Amplification Of Internal Transcribed Spacer Research Articles

Soil Structure and Ectomycorrhizal Root Colonization of Pecan Orchards in Northern Mexico.

Pecan trees form a symbiotic relationship with ectomycorrhizal fungi (ECM), which actively provide nutrition to the roots and protect them from phytopathogens. Although these trees originated in the southern United States and northern Mexico, information on their root colonization by ECM is insufficient in terms of a representative number of samples, both in these regions and worldwide. Therefore, the objectives of this study were to determine the percentage of ectomycorrhizal colonization (ECM) of pecan trees of different ages in conventional and organic agronomic orchards and to identify ectomycorrhizal sporocarps, both morphologically and molecularly. The rhizospheric soil properties and the ECM percentages were analyzed for 14 Western variety pecan tree orchards between 3 and 48 years of age and grouped according to the agronomic management method. DNA extraction, internal transcribed spacer amplification, and sequencing were conducted on the fungal macroforms. The ECM colonization percentage fluctuated between 31.44 and 59.89%. Soils with low phosphorus content showed higher ECM colonization. The ECM concentrations were relatively homogeneous in relation to the ages of the trees, and organic matter content did not affect the percentage of ECM colonization. The highest ECM percentages occurred with the sandy clay crumb texture soil, with an average of 55% ECM, followed by sandy clay loam soils with 49.5%. The Pisolithus arenarius and Pisolithus tinctorius fungi were molecularly identified from sporocarps associated with pecan trees. This is the first study that reports Pisolithus arenarius as being associated with this tree.

First report of Colletotrichum tropical causing leaf spot on Cariniana legalis in Brazil.

Cariniana legalis (Mart.) Kuntze (Lecythidaceae), commonly known as "Jequitibá Rosa," an endemic tree from Brazil, is one of the largest trees that grows in the Atlantic Rain Forest. Jequitibá Rosa has been extensively exploited due to the excellent quality of its wood, which has resulted in the species being placed as "vulnerable" on the IUCN red list of threatened species (IUCN, 2021). Thus, conservation of the species is paramount. In October 2018, in the municipality of Ilhéus, Bahia (14º 79' 67" S, 39º 17' 32" W), trees of C. legalis were observed with approximately 80% of leaves presenting light to dark brown necrotic lesions with yellow edges at the tips and margins of the leaves; the lesions gradually expanded through the leaves and coalesced to form wider lesions, which resulted in death of the leaves and weakening of the trees. The symptoms indicate infection caused by a Colletotrichum spp., important pathogens known to cause diseases in several economically important plants. Symptomatic leaves were collected and lesions examined under a stereomicroscope at 20x magnification (Supplementary Figure S1. A). Conidia were transferred directly and aseptically from the leaf spots to potato-dextrose-agar (PDA) and incubated in the dark at 25 ± 1 ºC for 72 h. Subsequently, pure cultures were obtained by monosporic isolation. All fungal structures were measured using a Leica DM500 microscope at 1000x magnification. A pathogenicity test was performed both on hosts in the field and using detached leaves by inoculation with a conidial suspension 106 conidia/mL prepared from a culture grown on PDA incubated in the dark at 25 ± 1 ºC for 10 days. Six healthy and fully developed detached leaves were inoculated with two 10 μL drops of conidial suspension on the adaxial surface. Six leaves were inoculated with two drops of sterile water were used as controls. The inoculated leaves were kept in a humid chamber at 25º C with a 12 h photoperiod. Four trees of C. legalis growing in the field were selected and 120 healthy leaves (30 per tree) sprayed with a conidial suspension and covered with transparent polyethylene plastic bags, with a piece of wet cotton inside, to maintain moisture for 72 h. A further 30 leaves per tree were sprayed with sterile water as controls. DNA was extracted using the cetyltrimethylammonium bromide (CTAB) method following the protocol described by Oliveira et al. (2016). Internal transcribed spacer (ITS), partial histone3 (HIS3), and partial glyceraldehyde-3-phosphatedehydrogenase (GAPDH) gene sequences were amplified by polymerase chain reaction (PCR) using ITS1/ITS4 (White et al. 1990), CYLH3F/CYLH3R (Crous et al. 2004), and GDF1/GDR1 (Guerber et al. 2003) primers. The PCR for the ITS amplification were performed according to Oliveira et al. (2014), and for the HIS3 and GAPDH according Damm et al. (2012). Maximum likelihood analysis (with support estimated by a bootstrap analysis with 1,000 replicates) was performed using PhyML 3.0 (Guindon and Gascuel 2003) and launched from Topali 2.5. The colony produced abundant white to light gray aerial mycelium, and an orange viscous mass of conidia (Supplementary Figure S1. B). Conidia were single-celled, smooth, hyaline and sub-cylindrical with rounded ends, 13 (11-15) × 3.5 (3-4) µm (Supplementary Figure S1. C); appressoria were aseptate, brown, subglobose to clavate, 11 (10-12) × 7 (6-8) µm (Supplementary Figure S1. D). BLASTn analysis revealed that the partial gene sequences of ITS (URM 8381 ‒ MZ158701), GAPDH (URM 8381 ‒ MZ189259) and HIS3 (URM 8381 ‒ MZ189260) were 100% identical to Colletotrichum tropicale (CPO 27.830 ‒MN744296/CBS 129983 ‒ MH865615), (CMM 4071 ‒ KC517181/CPO 27.719 ‒MN737355) and (CBS 124949 ‒ KY856395). A maximum likelihood phylogenetic tree was generated by combining all sequenced loci. The phylogenetic tree revealed that sequences of the isolate URM8381 formed a clade with the sequences from the type species of C. tropicale E.I. Rojas, S.A. Rehner & Samuels (CBS 124949) with a high support value (95), which is distinct from other related species (Supplementary Figure S1. E). The sequences from the isolate were deposited in GenBank under the following accession numbers: ITS: MZ158701; GAPDH: MZ189259 and HIS3: MZ189260. C. tropicale was reisolated from the inoculated leaves, and had the same cultural and morphological characteristics as the original isolate. Both detached leaves and leaves on trees were inoculated in the field and presented leaf spot symptoms (Supplementary Figure S1.F), at 6 and 8 days after inoculation, respectively, which further confirms C.tropicale as the causal agent of the symptoms observed on the leaves of C. legalis. The controls did not develop any symptoms (Supplementary Figure S1. G). C. tropicale belongs to the C. gloeosporioides species complex. In Brazil, C. tropicale causes anthracnose on various hosts, including Annona muricata L. (soursop) and Myrciaria dubia (Kunth) McVaugh ("camu-camu") (Costa et al. 2019; Matos et al. 2020). To our knowledge, this is the first report of C. tropicale causing leaf spot on C. legalis.

