Biochemical Characterization and Phylogenetic Analysis Based on 16S rRNA Sequences for V-Factor Dependent Members of <Emphasis Type="Italic">Pasteurellaceae</Emphasis> Derived from Laboratory Rats

Phylogenetic analysis based on 16S rRNA sequences with sequence data of some bacterial species of Pasteurellaceae related to rodents deposited in GenBank was performed along with biochemical characterization for the 20 strains of V-factor dependent members of Pasteurellaceae derived from laboratory rats to obtain basic information and to investigate the taxonomic positions. The results of biochemical tests for all strains were identical except for three tests, the ornithine decarboxylase test, and fermentation tests of D(+) mannose and D(+) xylose. The biochemical properties of 8 of 20 strains that showed negative results for the fermentation test of D(+) xylose agreed with those of Haemophilus parainfluenzae complex. By phylogenetic analysis, the strains were divided into two clusters that agreed with the results of the fermentation test of xylose (group I: negative reaction for xylose, group II: positive reaction for xylose). The clusters were independent of other bacterial species of Pasteurellaceae tested. The sequences of the strains in group I showed 99.7–99.8% similarity and the strains in group II showed 99.3–99.7% similarity. None of the strains in group I had a close relation with Haemophilus parainfluenzae by phylogenetic analysis, although they showed the same biochemical properties. In conclusion, the strains had characteristic biochemical properties and formed two independent groups within the “rodent cluster” of Pasteurellaceae that differed in the results of the fermentation test of xylose. Therefore, they seemed to be hitherto undescribed taxa in Pasteurellaceae.     

Numerical taxonomy of psychrotrophic lactic acid bacteria from prepacked meat and meat products

Ninety-four strains of lactic acid bateria isolated from refrigerated, prepacked meat and meat products were together with 59 reference strains of Brochothrix, Lactobacillus, Leuconostoc, Pediococcus and Streptococcus phenotypically classfied, using 96 unit characters. Data were examined using Simple Matching (S_SM) or Jaccard coefficient (S_J), and unweighted pair group algorithm with arithmetic averages. Twenty-three clusters with two or more members were defined at the 84% S_SM-similarity level which corresponded to the S_J-similarity level of 61%. Based on S_SM, most field strains were included in nine clusters, and with three unsignificant exceptions these contained no reference strains. The field clusters were designated Carnobacterium piscicola (cluster 1; 5% of field isolates), Carnobacterium divergens(cluster 2; 9% of field isolates), Leuconostoc (cluster 9; 18% of field isolates) and Lactobacillus (cluster 4, 10, 11, 12, 13 and 14; together 60% of field isolates). The Lactobacillus clusters had many features in common with cluster II of Shaw & Harding (1984). Phenotypical characteristics of major clusters are given. The S_SM and S_J based classifications basically coincided for the field strains; the exception was cluster 4 which now were split in two parts. Fourteen clusters were made up of mainly reference strains (S_SM). Most of them included more than one type strain on species level; exceptions were Brochothrix thermosphacta (cluster 3), Lactobacillus salivarius (cluster 17) and Leuconostoc mesenteroides (cluster 18). Several rearrangements were seen amongst the clusters of the reference strains when S_J, instead of S_SM, was used for clustering.     

REMARKABLE CONSERVATION OF INTERNALLY TRANSCRIBED SPACER SEQUENCES OF ARTHROSPIRA (“SPIRULINA” ) (CYANOPHYCEAE,CYANOBACTERIA) STRAINS FROM FOUR CONTINENTS AND OF RECENT AND 30‐YEAR‐OLD DRIED SAMPLES FROM AFRICA1

