degrees C, were identified as members of the B. subtilis group (five isolates), B. sporothermodurans (three isolates), B. amyloliquefaciens (one isolate), B. oleronius (one isolate) and B. pallidus (one isolate). Bacillus cereus was present in each feed concentrate sample and was isolated using a selective mannitol egg yolk polymyxin agar medium. CONCLUSIONS: Feed concentrate for dairy cattle contains known as well as as yet unknown species of Bacillus and related genera with properties relevant to the dairy sector. SIGNIFICANCE AND IMPACT OF THE STUDY: The results formulate the hypothesis that feed concentrate can be a contamination source of spores, including those of B. sporothermodurans, for raw milk at the farm level.     

RAPD (arbitrary primer) PCR is more sensitive than multilocus enzyme electrophoresis for distinguishing related bacterial strains.

The RAPD (random amplified polymorphic DNA) fingerprinting method, which utilizes low stringency PCR amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments, was calibrated relative to the widely used, protein-based multilocus enzyme electrophoretic (MLEE) typing method. RAPD fingerprinting was carried out on five isolates from each of 15 major groups of Escherichia coli strains that cause diarrheal disease worldwide (75 isolates in all). Each group consisted of isolates that were not distinguishable from one another by MLEE typing using 20 diagnostic enzyme markers. In our RAPD tests, three or more distinct subgroups in each MLEE group were distinguished with each of five primers, and 74 of the 75 isolates were distinguished when data obtained with five primers were combined. Thus, RAPD typing is far more sensitive than MLEE typing for discriminating among related strains of a species. Despite their different sensitivities, the same general relationships among strains were inferred from MLEE and RAPD data. Thus, our results recommend use of the RAPD method for studies of bacterial population genetic structure and evolution, as well as for epidemiology.     

中国耐多药结核分枝杆菌临床分离株rpoB基因突变特点

为阐明中国耐多药结核分枝杆菌临床分离株rpoB基因的突变特征,对86株结核分枝杆菌临床分离株rpoB基因两个区域,包括81个碱基利福平抗药性决定区(rifampin resistance determining region,RRDR)和V176F区进行序列测定。其中72株耐多药分离株中的65株rpoB基因的RRDR区存在22种不同类型突变、21种点突变和一个插入突变。最常见的突变部位分别位于密码子531(41％)、526(40％)和516(4％),10％耐药分离株未检测到突变。鉴定了RRDR内6个新的等位基因,以及RRDR外部区域5个新的突变。所有分离菌株V176均无突变。     

Allelic polymorphism of the tem(M) determinant in Mycoplasma hominis and Ureaplasma urealyticum clinical isolates resistant to tetracyclines

Of the 130 clinical isolates of Mycoplasma hominis from patients with nonspecific inflammatory diseases of the urogenital tract (UGT), approximately 10% contained the tet(M) gene after the course of treatment with tetracyclines. This gene was found in nine (25%) of the 36 Ureaplasma urealyticum clinical isolates. The nucleotide sequence of 13 tet(M) genes in TcR clinical isolates of M. hominis and five genes in U. urealyticum TcR clinical isolates was determined. A comparison of nucleotide sequences of eight tetM genes of different origin and tet(M) genes of Gardnerella vaginalis and M. hominis and U. urealyticum clinical isolates showed that the mosaic structure of the tet(M) gene is completely identical in 11 of 13 M. hominis TcR isolates but belongs to an unidentified allele different from those described earlier, Another new allelic variant of tet(M) was found in two isolates. In three of five TcR clinical isolates of U. urealyticum, a tet(M) gene, whose mosaic structure was identical to that of tet(M) reported previously for ureaplasmas, and also two new allelic variants, which have not been described so far, were found.     