Differentiation Among Rodentibacter Species Based on 16S-23S rRNA Internal Transcribed Spacer Analysis.

The internal transcribed spacer (ITS) regions of Rodentibacter pneumotropicus, R. heylii, R. rarus, R. ratti, and R. heidelbergensis and of a Rodentibacter- related β-hemolytic Pasteurellaceae taxon isolated from laboratory rodents were studied for their feasibility to discriminate among these species. The 6 species analyzed showed species-specific ITS patterns that were shared by the type strains and clinical isolates and that allowed their identification. Nevertheless, differentiating between the ITS band patterns of R. pneumotropicus and R. ratti is visually challenging. In all species tested, sequence analysis of the ITS fragments revealed a larger ITSile+ala, which contained the genes for tRNAIle(GAU) and tRNA Ala(UGC), and a smaller ITSglu with the tRNAGlu(UUC) gene. The ITS sequences varied among the 6 species evaluated, displaying identity levels ranging from 62% to 86% for ITSile+ala and 68% to 90% for ITSglu. Overall, ITS amplification proved to be a reliable method to differentiate among these important Pasteurellaceae species of laboratory rodents. Moreover, the ITS sequence variations recorded here might facilitate the design of probes for specific identification of these species. The ability to diagnose these organisms to the species level could increase our understanding of their clinical significance.

First Report of Mycoleptodiscus terrestris Causing Crown and Root Rot of Alfalfa (Medicago sativa) in Minnesota.

Mycoleptodiscus terrestris (Gerd.) Ostaz. has been studied extensively as a potential mycoherbicide against aquatic weeds since the early 1970s (Mathur and Gehlot 2018; Shearer 1998). However, it is also a pathogen on many legumes including alfalfa (Gerdemann 1953; Smith et al. 1998). In August 2019, alfalfa plants with stunted yellow foliage and rotted stems at the base of the crown were observed in a variety trial planted in spring 2018 at the University of Minnesota, St. Paul, Minnesota. Affected plants were in patches across the field with approximately 20% of plants showing symptoms. Plants from patches had few lateral and fibrous roots and dark lesions appeared in the crown and root tissue. Tissue samples (5 mm2) from 10 plants with symptomatic crown and root tissues were surface disinfested with 70% ethanol for 5 min, followed by 30 s in 10% NaOCl, and then rinsed three times in sterile distilled water. Samples were air-dried and placed on water agar (WA) amended with 25 µg/ml rifampicin. Plates were incubated at room temperature for 3 days and fungal hyphal tips from tissue samples were transferred to potato dextrose agar (PDA). After 7 days, isolates were tentatively identified by morphological characteristics as M. terrestris (Ostazeski 1967). The hyaline mycelia turned from olive-gray to dark gray with age. Abundant dark microsclerotia formed 5 days after incubation that varied in size and shape, measuring 300-860 x 270-600 µm. Molecular identification of two representative isolates (DAZ5 and DAZ9) was done by sequencing the internal transcribed spacer (ITS) regions of the rDNA, the translation elongation factor 1α (TEF1), and the second largest subunit of RNA polymerase II (RPB2) genes. For both isolates the ITS, TEF1, and RPB2 genes were amplified and sequenced with primers ITS1/4 (White et al. 1990), 983F/1567R (Rehner and Buckley 2005), and fRPB2-7cR/RPB-5F2 (Liu et al. 1999; Sung et al. 2007), respectively. ITS amplification conditions followed White et al. (1990), the TEF and the partial RPB2 gene was obtained by using a touchdown PCR protocol as described in Rehner and Buckley (2005) and Woudenberg et al. (2017), respectively. Based on a BLAST search of the NCBI nucleotide database, the ITS sequences (GenBank MN851265.1 and MN851266.1) had 100% identity with M. terrestris strain CBS 231.53 (MK487754.1). The TEF1 (MN873019, MN873020) and RPB2 sequences (MN873021, MN873022) had 100% identity with M. terrestris strain IMI 159038 (MK495977.1, MK492735.1). A pathogenicity test was performed by inoculating five 3-week-old alfalfa plants per cultivar (cv. DKA44-16RR, Vernal, 53V52, and Agate) with isolates DAZ5 and DAZ9. Plants were inoculated around the exposed stem base with three 5 mm diameter PDA plugs from a culture of M. terrestris covered with microsclerotia. Control plants were inoculated with sterile PDA plugs. After inoculation plants were incubated at 25 0C with a 16-h photoperiod in a growth chamber. The first symptoms appeared two months after inoculation on all cultivars as a dark lesion at the stem base followed by yellowing and rotting of stems. Inoculated plants had more fibrous roots than the controls. The control plants were symptomless with healthy root development. The pathogen was re-isolated from all infected alfalfa cultivars and had the same morphology as isolates DAZ5 and DAZ9, fulfilling Koch's postulates. To our knowledge, this is the first report of M. terrestris causing crown and root rot disease of alfalfa in Minnesota.