The internally transcribed spacer (ITS) sequences of 21 Arthrospira clonal strains from four continents and assigned to four different species (A. platensis, A. maxima, A. fusiformis, A. indica) in the culture collections were determined. Two main clusters, I and II, were differentiated by 49 positions out of 475 nt or 477 nt, respectively. Each cluster was further subdivided into two subclusters. Subclusters I.A and I.B were separated by two substitutions, whereas subclusters II.A and II.B were distinguished by four substitutions. After direct sequencing of the PCR products, three dried samples from Chad aged between 3 months and 35 years yielded a sequence belonging to subcluster I.A, as did a recent commercial product. The strains grown in production plants belonged to the same (sub)clusters as strains from culture collections, mainly I.A and II. PCR primers specific for each cluster and subcluster were designed and tested with crude cell lysates of Arthrospira strains. One dried sample (“dihé” 1) and a herbarium sample from Lake Sonachi (Kenya) only contained I.A sequences, whereas the commercial product was a mixture of the four genotypes and the other two dried samples contained minor polymorphisms characteristic of different clusters. Five clonal Arthrospira strains, thought to be duplicates, showed the simultaneous presence of the two forms of the four diagnostic positions that distinguish subclusters genotype II.A and genotype II.B. This is likely to be caused by multiple copies of the rDNA operon, in a intermediate stage of homogenization between subcluster II.A and subcluster II.B. The high conservation of ITS sequences is in contrast with the assignment to four different species, the great morphological variability of the strains, and their wide geographic distribution.     

GENETIC STRUCTURE AND DIVERSITY WITHIN LOCAL POPULATIONS OF BACILLUS MYCOIDES

Sixty strains of Bacillus mycoides were isolated from each of two sites and characterized by their responses to standard metabolic tests used in bacterial taxonomy, by multilocus enzyme electrophoresis (MLEE), and by restriction-fragment-length polymorphism (RFLP) analysis of Southern blots probed with both a conserved DNA fragment derived from a Salmonella typhimurium ribosomal cistron and with two cosmid probes derived from B. mycoides ATCC strain 6463. Both MLEE and RFLP analyses indicated that the collection contained two genetically distinct sets of strains (I and II); one of these sets was further differentiated genetically by the same analyses (IIA and IIB). Standard taxonomic analysis did not distinguish these sets of strains; biochemical test profiles were similar for all isolates. The genetic distance between groups I and II is as great as that observed for recognized species of bacteria. It is proposed that these groups are sibling species having a common evolutionary descent and that their metabolic phenotype has been conserved, whereas their DNA and protein sequences have diverged. No strong evidence of geographic differentiation between strains from the two sites appeared in either genetic or phenetic characters.     

Carbon and Sulfur Metabolism in Representatives of Two Clusters of Bacteria of the Genus Leucothrix: A Comparative Study

Major pathways of carbon and sulfur metabolisms were studied in representatives of two clusters of bacteria: Leucothrix thiophila (cluster I, strains 2WS, 4WS, and 6WS) and Leucothrix sp. (cluster II, strains 1WS, 3WS, and 5WS). All strains were capable of chemoorganoheterotrophic growth, as well as of chemolithoheterotrophic growth in the presence of reduced sulfur compounds. The bacteria were found to possess a complete set of the enzymes of the tricarboxylic acid cycle and glyoxylate cycle. The dehydrogenase activity in cells of cluster I strains was an order of magnitude lower than in cluster II strains and in other known heterotrophic bacteria. Cells of bacteria of both clusters exhibited high activity levels of enzymes involved in the energy metabolism of sulfur. The oxidation of sulfur compounds and the operation of the electron-transport chain were shown to be related. Cluster II bacteria more efficiently use organic compounds in their energy metabolism, whereas cluster I bacteria are characterized by more efficient utilization of reduced sulfur compounds. During sulfite oxidation, cluster I bacteria can synthesize ATP both via substrate-level phosphorylation and oxidative phosphorylation, whereas cluster II bacteria synthesize ATP only via the latter process.     

Genetic diversity of root-nodulating bacteria isolated from pea (<Emphasis Type="Italic">Pisum sativum</Emphasis>) in subtropical regions of China

Diversity of 42 isolates from effective nodules of Pisum sativum in different geographical regions of China were studied using 16S rRNA gene RFLP patterns, 16S rRNA sequencing, 16S–23S rRNA intergenic spacer (IGS) region RFLP patterns and G-C rich random amplified polymorphic DNA (RAPD). The isolates were distributed in two groups on the basis of their 16S rRNA gene RFLP patterns. The 16S rRNA gene sequences of strains from 16S rRNA gene RFLP patterns group I were very closely related (identities higher than 99.5%) to Rhizobium leguminosarum USDA 2370. Group II consisting of WzP3 and WzP15 was closely related to Rhizobium etli CFN42. The analysis of the 16S-23S IGS RFLP patterns divided the isolates into 18 genotypes and four groups. Group I was clustered with R. leguminosarum USDA2370. Group II consisted of YcP2, YcP3 and CqP7. The strains of group III were distributed abroad. Group IV consisted of WzP3, WzP15 and R. etli CFN42. RAPD divided the isolates into nine clusters in which group IV only consisted of YcP2 and the strains of group V and IX were from Wenzhou and Xiantao, respectively. This assay demonstrated the geographical effect on genetic diversity of pea rhizobia.     