Distribution of chymoelastases and trypsin-like enzymes in five species of entomopathogenic deuteromycetes

Nine isolates of the entomopathogenic deuteromycetes Metarhizium anisopliae, Beauveria bassiana, Verticillium lecanii, Nomuraea rileyi, and Aschersonia aleyrodis produced basic (pI greater than 7.0) chymoelastases that possessed extended binding sites, comprising at least four or five subsites, with preference for hydrophobic residues at the primary binding site. Most isolates also produced additional acidic enzymes with similar specificities against ester and amide substrates but which lacked activity against elastin. Both acidic and basic enzymes degraded high protein azure or locust cuticle and, as shown by inhibition studies, possessed essential serine and histidine residues in the active site. In spite of similarities in catalytic properties antibodies generated against a Metarhizium chymoelastase cross-reacted only with enzymes from two (out of four) Metarhizium isolates; enzymes from all other isolates did not cross-react. Two isolates of Metarhizium produced a third class of protease which degraded Bz-AA-AA-Arg-NA substrates (AA, various amino acids) and hide protein azure. Analogous peptidases were produced by other isolates but they were specific for Bz-Phe-Val-Arg-NA and showed less sensitivity to trypsin inhibitors. The possible significance to pathology of the presence of diverse yet similar protease forms in five genera of entomopathogens is discussed.     

Characterisation,genetic diversity and antagonistic potential of 2,4-diacetylphloroglucinol producing Pseudomonas fluorescens isolates in groundnut-based cropping systems of Andhra Pradesh,India

This study is focused on isolation and characterisation of 2,4-diacetylphloroglucinol (2,4-DAPG)-producing Pseudomonas fluorescens isolates from different soils of groundnut-based cropping systems in Andhra Pradesh. In our studies, 21 isolates of P. fluorescens were isolated and confirmed through various biochemical tests, of which five were tested positive for 2,4-DAPGproduction with specific primers. Biocontrol potential of these isolates on groundnut stem rot pathogen (Sclerotium rolfsii) was determined through in vitro dual culture assays. The eight isolates were found effective against S. rolfsii (up to 75% inhibition) in dual culture method. All the five 2,4-DAPG-producing Plant Growth-Promoting Rhizobacteria isolates were highly antagonistic to S. rolfsii. Genetic diversity of these P. fluorescens isolates was determined by random amplification of polymorphic DNA analysis. Overall, our results suggest that the prevalence of 2,4-DAPG-producing fluorescent Pseudomonads in different crop rhizospheres of groundnut-based cropping systems.     

Isozyme Analysis and Soluble Mycelial Protein Pattern in Iranian Isolates of Several formae speciales of Fusarium oxysporum

A total of 13 representative isolates of Fusarium oxysporum f. sp. melonis (FOM) from Iran, USA and France, eight isolates of seven formae speciales from Iran and one isolate of F. oxysporum f. sp. niveum from the USA were compared based on isozyme analysis and soluble mycelial protein pattern. Isozyme analyses of alkaline phosphatase (ALP), catalase (CAT), esterase (EST), malate dehydrogenase (MDH), superoxide dismutase (SOD) and xanthine dehydrogenase (XDH) revealed polymorphism among the F. oxysporum isolates in which 22 electrophoretic phenotypes (EP) were determined. At least 10 putative loci for these six enzymes were detected and they were all polymorphic. Maximum genetic diversity was observed in CAT, EST and XDH loci. Using UPGMA, the 22 isolates were separated into three main groups with one of the groups divided into two subgroups. Group I included isolates belonging to five formae speciales from Iran, whereas group II that included FOM isolates from both Iran and the USA was divided into two subgroups each containing the vast majority of the respective isolates from either country. Group III constituted FOM isolates from France and one pathogenic isolate on pepper from Iran. FOM isolates representing five different geographical regions from Iran belonged to two different races of 1 and 1,2Y and one vegetative compatibility group (VCG)0134 and thus were genetically homologous. Isozyme polymorphism in these isolates was highly correlated with VCG and geographical origins and to a lesser extent with races. Variations in soluble protein profile in FOM isolates were correlated with genetic distances determined in isozyme analysis. This study suggests that isozyme analysis could be a useful tool for identifying genetic diversity not only in FOM but also several formae speciales of F. oxysporum.