First Report of Leaf Spot on Sorghum bicolor Caused by Alternaria tenuissima in China

Sorghum bicolor (L.) is an important crop used in renewable fuels, which is widely planted in Africa, North America, and Asia for its resistance to stress (Dahlberg 2019). A foliar disease on sorghum was observed in 2019, affecting approximately 11,000 ha, in Daqing, Heilongjiang Province, China. Disease incidence averaged approximately 50% among all affected fields and caused 10 to 20% economic loss. At the initial stage of the infection, small brown spots with light yellow halos appeared on the leaves, which gradually enlarged and coalesced to form large areas of lesions, 2 to 20 mm long and 2 to 5 mm wide, on leaves in the advanced stage of the infection. To identify the pathogen, 10 symptomatic leaves were collected and surface disinfected with 1% sodium hypochlorite for 1 min followed by 70% ethanol for 30 s, rinsed in sterile distilled water, and dried on filter paper. Leaf spot fragments were then placed onto potato dextrose agar (PDA) and incubated at 28°C in darkness for 3 days. Four fungal isolates were obtained from the diseased leaves by a single-spore isolation method. The fungal colonies of the isolates had round margins with abundant, fluffy, and olive-green to brown aerial mycelia after 7 days on PDA. Conidiophores were pale brown with septa, straight or flexuous, single or in clusters, with branches forming occasionally. Numerous pale brown, obclavate to obpyriform shaped conidia were produced on conidiophores and occurred in long chains. Conidia ranged in size from 14.5 to 49.6 × 7.5 to 17.6 μm, with longitudinal and transverse septa varying from zero to three and from one to six, respectively (n = 50). Based on morphological characteristics, all the fungal isolates were preliminarily identified as Alternaria spp. (Simmons 2007). The internal transcribed spacer (ITS) region of rDNA and the partial coding sequences of allergen (Alt) and glyceraldehyde 3-phosphate dehydrogenase (G3PDH) genes of isolates were amplified and sequenced with primers ITS1/ITS4, Alt a/b, and G3PDH a/b, respectively (Woudenberg et al. 2013). DNA sequences from amplification of ITS from two isolates were deposited in GenBank (MN816298 and MN939684). BLAST analysis of the sequences from isolates AT1 and AT2 (MN816298 and MN939684) showed 99.64% (557/559 bp) and 100% (558/558 bp) similarity with the ITS sequence (MN907695) of Alternaria tenuissima (ZZ9-5-1). Sequences of Alt (MT109294) and G3PDH (MT109295) of isolate AT2 were 99.59% (486/488 bp) and 99.67% (596/598 bp) similar to the Alt and G3PDH sequences from A. tenuissima SY-4 (MK593137.1) and 15-238 (LC134315.1), respectively. Therefore, the pathogen was identified as A. tenuissima on the basis of the morphological characteristics and the sequences of ITS, Alt gene, and G3PDH gene. Pathogenicity of the isolates was tested on leaves of five sorghum seedlings by spraying with aqueous conidial suspensions (105 conidia/ml), whereas negative control plants were sprayed with sterile distilled water and then incubated in chambers at 25°C and 95% relative humidity. Plants inoculated with the fungus developed brown lesions on leaves within 8 days, whereas the negative controls were symptomless. To fulfill Koch’s postulates, reisolations from margins of necrotic leaf spot tissue of all tested strains were streaked on V8 agar (Blagojevic et al. 2015). Fungi isolated from lesions showed the same colony morphology as described above and were identified by morphological characters or DNA sequences as A. tenuissima. The control leaves remained asymptomatic, and the pathogen was not reisolated. The pathogenicity test was repeated with similar results. A. tenuissima could potentially cause leaf spots on many plants (Sun et al. 2019). However, this is the first report of A. tenuissima causing leaf spots on sorghum in China. Identification of this disease pathogen is important to prevent its spread to other areas.