Comparison of Three Methods for Epidemiological Typing of <Emphasis Type="Italic">Campylobacter jejuni</Emphasis> and <Emphasis Type="Italic">C. coli</Emphasis>

A total of 168 Campylobacter strains (154 C. jejuni and 14 C. coli) isolated from human clinical samples and chicken meat were typed using Penner serotyping, randomly amplified polymorphic DNA (RAPD), and pulsed-field gel electrophoresis (PFGE) with four restriction enzymes (Sac II, Sal I, Sma I, Kpn I).The 168 strains were found to represent 13 different Penner-types and 72 different RAPD-types. However, the discriminatory potential of PFGE was dependent on the restriction enzymes used. The 168 strains were divided into 74 (Sac II), 73 (Sal I), 72 (Sma I) and 69 (Kpn I) types. The DNA of some strains was not digested by Sal I, Sma I and Kpn I. Although three RAPD-types were further subdivided by PFGE, RAPD showed good discriminatory power and a high level of agreement with PFGE patterns in terms of strain differentiation.To compare the similarities of PFGE patterns (Sac II) among the strains, a dendrogram was constructed based on the unweighted pair group method with averages (UPGMA). In most cases, DNA types of C. coli were different from those of C. jejuni. The similarities between human and meat isolates were less than 0.42 except for one outbreak in which the isolates from both patients and chicken meat showed the same DNA types.     

The human carbonic anhydrase isoenzymes I and II inhibitory effects of some hydroperoxides,alcohols, and acetates

The carbonic anhydrases (CAs, EC 4.2.1.1) represent a superfamily of widespread enzymes, which catalyze a crucial biochemical reaction, the reversible hydration of carbon dioxide to bicarbonate and protons. Human CA isoenzymes I and II (hCA I and hCA II) are ubiquitous cytosolic isoforms. In this study, a series of hydroperoxides, alcohols, and acetates were tested for the inhibition of the cytosolic hCA I and II isoenzymes. These compounds inhibited both hCA isozymes in the low nanomolar ranges. These compounds were good hCA I inhibitors (K_is in the range of 24.93–97.99?nM) and hCA II inhibitors (K_is in the range of 26.04–68.56?nM) compared to acetazolamide as CA inhibitor (K_i: 34.50?nM for hCA I and K_i: 28.93?nM for hCA II).     

Multilocus microsatellite typing shows three different genetic clusters of Leishmania major in Iran

Ten polymorphic microsatellite markers were used to analyse 25 strains of Leishmania major collected from cutaneous leishmaniasis cases in different endemic areas in Iran. Nine of the markers were polymorphic, revealing 21 different genotypes. The data displayed significant microsatellite polymorphism with rare allelic heterozygosity. Bayesian statistic and distance based analyses identified three genetic clusters among the 25 strains analysed. Cluster I represented mainly strains isolated in the west and south-west of Iran, with the exception of four strains originating from central Iran. Cluster II comprised strains from the central part of Iran, and cluster III included only strains from north Iran. The geographical distribution of L. major in Iran was supported by comparing the microsatellite profiles of the 25 Iranian strains to those of 105 strains collected in 19 Asian and African countries. The Iranian clusters I and II were separated from three previously described populations comprising strains from Africa, the Middle East and Central Asia whereas cluster III grouped together with the Central Asian population. The considerable genetic variability of L. major might be related to the existence of different populations of Phlebotomus papatasi and/or to differences in reservoir host abundance in different parts of Iran.     

