Tenacibaculum maritimum CRISPR loci analysis and evaluation of isolate spoligotyping.

AIMS: We performed in silico analysis of CRISPRcas loci from Tenacibaculum maritimum, evaluated spoligotyping as a subtyping method and genotyped uncharacterized Turkish isolates from European sea bass by multilocus sequence typing (MLST). METHODS AND RESULTS: Spoligotyping was performed with primers designed to allow amplification and sequencing of whole CRISPR-arrays from 23 T. maritimum isolates. Twenty-three completed/draft genomes were also downloaded from the NCBI database and analysed. MLST of Turkish isolates was achieved with a well-established 7-gene scheme. Tenacibaculum maritimum genomes carry a structurally complete but partially defective class II CRISPRcas locus due to known amino acid substitutions in encoded Cas9 proteins. Our spacer identification suggests that the host range of bacteriophage P2559Y and Vibrio phage nt-1 include T. maritimum and that the most recurrent infection recorded by isolates has been with Tenacibaculum phage PTm5. Thirty-eight isolates with this CRISPRcas locus belonged to 25 spoligotypes and to 24 sequence types by MLST, respectively. According to MLST, T. maritimum isolates from Turkey are most related to previously defined sequence types ST3, ST40 and ST41 isolates from Spain, Malta and France. CONCLUSIONS: The evaluated spoligotyping offers discriminatory power comparable to MLST. SIGNIFICANCE AND IMPACT OF THE STUDY: Spoligotyping has potential as a quick, easy and cheap tool for subtyping of T. maritimum isolates.

Environmental biofilm communities associated with early-stage common dentex (Dentex dentex) culture.

AIMS: To describe the biofilm microbiota associated with various feeding phases during larval common dentex (Dentex dentex) culture. METHODS AND RESULTS: A targeted metagenomic (metagenetic) study was performed by means of 16S rRNA gene-based PCR and NextGen pyrosequencing. The resulting dataset was scrutinized with microbial community analysis software (r packages) using r/Rstudio. While median observed and estimated alpha-diversities were 171 ± 38 and 207 ± 27 taxa, respectively, 72·1-85·8% of individual biofilm communities comprised only 27-46 taxa. Members of the genus Methylobacterium and family Rhodobacteraceae dominated biofilms formed during all feeding phases while genera Nannochloropsis and Tetraselmis microalgae were major constituents of biofilms during rotifer live feeding. Both potential fish pathogenic genera, for example, Vibrio and putatively probiotic taxa, for example, Phaeobacter gallaeciensis were identified. CONCLUSIONS: Relatively stable biofilm communities were identified during each feeding phase but varied significantly between feeding phases, most likely in response to the introduction of live feed/microalgae-associated bacteria into rearing tanks. SIGNIFICANCE AND IMPACT OF THE STUDY: The structure of the bacterial communities identified represents a 'template' for successful larval dentex culture and provides a foundation for future investigations into failed production cycles.

First Report of Leaf Blotch on Sorghum Caused by Bipolaris spicifera in Turkey.

In July 2009, a leaf blotch disease was observed on sorghum in Sakarya Province, Turkey. Disease incidence and severity were rated at 45% and 25 to 75%, respectively. Typical symptoms included elliptical, straw-colored, necrotic lesions with darker margins. The lesions eventually coalesced, resulting in drying of leaves. A fungus was isolated from the lesions on potato dextrose agar (PDA) incubated under near ultraviolet light for 12 h daily at 22°C for 2 weeks. Flexuous conidiophores of the fungus were solitary or produced in small groups. They were geniculate with numerous well-defined scars, medium to dark brown, ≥300 µm long, and 4 to 9 µm thick. Five to eight or more conidia were produced on the apices of the conidiophores. The conidia were straight, oblong or cylindrical, rounded at the ends, golden brown at maturity except for a small area just above the dark scar, pseudoseptate, and 20 to 31 × 7.5 to 12.5 µm (1). The causal fungus was identified as Bipolaris spicifera (Bain) Subram. (teleomorph Cochliobolus spicifer Nelson). The identification was confirmed with specific PCR primers (Bipol-1 F: 5'-CAGTTGCAATCAGCGTCAGT-3', R: 5'-AAGACAAAAACGCCCAACAC-3', Bipol-2 F: 5'-GTGTTGGGCGTTTTTGTCTT-3', R: 5'-CCTACCTGATCCGAGGTCAA-3', Bipol-3 F: 5'-GATGAAGAACGCAGCGAAAT-3', R: 5'-AAGACAAAAACGCCCAACAC-3'). These primers were designed by the authors using Primer3 primer design software and sequences of B. spicifera found in GenBank. PCR products were amplified from nuclear DNA of the cultured fungus and were sequenced after cleaning with a Beckman 8000 CEQ DNA sequencer. Sequences amplified using Bipol-1 and Bipol-2 showed 99 to 100% similarity with B. spicifera sequences from GenBank. The DNA sequence amplified using Bipol-2 was deposited in GenBank (Accession No. HQ538774). B. spicifera has been reported previously as pathogenic in Africa, North and South America, Asia, Australia, Oceania, and the West Indies on Agrostis, Avena, Cymbopogon, Cynodon, Dactylis, Desmostachya, Eleusine, Holcus, Hordeum, Oryza, Panicum, Pennisetum, Phleum, Poa, Saccharum, Sorghum, Triticum, and Zea spp. (3). Pathogenicity tests were conducted on sorghum (Sorghum bicolor (L.) Moench) and Sorghum × sudangrass hybrid cultivars. From PDA cultures, conidia were collected in sterile distilled water with a concentration of 3% Tween 20. Twenty-five plants (five per pot) were inoculated by spraying the conidia (105 ml-1) onto 21-day-old plants, which were then maintained at 25 ± 2°C in a greenhouse following 48 h in a humid chamber. The test was repeated once. Control plants were sprayed with sterile distilled water. Typical symptoms (2) were obtained from all inoculated plants 7 days after inoculation. No symptoms developed on the control plants. The pathogen was reisolated from inoculated leaves to fulfill Koch's postulates. To our knowledge, this is the first report of B. spicifera on sorghum in Turkey. References: (1) M. B. Ellis. Dematiaceous Hyphomycetes. Commonwealth Mycological Institute, Kew, Surrey, England, 1971. (2) H. Koo et al. Plant Pathol. J. 19:133, 2003. (3) A. Sivanesan. Mycologia Papers 158:1, 1987.

Endogenous ochronosis.

Endogenous ochronosis or alkaptonuria is a rare, autosomal recessive disease of tyrosine metabolism that is caused by a deficiency of the enzyme homogentisic acid oxidase. The disease results in the accumulation and deposition of homogentisic acid in the cartilage, eyelids, forehead, cheeks, axillae, genital region, buccal mucosa, larynx, tympanic membranes, and tendons. The disease generally presents in adults with arthritis and skin abnormalities; occasionally, involvement of other organs may be seen. A 49-year-old man was referred to our clinic with verrucous lesions on his hands. On physical examination, caviar-like ochronotic papules were found around his eyes and the helix cartilage of his ears, and on the dorsa of both hands. There were brown macules on the sclera (Osler's sign). The patient had arthritis and nephrolithiasis, and a sample of his urine darkened upon standing. Histopathological examination showed deposition of ochronotic pigment. High-dose ascorbic acid was given, and the patient showed improvement on follow-up examination 6 months later.