Isolation and identification of endophytic fungi from two medicinally important orchids, Satyrium nepalense D. Don and Herminium lanceum (Thunb. ex sw.)Vuijk

Endophytic fungi isolated from medicinal plants can be good sources of medicine. Satyrium nepalense and Herminium lanceum are two medicinally important orchids. Decoction of stems, roots and tubers of Satyrium nepalense, locally known as ‘Salam mishri’, is prescribed in various ailments and also as dietary supplement since ancient times. H. lanceum, locally known as ‘Jalya’, is used for the treatment of urinary problems, diabetes, fever and haemorrhagia. A total of 12 fungal species, eight and four, respectively, were isolated from the root cultures of S. nepalense and H. lanceum. For the identification of these isolates, nuclear internal transcribed spacer (ITS) from each of these was amplified and sequenced. The amplification and sequencing of ITS was successful from 11 of the 12 fungi. All the amplicons yielded barcode quality sequences, which have been submitted to the GenBank, NCBI. The fungi were identified by BLAST method on NCBI as well as BOLD. Five fungal species, Ilyonectria estremocensis, Cryptosporiopsis ericae, Thanatephorus cucumeris, Phialophora mustea, Aspergillus species from S. nepalense, and two from H. lanceum, Fusarium falciforme and Aspergillus flavus, were identified. Most of these fungi have been shown to be antibacterial and/or anti-cancerous, and a few are the known to be sources of bioactive molecules.

First Report of Colletotrichum fructicola Causing Bitter Rot of Pear (Pyrus bretschneideri) in China.

Pyrus bretschneideri cv. Dangshansuli is the most important commercial Asiatic pear cultivar worldwide. In recent years, a fruit rot disease of unknown etiology have caused considerable fresh market losses in the 'Dangshansuli' production operations in Dangshan county, Anhui Province, China. Fresh market losses typically range from 60 to 90% and in 2008 were estimated at US$150 million. Symptomatic mature 'Dangshansuli' pears were collected from an orchard in Dangshan County in February 2008. A thin section (about 1 mm3) of symptomatic tissue was sterilized in a bleach and placed on potato dextrose agar (PDA) medium for isolation. From all fruit, a single fungus was recovered displaying gray-white dense aerial mycelium. Identical fungi were isolated from six additional symptomatic 'Dangshansuli' pears collected from other orchards in the county. Pathogenicity tests using one isolate (DS-0) were conducted in triplicate by placing 4 mm diameter discs from 7-day-old PDA plates onto the mature 'Dangshansuli' pear fruit that were incubated in an incubator at 25°C with a 12-h photoperiod for 30 days. An equal number of noncolonized PDA inoculations were included as a control. Isolate DS-0 caused symptoms similar to those in the field within 7 days and complete collapse of cortical tissues within 30 days. No symptoms were observed on control fruit. Round brownish lesions with a diameter of about 3 cm on inoculated fruit was populated by sunken, rotiform acervuli on which numerous, colorless, oblong single cell shape conidia with width/length of 6 × 20 μm were produced. A comparison of morphology and sequence analysis of the ribosomal internal transcribed spacer (ITS) regions in pre- and post-inoculation cultures from inoculated fruit confirmed the presence DS-0. To further characterize DS-0, aliquots of extracted genomic DNA from the fungus were subjected to PCR amplification and sequencing of seven gene regions from the ITS, actin (ACT), β-tubulin 2 (TUB2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), manganese-superoxide dismutase (SOD2), chitin synthase (CHS-1), and calmodulin (CAL), using the primers listed by Weir et al (4), except for the primer pair of ITS1 (5'-TCCGTAGGTGAACCTGCGG-3') and ITS4 (5'-TCCTCCGCTTATTGATATGC-3') for ITS amplification, and SODglo2-R (5'-TAGTACGCGTGCTCGGACAT-3') and SODglo2-R (5'-TAGTACGCGTGCTCGGACAT-3') for TBU2 amplification. Two or three clones of PCR products of each gene were sequenced and compared (GenBank Accession Nos. KC410780 to KC410786) to published data at http://www.cbs.knaw.nl/colletotrichum . The result indicated that DS-0 shared the highest similarity of 99.91% with Colletotrichum fructicola, corroborating numerous reports of Colletotrichum spp. causing bitter rot of pear on P. pyrifolia (1,2,3,4). C. fructicola was only recently reported as causing bitter rot of P. pyrifolia (4) and to our knowledge, this is the first report of C. fructicola causing bitter rot of P. bretschneideri, which will help producers select the best management practices for this devastating disease.

Rapid and Accurate Identification of Mycobacterium tuberculosis Complex and Common Non-Tuberculous Mycobacteria by Multiplex Real-Time PCR Targeting Different Housekeeping Genes

Rapid and accurate identification of mycobacteria isolates from primary culture is important due to timely and appropriate antibiotic therapy. Conventional methods for identification of Mycobacterium species based on biochemical tests needs several weeks and may remain inconclusive. In this study, a novel multiplex real-time PCR was developed for rapid identification of Mycobacterium genus, Mycobacterium tuberculosis complex (MTC) and the most common non-tuberculosis mycobacteria species including M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and the M. gordonae in three reaction tubes but under same PCR condition. Genetic targets for primer designing included the 16S rDNA gene, the dnaJ gene, the gyrB gene and internal transcribed spacer (ITS). Multiplex real-time PCR was setup with reference Mycobacterium strains and was subsequently tested with 66 clinical isolates. Results of multiplex real-time PCR were analyzed with melting curves and melting temperature (T (m)) of Mycobacterium genus, MTC, and each of non-tuberculosis Mycobacterium species were determined. Multiplex real-time PCR results were compared with amplification and sequencing of 16S-23S rDNA ITS for identification of Mycobacterium species. Sensitivity and specificity of designed primers were each 100% for MTC, M. abscessus, M. fortuitum, M. avium complex, M. kansasii, and M. gordonae. Sensitivity and specificity of designed primer for genus Mycobacterium was 96 and 100%, respectively. According to the obtained results, we conclude that this multiplex real-time PCR with melting curve analysis and these novel primers can be used for rapid and accurate identification of genus Mycobacterium, MTC, and the most common non-tuberculosis Mycobacterium species.