Proteomic Adaptation of Australian Epidemic Bordetella pertussis

Bordetella pertussis causes whooping cough. The predominant strains in Australia changed to single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele ptxP3/pertactin gene allele prn2) from cluster II (non‐ptxP3/non‐prn2). Cluster I was mostly responsible for the 2008–2012 Australian epidemic and was found to have higher fitness compared to cluster II using an in vivo mouse competition assay, regardless of host's immunization status. This study aimed to identify proteomic differences that explain higher fitness in cluster I using isobaric tags for relative and absolute quantification (iTRAQ), and high‐resolution multiple reaction monitoring (MRM‐hr). A few key differences in the whole cell and secretome were identified between the cluster I and II strains tested. In the whole cell, nine proteins were upregulated (>1.2 fold change, q < 0.05) and three were downregulated (<0.8 fold change, q < 0.05) in cluster I. One downregulated protein was BP1569, a TLR2 agonist for Th1 immunity. In the secretome, 12 proteins were upregulated and 1 was downregulated which was Bsp22, a type III secretion system (T3SS) protein. Furthermore, there was a trend of downregulation in three T3SS effectors and other virulence factors. Three proteins were upregulated in both whole cell and supernatant: BP0200, molybdate ABC transporter (ModB), and tracheal colonization factor A (TcfA). Important expression differences in lipoprotein, T3SS, and transport proteins between the cluster I and II strains were identified. These differences may affect immune evasion, virulence and metabolism, and play a role in increased fitness of cluster I.     

Statistical analysis of the envelope gene and the prM region of Japanese encephalitis virus: Evidence suggestive of positive selection

The variation in nucleotide sequence observed in the envelope (E) gene and the prM (precursor of M protein) region of different strains of Japanese encephalitis virus (JEV) was analysed. Presence of selective forces acting on these regions was investigated by computing the relative rates of synonymous (K _s) and nonsynonymous (K _a) substitutions. The ratioK _s/K _a was used as an indicator of the overall selective constraints on the amino acid sequence of JEV proteins. The possibility that different regions of the gene may be subject to varying selective pressures was tested by dividing the gene into three regions and estimating theK _s/K _a ratio for each region. On the basis of analysis of a limited number (17) of strains of JEV, evidence suggestive of positive selection acting on certain regions of the E gene of the virus, and in some cases on the entire gene, was obtained. Analysis ofK _a diversity in the prM region of 46 JEV strains grouped into three genotypes revealed that strains included in genotype II were more heterogeneous than strains belonging to genotype I, while the differences between meanK _a values for genotypes I and III and genotypes II and III were not statistically significant. Analysis of host-specific heterogeneity in the prM region revealed that pig isolates were more X_a-diverse than human isolates.     

Production of Fumonisins by Fusarium moniliforme Strains Isolated from Corn Grain

Fusarium moniliforme is the predominant fusarium species in the grain mycoflora of corn grown in the northern Caucasus, accounting for 95% of fusarium isolates. Eighty-five Fusarium moniliforme strains were grown on a grain substrate and checked for the presence of fumonisins (B₁ + B₂ + B₃) by indirect solid-phase enzyme immunoassay. All strains were capable of producing fumonisins (0.95 to 32 500 mg/kg). Strains sampled in Krasnodar krai produced the highest fumonisin levels (averaging 5490 mg/kg). Fusarium moniliforme strains were subdivided into three morphological types. The types differed significantly in the rate of fumonisin production. Strains belonging to the mycelial type (I) produced the greatest amount of the toxin, and those of the pionnotal type (III) were the least active. Strains of the sporodochial type (II) had an intermediate activity. The mean levels of fumonisin accumulation (mg per kg) for each type were I, 7460; II, 1150; and III, 227.     

New variants of polar glycopeptidolipids detected in Mycobacterium simiae, including 'habana' strains, as evidenced by electrospray ionization-ion trap-mass spectrometry