독도의 자생식물 뿌리에서 분리한 내생진균의 다양성과 생장촉진활성

독도에 자생하고 있는 식물의 뿌리로부터 내생진균의 분리를 시도하여, 동도로 부터 참억새, 돌피, 쇠무릎과 서도에서 갯별꽃 및 율무쑥등을 연구재료로 사용하였다. 총 21종의 내생진균을 분리하였고, universal primers ITS-1과 ITS-4를 사용하여 ITS 영역을 PCR로 증폭하여 동정하였다. 염기서열 분석결과, 동도에 자생하는 참억새에서는 Penicillium 속 균주가 75%, Aspergillus 균주가 25%, 분리되었고, 돌피에서는 Penicillium 속 균주가 55%, Aspergillus 속 균주가 30%, Zygorhynchus 속 균주가 15%가 분리되었으며, 쇠무릎에서는 Penicillium 속 균주가 50%, Aspergillus 속 균주가 12%, Gibberella 속 균주가 13%, Talaromyces 속 균주가 9%, Umbelopsis 속 균주가 8% 분리되었다. 서도에 자생하는 갯별꽃에서는 Penicillium 속 균주가 76%, Pestalotiopsis 속 균주가 24% 분리되었고, 율무쑥에서는 Penicillium 속 균주가 81%, Mucor 속 균주가 19% 분리되었다. Bioassay결과, 돌피에서 분리된 Ec-3-1균주가 식물생장촉진활성을 나타내었다. 그리고 독도의 5종류 식물에서 Penicillium 속의 내생진균이 가장 많이 존재함을 알 수 있었다. Endophytic fungi were isolated from the roots of plants growing naturally on the island of Dokdo. Plant samples, such as Miscanthus sinensis, Achyranthus japonica and Echinochloa crusgali were isolated from Dongdo, and those such as Honkenya peploides and Artemsia koidzumii were isolated from Seodo. Twenty one strains of endophytic fungi were isolated from these plants. To identify the strains, PCR (polymerase chain reaction) amplification of the partial ITS (Internal Transcribed Spacer) regions was done with universal primers ITS-1 and ITS-4 to determine the nucleotide sequence of the ITS regions. Of the strains isolated from Miscanthus sinensis, 75% were Penicillium sp. and 25% were Aspergillus sp. Fifty five percent of strains isolated from Achyranthus japonica were Penicillium sp., 30% were Aspergillus sp. and 15% were Zygorhynchus sp. Strains isolated from Echinochloa crusgali were Penicillium sp. (50%), Aspergillus sp. (12%), Giberella sp. (13%), Talaromyces sp. (9%) and Umbelopsis sp. (8%). Of the strains isolated from Honkenya peploides, 76% were Penicillium sp. and 24% were Pestalotiopsis sp. Strains isolated from Artemisia koidzumii were Penicillium sp. (81%) and Mucor sp. (19%). As a result of bioassay, Ec-3-1 strain isolated from Echinochloa crusgalli showed plant growth-promotion activity. Of all the endophytic fungi isolated, Penicillium sp. was the most abundantly distributed fungal strain in all plants used in this study.

ITS Length Polymorphism in Oysters and its Use in Species Identification

In an effort to develop genetic markers for oyster identification, we studied length polymorphism in internal transcribed spacers (ITS) between major ribosomal RNA genes in 12 common species of Ostreidae: Crassostrea virginica, C. rhizophorae, C. gigas, C. angulata, C. sikamea, C. ariakensis, C. hongkongensis, Saccostrea echinata, S. glomerata, Ostrea angasi, O. edulis, and O. conchaphila. We designed two pairs of primers and optimized PCR conditions for simultaneous amplification of ITS 1 and ITS2 in a single PCR. Amplification was successful in all 12 species, and PCR products were visualized on high-resolution agarose gels. ITS2 was longer than ITS 1 in all Crassostrea and Saccostrea species, whereas they were about the same size in the three Ostrea species. No intraspecific variation in ITS length was detected. Among species, the length of ITS I and ITS2 was polymorphic and provided unique identification of 8 species or species pairs: C. ariakensis, C. hongkongensis, C. sikamea, O. conchaphila, C. virginica/C. rhizophorae, C. gigas/C. angulata, S. echinata/S. glonzerata, and O. angasi/O. edulis. The ITS assay provides simple, rapid and effective identification of C. ariakensis and several other oyster species. Because the primer sequences are conserved, the ITS assay may be useful in the identification of other bivalve species.

Digestion of DNA regions to discriminate ochratoxigenic and non-ochratoxigenic strains in the Aspergillus niger aggregate

Aspergillus strains belonging to the Aspergillus niger aggregate, either isolated from Italian grapes or received from public collections, were analysed in order to discriminate between the ochratoxin A (OTA) producing and the non-producing strains by means of the analysis of Internal Transcribed Spacers (ITS), Intergenic Spacers (IGS) and of a β-tubulin gene portion. A. niger and Aspergillus awamori were identified observing the macro- and microscopic features of the colonies and the strains ochratoxigenicity was evaluated through Thin Layer Chromatography and/or High Performance Liquid Chromatography. PCR amplification of ITS, IGS and β-tubulin gene portion produced 600, 440 and 550 bp amplicons, respectively, in all the analysed strains. The digestion of the IGS amplicon with Hinf I and of the other two amplicons with Rsa I, revealed one main profile type (“T–C–C”) associated with the A. niger aggregate strains which lack the ability to produce OTA.

PCR-based Species-Specific Amplification of ITS of Mecistocirrus digitatus and Its Application in Identification of GI Nematode Eggs in Bovine Faeces

Differential diagnosis of Mecistocirrus digitatus infection relies on morphological examination of either eggs in faecal samples or L3 larvae developed in vitro. Technical limitations hinder the practicability of these approaches. Hence, in order to develop a specific diagnostic measure for M. digitatus infection, we determined the sequence of the internal transcribed spacer (ITS) of its ribosomal DNA (rDNA) and designed primers for PCR-based species-specific amplification of the ITS to differentiate between M. digitatus and other common gastrointestinal (GI) nematode species. The newly designed primers amplified a single specific 520 base pair (bp) fragment from the M. digitatus ITS, and its detection limit was as low as 0.001 ng. Further, this sensitivity suggested that the specific fragment could be amplified even from a unicellular egg that collected directly from uteri of an adult M. digitatus female. In fact, we designed a method that employs a small piece of a cover slip and a filter paper by which we could differentially amplify a PCR fragment from a unicellular egg. The reliability of the specific PCR assay was also demonstrated with 10 oval samples that collected from bovine faeces by using sugar flotation method. These data suggested that the specific PCR assay of the ITS region of M. digitatus rDNA could be useful for the identification of GI nematodes.

Molecular characterization of Cylindrospermopsis raciborskii strains isolated from Portuguese freshwaters

Cylindrospermopsis raciborskii is a toxic bloom forming cyanobacteria that is a common component of the phytoplankton assemblage in temperate freshwaters, as well as in temperate climates. This species is of major concern in public health, due to its known ability to produce toxins, including cylindrospermopsin and paralytic shellfish poisoning toxin (PSP). In this study, M13 PCR fingerprinting, ERIC PCR fingerprinting and amplification of the internal transcribed spacer (ITS) region were used to characterize nine cultured strains of C. raciborskii, sourced from several freshwater lakes and rivers in Portugal, and two other Australian. Strains belonging to other taxa including Microcystis aeruginosa, Aphanizomenon spp., Planktothrix agardhii and Oscillatoria neglecta were also analysed to evaluate the taxonomical potential of the fingerprinting methods. Data obtained from genomic fingerprinting were used to perform hierarchical cluster analysis and demonstrated ability to differentiate strains at intra-specific level. However, the high level of variability prevents their use as an identification tool. ITS amplification displayed intra-specific polymorphism both in number and length of the obtained amplicons, but revealed itself as a good method for strain clustering. The unsuccessful amplification of peptide synthetase (PS) and polyketide synthase (PKS) genes pointed to the inability of Portuguese C. raciborskii strains to produce cylindrospermopsin. HPLC analysis further confirmed this lack of toxicity, since negative results were obtained for cylindrospermopsin and PSP toxins.

Genetic analysis of housekeeping genes reveals a deep‐sea ecotype of Alteromonas macleodii in the Mediterranean Sea

The genetic diversity of 19 strains belonging to Alteromonas macleodii isolated from different geographic areas (Pacific and Indian Ocean, and different parts of the Mediterranean Sea) and at different depths (from the surface down to 3500 m) has been studied. Fragments of the 16S rRNA gene, the internal transcribed spacer (ITS) between 16S and 23S rDNA genes, the gyrB and the rpoB genes, have been sequenced for each strain. Amplified fragment length polymorphisms were used to characterize similarity at the level of the whole genome. Most of the diversity reflected the existence of a cluster of strains isolated from deep Mediterranean waters and two isolates from the Black Sea. Particularly the isolates from the deep sites were consistently different from all the others indicating the existence of a specific ecotype adapted to these conditions. Amplification of gyrB gene and ITS directly from DNA retrieved from deep Mediterreanean waters and one Atlantic sample showed that presence of this deep-sea ecotype is widespread and is not a product of culture bias. On the other hand, strains isolated from surface tropical waters showed a remarkable level of resemblance to the first isolate of this species obtained from Hawaii in 1972. The results indicate the existence of both lineages of global distribution and ecotypes adapted to specific conditions such as deep or more diluted (the Black Sea) waters.