Aims: To determine the composition of polar glycopeptidolipids (pGPLs) of Mycobacterium simiae and, particularly, those of ‘habana’ strains, in a search for specific markers given the immunogenic potential of ‘habana’ TMC 5135 in experimental tuberculosis. Methods and Results: pGPLs were determined in free lipid extracts using electrospray ionization‐ion trap‐mass spectrometry (ESI‐IT‐MS), working in both negative‐ and positive‐ion mode. In the case of TMC 5135, the presence of the previously characterized GPL‐II (containing 2,4‐di‐O‐CH₃ glucuronic acid as distal sugar in the oligosaccharide antigenic moiety) and GPL‐III (containing 4‐O‐CH₃ glucuronic acid as distal sugar) was confirmed using MS/MS and MS/MS/MS approaches. Interestingly, some ‘habana’ strains presented variants of GPL‐II, designated GPL‐II′‐A and GPL‐II′‐B. A di‐O‐CH₃‐deoxy‐hexose (tentatively, 2,3‐di‐O‐CH₃‐fucose) was identified as the penultimate sugar in the oligosaccharide moiety of GPL‐II′‐A, whereas in GPL‐II′‐B the penultimate sugar was fucose (tentative identification). On the contrary, the distal sugar of the oligosaccharide chain of pGPLs of Myco. simiae ATCC 25275^T was identified as tri‐O‐CH₃‐glucuronic acid (designated GPL‐sim^T‐I, with two variants: GPL‐sim^T‐I‐A and GPL‐sim^T‐I‐B), O‐CH₃‐glucuronic acid (designated GPL‐sim^T‐II) and di‐O‐CH₃‐glucuronic acid (GPL‐II′‐A and GPL‐II′‐B). The penultimate sugar of the oligosaccharide chain of GPL‐sim^T‐I‐A and GPL‐sim^T‐II was identified as di‐O‐CH₃‐deoxy‐hexose (tentatively, 2,3‐di‐O‐CH₃ fucose), and that of GPL‐sim^T‐I‐B as deoxy‐hexose (tentatively, fucose). In all strains studied, each [M‐H]^? and [M+Na]⁺ ion was revealed as a mixture of homologous compounds varying in the number of –O‐CH₃ groups present in the oligosaccharide moiety and in the length of the fatty acyl linked to the peptide. Conclusions: The present work indicates that, within a similar general pattern of pGPLs, different strains of Myco. simiae present some variations, so that new compounds (GPL‐II′‐A, GPL‐II′‐B, GPL‐sim^T‐I‐A, GPL‐sim^T‐I‐B and GPL‐sim^T‐II) were defined. Noteworthy was the fact that the ‘habana’ strains clearly differed from the type strain of Myco. simiae. Significance and Impact of the Study: The data obtained can be used in the delineation of the ‘habana’ group of Myco. simiae, including the quality control of the immunogenic strain ‘habana’ TMC 5135.     

Characterization of microbial traits associated with glyphosate biodegradation in industrial activated sludge

Summary The microorganisms from two industrial (I1, I2) activated sludges that treat glyphosate (N-phosphonomethyl glycine) wastes and one domestic (D1) sludge were enumerated by microscopic examination and by the use of eight selective media. I1 and I2 had higher total counts but fewer pseudomonads and no yeasts. The enumerations correlated directly with traditional biological performance measurements. A total of 393 microbial strains were isolated from the sludges to correlate the occurrence and relationship of glyphosate-degrading activity (GDA) to 155 biochemical and morphological characteristics. Each activated sludge contained unique bacterial populations with the microbes treating industrial wastes, capable of utilizing a wide range of carbohydrates. Numerical taxonomy (arithmetic average linkage) using simple matching and Jaccard coefficients confirmed that there were five (D1), three (I1), and 12 (I2) clusters. GDA was found in only a small portion of the industrial clusters and did not correlate with any other characteristic tested, even though the GDA strains had a large phenotypic diversity. This suggests that GDA is not a universal trait and its expression requires enrichment through specific selective pressures.     

Identification of lactic acid bacteria isolated from human vaginal secretions

A total of 57 lactic acid bacteria were isolated from the vaginal secretions of 259 patients. Of these strains, 37 were isolated from patients attending pre-natal clinics and the remaining strains from patients attending post-natal clinics. The strains were identified by using simple physiological and biochemical tests and their phenotypic relatedness determined by numerical analysis of total soluble cell protein patterns. The genotypic relatedness of representative strains selected from each of the protein profile clusters was determined by numerical analysis of the DNA banding patterns obtained from RAPD-PCR. The majority of lactobacilli isolated belonged to the species Lactobacillus pentosus, Lactobacillus fermentum and Enterococcus faecium. A few strains of Lactobacillus plantarum and Weissella viridescens were also isolated. One strain, TV 1029, grouped into the same protein profile cluster as E. faecium, but revealed a DNA banding pattern closer related to Enterococcus faecalis. This is the first report of W. viridescens associated with the human vagina. This revised version was published online in June 2006 with corrections to the Cover Date.     

Two Distinct <Emphasis Type="Italic">Photobacterium</Emphasis> Populations Thrive in Ancient Mediterranean Sapropels

Eastern Mediterranean sediments are characterized by the periodic occurrence of conspicuous, organic matter-rich sapropel layers. Phylogenetic analysis of a large culture collection isolated from these sediments revealed that about one third of the isolates belonged to the genus Photobacterium. In the present study, 22 of these strains were examined with respect to their phylogenetic and metabolic diversity. The strains belonged to two distinct Photobacterium populations (Mediterranean cluster I and II). Strains of cluster I were isolated almost exclusively from organic-rich sapropel layers and were closely affiliated with P. aplysiae (based on their 16S rRNA gene sequences). They possessed almost identical Enterobacterial Repetitive Intergenic Consensus (ERIC) and substrate utilization patterns, even among strains from different sampling sites or from layers differing up to 100,000 years in age. Strains of cluster II originated from sapropels and from the surface and carbon-lean intermediate layers. They were related to Photobacterium frigidiphilum but differed significantly in their fingerprint patterns and substrate spectra, even when these strains were obtained from the same sampling site and layer. Temperature range for growth (4 to 33°C), salinity tolerance (5 to 100‰), pH requirements (5.5–9.3), and the composition of polar membrane lipids were similar for both clusters. All strains grew by fermentation (glucose, organic acids) and all but five by anaerobic respiration (nitrate, dimethyl sulfoxide, anthraquinone disulfonate, or humic acids). These results indicate that the genus Photobacterium forms subsurface populations well adapted to life in the deep biosphere.     

Structural variation in the O-specific polysaccharides of Klebsiella pneumoniae serotype O1 and O8 lipopolysaccharide: evidence for clonal diversity in rfb genes

The O-polysaccharide fraction of the lipopolysaccharide from Klebsiella pneumoniae serotype O8 was found to comprise two galactose-containing homopolymers. Structural analysis, using chemical and high-field nuclear magnetic resonance (NMR) techniques, established that the K. pneumoniae O8 polysaccharides are composed of the linear, disaccharide repeating units OAc 1 2/6 →3)-β-d -Galf-(1 →3)-α- d -Galp-(1→d -Galactan I-OAc →3)-α-d -Galp-(1 →3)-β-d -Galp-(1→d -Galactan II. K. pneumoniae O8 mutant RFK-1 was isolated by resistance to phage KO1-2; strain RFK-1 expressed only d -galactan I-OAc. The ¹H- and ¹³C-NMR resonances from this O-polysaccharide indicate that all of the O-acetyl groups within the K. pneumoniae O8 polysaccharide are carried on d -galactan I and O-acetylation occurs only on the β- d -galactofuranose residues; 60% of the available β- d -galactofuranose residues are non-acetylated. The O-acetylation of the remaining residues is equally distributed between the O-2 and O-6 positions. The carbohydrate backbone structures in the O8 polysaccharide are identical to d -galactan I and II expressed by K. pneumoniae O1, accounting for the antigenic cross-reaction between strains belonging to serotypes O1 and O8. However, the O1 polysaccharides are not acetylated and the O-acetyl groups present in the K. pneumoniae serotype O8 polysaccharides provide a structural basis for their recognition as distinct serotypes. The rfb (O-polysaccharide biosynthesis) gene cluster of K. pneumoniae serotype O1 determines the synthesis of d -galactan I. rfb_Kpo1-specific gene probes were used to examine conservation in the rfb gene clusters of other K. pneumoniae serotypes which produce d -galactan I. Six O1 strains were examined and all showed hybridization with rfb_KpO1 probes under conditions of high stringency. Three serotype O2 strains produce d -galactan I and these strains also contained DNA sequences recognized by rfb_KpO1 probes under high stringency. The physical maps of these homologous rfb chromosomal regions showed some polymorphism. Surprisingly, the rfb_KpO8 region from K. pneumoniae serotype O8 was only recognized by rfb_KpO1 probes under low-stringency hybridization conditions, providing evidence for two substantially different clonal groups of rfb genes from K. pneumoniae strains with structurally related O-antigens.     