Bartonella clarridgeiaeandB. henselaein Dogs, Gabon

To the Editor: The genus Bartonella contains several recently described species, many of which are emerging human pathogens. Human infections are mostly due to Bartonella henselae and B. quintana. Like many vectorborne disease agents, Bartonella species have a natural cycle. This cycle contains a reservoir host, in which Bartonella species cause an intraerythrocytic bacteremia, and a vector, which transmits the bacteria from the reservoir host to a new susceptible host (usually the uninfected reservoir host) (1). In the case of B. quintana and B. bacilliformis, the natural host is human. In Bartonella diseases, humans act as accidental hosts. Among the nonhuman Bartonella species that infect humans, B. henselae is most commonly encountered and usually causes cat-scratch disease. However, several cases of infections in humans attributable to other Bartonella species, including B. elizabethae, B. grahamii, B. vinsonii arupensis, B. vinsonii berkhoffii, and possibly B. clarridgeiae, have been reported (1). Isolation of Bartonella species in animals that have contact with humans can help identify new human pathogens or new diseases. We report results of isolation of Bartonella spp. from the blood of 258 dogs in Gabon. The study was performed in the Ogooue-Ivindo province of Gabon, a country of Central Africa with an equatorial climate. Blood samples were taken from dogs in the town of Mekambo and in all villages connecting Mekambo and Mazingo (nine villages) and Mekambo and Ekata (seven villages) during July and August 2003. Each dog brought by its owner for the study was weighed and sedated by injection with 50 μg/kg of medetomidine (Pfizer Sante Animal, Orsay, France). After the dog was examined, a blood sample was drawn from the jugular vein by Vacutainer (Becton Dickinson, Meylan, France). Each dog was tattooed with an identification number and given both antihelminthic and external antiparasitic treatments. During the examination, the dogs were treated with care; upon completion of the examination, the dogs were given 250 μg/kg of the reversal agent atipamezola (Pfizer Sante Animal) intramuscularly. A physical examination form and a questionnaire were completed for each test participant by its owner. A total of 258 dogs (155 males and 103 females) were examined and had blood samples drawn during the study. All animals were of mixed breeds and were 6 months to 14 years old (average 3 years 1 month). The Vacutainer tubes were kept on ice until blood samples were dispensed into cryotubes and frozen in liquid nitrogen. Samples were stored at –80°C until isolation attempts were made on Columbia agar (Biomerieux, Marcy l'etoile, France) as described previously (2). In this study, six Bartonella isolates were obtained and identified as B. clarridgeiae (five isolates) and B. henselae (one isolate), by internal transcribed spacer amplification and sequencing (3). B. vinsonii subsp. berkhoffii was the first Bartonella species found in dogs (1). Isolation of B. clarridgeiae (4,5) and B. washoensis (6) in dogs was recently reported. Infection of dogs by other Bartonella species was also detected in the DNA of B. henselae (7,8), B. clarridgeiae (7), and B. elizabethae (8). The presence of these Bartonella species is not surprising, since Ctenocephalides felis, the vector of B. henselae in cats, has a wide range of hosts, including the domestic dog. However, attempts to isolate this species in samples collected from 211 dogs in the United Kingdom failed (9). Bartonella species are supposedly difficult to isolate in dogs because of a low concentration of bacteria in the blood (1). This supposition was apparent in our study; we identified approximately 100 bacterial colonies per milliliter of blood from three of the six dogs in our study. From the other three dogs in our study, including the dog infected with B. henselae, we identified two to four bacterial colonies per milliliter of blood. Most of the data pertaining to Bartonella have been obtained in the United States and Europe. Increasingly, Bartonella infections are being reported in Africa, especially in southern Africa (10). We report here the first isolation of B. henselae from a dog and the first isolation of B. clarridgeiae in Central Africa. That dogs also act as reservoirs of B. henselae likely has implications in Africa where HIV infections are prevalent.

Internal transcribed spacer 2 amplicon as a molecular marker for identification of Peronospora parasitica (crucifer downy mildew).

The purpose of the study was to characterize the internal transcribed spacer (ITS) regions of Peronospora parasitica (crucifer downy mildew) in order to evaluate their potential as molecular markers for pathogen identification. PCR amplification of ribosomal RNA gene block (rDNA) spacers (ITS1 and ITS2) performed in 44 P. parasitica isolates from different Brassica oleracea cultivars and distinct geographic origins, revealed no length polymorphisms. ITS restriction analysis with three endonucleases, confirmed by sequencing, showed no fragment length polymorphisms among isolates. Furthermore, ITS amplification with DNA isolated from infected host tissues also allowed the detection of the fungus in incompatible interactions. The combination of the universal ITS4 and ITS5 primers, for amplification of full ITS, with a new specific forward internal primer for ITS2 (PpITS2F), originates a P. parasitica specific amplicon, suitable for diagnosis. As ITS2 regions of P. parasitica, B. oleracea, other B. oleracea fungal pathogens and other Peronospora species are clearly distinct, a fast and reliable molecular identification method based on multiplex PCR amplification of full ITS and P. parasitica ITS2 is proposed for the diagnosis of crucifer downy mildew. The method can be applied to diagnose the disease in the absence of fungal reproductive structures, thus being useful to detect nonsporulating interactions, early stages of infection on seedlings, and infected young leaves packed in sealed plastic bags. Screening of seed stocks in sanitary control is also a major application of this diagnostic method.