Genetic diversity of the common bacterial blight pathogen of bean, <Emphasis Type="Italic">Xanthomonas axonopodis</Emphasis> pv. <Emphasis Type="Italic">phaseoli</Emphasis>, in Iran revealed by rep-PCR and PCR–RFLP analyses

Xanthomonad-like bacteria that are associated with common bacterial blight of bean in Iran were identified on the basis of their colonial morphology, biochemical and serological properties, presence of a specific DNA fragment using PCR primers and pathogenicity on bean. Xanthomonas axonopodis pv. phaseoli (Xap) strains were further characterized using rep-PCR and restriction fragment length polymorphism (RFLP). RFLP profiles generated by the restriction endonucleases RsaI, TaqI, HaeIII and Sau96I and rep-PCR analysis revealed that Iranian strains were relatively genetically homogenous. The similarity coefficients among the strains ranged from 0.87 to 1. The genetic diversity coefficients among strains from three infected provinces, Isfahan, Markazi and Lorestan, were 0.019, 0.072 and 0.033, respectively. The low overall level of polymorphism within Xap isolates collected from the three Iranian infected regions could suggest that few initial inoculum introductions might have distributed among these different bean-growing areas in Iran.     

Stress Tolerance and Genetic Variability of Phosphate-solubilizing Fluorescent Pseudomonas from the Cold Deserts of the Trans-Himalayas

Nineteen efficient phosphate-solubilizing fluorescent Pseudomonas from the cold deserts of the trans-Himalayas were screened for stress tolerance against temperature, alkalinity, salinity, calcium salts, and desiccation. Phylogenetic analysis based on 16S rRNA gene sequencing placed these bacteria under three groups with fourteen strains in Group I including Pseudomonas trivialis and P. poae, two strains in Group II together with Pseudomonas kilonensis and P. corrugata, and three strains in Group III along with Pseudomonas jessenii and P. moraviensis. Genetic diversity assessed by ERIC and BOX-PCR revealed variability among strains belonging to the same phylogenetic groups. Cluster analysis based on the growth characteristics under regimes of different stress levels placed the strains into three distinct clusters displaying no correlation to their phylogenetic groups. Stress-tolerant strains differed in the level of decline in phosphate solubilization under increasing intensity of various stress parameters. The highest decrease occurred with 5% CaCO_3, followed by 2.5% CaCO₃, pH 11, 5% NaCl, temperature of 37°C, 40% PEG, 5% CaSO₄, 2.5% NaCl, 2.5% CaSO₄, pH 9 and temperature of 15°C. Two strains belonging to Phylogenetic Group I exhibited higher phosphate solubilization at lower temperature. The results revealed that stress-tolerance ability was not limited to any particular phylogenetic group. Knowledge about the genetic variants of phosphate-solubilizing fluorescent Pseudomonas with potential for tolerance to desiccation, alkalinity, temperature, and salinity could be useful in understanding their ecological role under stressful environments of low phosphate availability.     

Genetic diversity of Syrian Arabian horses

Although Arabian horses have been bred in strains for centuries and pedigrees have been recorded in studbooks, to date, little is known about the genetic diversity within and between these strains. In this study, we tested if the three main strains of Syrian Arabian horses descend from three founders as suggested by the studbook. We examined 48 horses representing Saglawi (n = 18), Kahlawi (n = 16) and Hamdani (n = 14) strains using the Equine SNP70K BeadChip. For comparison, an additional 24 Arabian horses from the USA and three Przewalski's horses as an out group were added. Observed heterozygosis (H_o) ranged between 0.30 and 0.32, expected heterozygosity (H_e) between 0.30 and 0.31 and inbreeding coefficients (F_is) between ?0.02 and ?0.05, indicating high genetic diversity within Syrian strains. Likewise, the genetic differentiation between the three Syrian strains was very low (F_st < 0.05). Hierarchical clustering showed a clear distinction between Arabian and Przewalski's horses. Among Arabian horses, we found three clusters containing either horses from the USA or horses from Syria or horses from Syria and the USA together. Individuals from the same Syrian Arabian horse strain were spread across different sub‐clusters. When analyzing Syrian Arabian horses alone, the best population differentiation was found with three distinct clusters. In contrast to expectations from the studbook, these clusters did not coincide with strain affiliation. Although this finding supports the hypothesis of three founders, the genetic information is not consistent with the currently used strain designation system. The information can be used to reconsider the current breeding practice. Beyond that, Syrian Arabian horses are an important reservoir for genetic diversity.