Molecular differentiation of clostridia associated with ‘blown pack’ spoilage of vacuum-packed meats using internal transcribed spacer polymorphism analysis

The 16S–23S rDNA internal transcribed spacer (ITS) polymorphism analysis was assessed for its suitability in rapid discrimination between species of psychrophilic and psychrotolerant clostridia associated with ‘blown pack’ spoilage of vacuum-packed meats. DNA isolated from 10 reference and 20 meat strains of psychrophilic and psychrotolerant clostridia were used as templates in PCR amplification with primers complementary to conserved regions of the 3′ end of the 16S rRNA and 5′ end of the 23S rRNA genes directly flanking the spacer. The majority of strains showed multi-band ITS patterns when products of spacer amplification were visualised on an agarose gel. With the majority of meat strains, PCR amplification generated single banding pattern for a single clostridial species. However, meat strains of Cl. algidicarnis produced four different ITS banding patterns. With reference strains of psychrophilic and psychrotolerant clostridia, variation in spacer length was also observed between nonproteolytic Cl. botulinum type B (17B), E (Beluga) and F (202F). On the other hand, the number and size of the ITS amplification products could not be used for a differentiation of Cl. laramiense ATCC 51254 T from Cl. estertheticum DSM 8809 T, Cl. putrefaciens DSM 1291 T from Cl. algidicarnis NCFB 2931 T, or Cl. frigidicarnis strains from nonproteolytic Cl. botulinum type B (17B). The presence of interstrain, and lack of interspecies, ITS polymorphism observed in the present study with some clostridial species may preclude the use of 16S–23S rDNA spacer amplification for species-level discrimination and identification, respectively, of psychrophilic and psychrotolerant clostridia associated with meat spoilage. However, where interstrain, intraspecies heterogeneity of ITS amplification products exists, ITS analysis could be useful for tracing back psychrophilic and psychrotolerant clostridia responsible for meat spoilage to their meat plant sources.

Genotyping of axenic and non-axenic isolates of the genus Prochlorococcus and the OMF-‘Synechococcus’ clade by size, sequence analysis or RFLP of the Internal Transcribed Spacer of the ribosomal operon The GenBank accession numbers for the ITS amplicon sequences reported in this paper are AF387607 (PCC 9511T), AF387610 (PCC 6307), AF387608 (PCC 7001) and AF387609 (PCC 7941).

PCR amplicons of the Internal Transcribed Spacer (ITS) of the rrn operon of three axenic OMF (oceanic, marine and freshwater) strains of 'Synechococcus' (WH7803, PCC 7001 and PCC 6307, respectively) differ greatly in length from that of the axenic Prochlorococcus marinus subsp. pastoris PCC 9511(T), although these four cyanobacteria cluster relatively closely in phylogenetic trees inferred from 16S rRNA gene sequences. The ITSs of three strains (PCC 9511(T), PCC 6307 and PCC 7001) were sequenced and compared with those available for strains Prochlorococcus MED4 (CCMP 1378) and MIT9313 from genome sequencing projects. In spite of large differences in length, sequence and mean DNA base composition, conserved domains important for transcriptional antitermination and folding of the rRNA transcripts were identified in all ITSs. A new group-specific primer permitted ITS amplification even with non-axenic isolates of Prochlorococcus and one OMF-'Synechococcus' strain. Prochlorococcus isolates of the high-light-adapted clade (HL) differed from representatives of the low-light-adapted clade (LL) by the length of their ITS. Restriction fragment length polymorphism (RFLP) of the ITS amplicons revealed three subclusters among the HL strains. Size, sequence data and RFLP of the ITS amplicons will therefore be valuable markers for the identification of different Prochlorococcus genotypes and for their discrimination from other cyanobacterial relatives with which they often co-exist in oceanic ecosystems.

Identification of Saccharomyces cerevisiae in bakery products by PCR amplification of the ITS region of ribosomal DNA

A non-conventional sensitive and specific method for the detection of Saccharomyces cerevisiae in food is proposed. Polymerase chain reaction (PCR) led to the identification of this yeast in some commercial bakery products. The comparative use of two methods of clean-up of DNA from Triticum spp., S. cerevisiae and some foods shows an improvement in extraction yield for the phenol-free method. Analysis of some sequences of ribosomal genes shows different amplified products for Triticum and S. cerevisiae. Internal transcribed spacer amplification (ITS1/ITS4) produced a single band of about 650 and 800 bp for Triticum and S. cerevisiae, respectively. ITS1/ITS2 universal fungal primers gave a single band of about 300 and 450 bp for Triticum and S. cerevisiae, respectively. Both amplification products are able to distinguish between the yeast and the DNA from T. aestivum and T. durum, showing polymorphism in the ITS1 region. Amplification on two primers designed using the sequence of the ITS1 region of S. cerevisiae rDNA (SC1/SC2) led to a single band of 300 bp, species-specific for the yeast. These primers enabled an unambiguous distinction between fermented foods containing S. cerevisiae and those leavened by baking powders to be made. We suggest that this PCR assay could be used for quality control and for the trace detection of S. cerevisiae as a potential food allergen.

Molecular characterization of Pisolithus spp. isolates by rDNA PCR-RFLP

Variation within ribosomal DNA (rDNA) genes of 19 isolates of Pisolithus from different geographic origins and hosts was examined by polymerase chain reaction (PCR) coupled with restriction fragment length polymorphism (RFLP) analysis. The primers utilized amplify rDNA regions in a wide range of fungi. One amplified region includes the internal transcribed spacer (ITS), which has a low degree of conservation. The ITS amplification products (640–750 bp) were digested with a variety of restriction endonucleases. Cluster analysis based on the restriction fragments grouped the isolates into three distinct groups: group I contained isolates collected in the northern hemisphere, except Pt 1, group II contained those collected in Brazil and group III contained isolate Pt 1. Additional analysis of other rDNA regions, IGS, 17 S and 25 S rDNA, resulted in similar groups. The data suggest that the taxonomy and systematics of this ectomycorrhizal fungus should be revised.