Publications

4478

A novel actinomycete, designated strain GLM-1T, was isolated from arbuscular mycorrhizal fungal spores from Funneliformis mosseae RYA08, collected from Aquilaria crassna Pierre ex Lec. rhizosphere soil in Klaeng, Rayong Province, Thailand. Morphological characteristics of this strain included long chains of rod-like cells and squarish elements. The cell-wall composition of this novel isolate contained meso-diaminopimelic acid. The whole-cell diagnostic sugars were arabinose and galactose. The predominant menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 and iso-C15 : 0. Only phosphatidylethanolamine was detected as a polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GLM-1T was closely related to Amycolatopsis rhabdoformis SB026T (99.11 %) with a low DNA–DNA hybridization value of 22.6–34.7 %. Genome sequencing revealed a genome size of 10 Mbp. There were obvious distinctions in the average nucleotide identity values between stain GLM-1T and its closely related strains at around 86–93 % (ANIb) and 89–94 % (ANIm). The digital DNA–DNA hybridization values between strain GLM-1T and type strains of phylogenetically related species were 34–55 %. The G+C content of the genomic DNA was 71.8 mol%. Based on these data, strain GLM-1T is considered to represent a novel species of the genus Amycolatopsis , for which the name Amycolatopsis eburnea sp. nov. is proposed. The type strain is GLM-1T (=TBRC 9315T=NBRC 113658T)

SUMMARYCandidatus Liberibacter spp. are Alphaproteobacteria associated with plants and psyllid vectors. Most cause plant diseases, including Ca Liberibacter asiaticus (Las) associated with citrus huanglongbing (HLB). Replacing HLB-infected by Las-free citrus trees results in fast re-infection despite psyllid control. To check if HLB could be soil-borne, we performed an insect-free greenhouse-experiment with 130 mandarin seedlings in two citrus-grove soils (A and B), non-autoclaved or autoclaved. Liberibacter-specific 16S-rDNA PCR primers to detect Las were used to search for Ca. Liberibacter spp. in mandarin leaves. Seven plants grown in non-autoclaved soil B showed HLB-like symptoms and tested positive after 2.5 and 8.5 months using three different primer systems: two based on the 16S-rDNA gene (primers HLBas/HLBr and OI2c/OI1) and one based on the rplA/rplJ gene (primers LAA2/LAJ5). DNA segments from these plants amplified by primers OI2c/OI1 were cloned and sequenced; they were 95.9 % similar to Las and 94.8% to Ca. Liberibacter africanus (Laf). The DNA product from Liberibacter-group specific PCR primers for the rplA/rplJ gene was 87.6% similar to that of Las and 78.2% of Laf. As the strain obtained originated from soil and was different from existing Ca. Liberibacter species, this strain may be a new species.

During 2015, samples from 22 apple trees showing proliferation symptoms were collected in southwest Bulgaria and Central and South Poland and tested for phytoplasma presence. ‘Candidatus Phytoplasma mali’ was identified in 18 samples based on results of restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene amplified in nested PCR using primer pair P1/P7 followed by R16F2n/R16R2 and F1/B6 primer pairs. The nitroreductase and rhodonase like genes and ribosomal protein genes rpl22 and rps3 were then analyzed using PCR-RFLP technique to study the genetic variability of the  phytoplasma strains. Two restriction profiles, P-I or P-II, were obtained for fragments of 16S rDNA plus 16S-23S spacer region digested with HpaII enzyme. Restriction fragment length polymorphism analysis of nitroreductase and rhodonase like genes using digestion with HincII endonuclease revealed that the all ‘Ca. P. mali’ strains belonged to subtype AP-15. Analysis of rpl22 and rps3 ribosomal protein genes digested with AluI enzyme resulted in classification of detected phytoplasma strains to rpX-A subgroup.

AbstractRickettsia typhi and Rickettsia felis (Rickettsiales: Rickettsiaceae) are flea-transmitted pathogens. They are important causes of acute febrile illness throughout the world. We, therefore, sought to identify the rickettsial species present in the fleas of dogs and cats in the department of Cauca, Colombia. In this study, we collected 1,242 fleas from 132 dogs and 43 fleas from 11 cats. All fleas were morphologically identified as Ctenocephalides felis (Bouché) adults and organized in pools for DNA extraction (234 pools from dogs and 11 from cats). The gltA gene from rickettsiae was targeted for screening amplification using conventional PCR. In total, 144 of the 245 pools (58.7%) were positive. The positive samples were then processed for the amplification of the 17kDa antigen gene (144/144; 100% positive) and sca5 gene (140/144; 97.2% positive). In addition, restriction enzyme length polymorphism analysis using NlaIV on the amplified product of the sca5 gene demonstrated several organisms: 21/140 (15%) were R. felis, 118/140 (84.3%) were Rickettsia asemboensis, and 1/140 (0.7%) were Candidatus Rickettsia senegalensis. Subsequent sequencing confirmed Candidatus Rickettsia senegalensis in C. felis collected from dogs the first reported from Colombia.

For Thaumarchaeota , the ratio of their glycerol dialkyl glycerol tetraether (GDGT) lipids depends on growth temperature, a premise that forms the basis of the widely applied TEX 86 paleotemperature proxy. A thorough understanding of which GDGTs are produced by which Thaumarchaeota and what the effect of temperature is on their GDGT composition is essential for constraining the TEX 86 proxy. “ Ca . Nitrosotenuis uzonensis” is a moderately thermophilic thaumarchaeote enriched from a thermal spring, setting it apart in its environmental niche from the other marine mesophilic members of its order. Indeed, we found that the GDGT composition of “ Ca . Nitrosotenuis uzonensis” cultures was distinct from those of other members of its order and was more similar to those of other thermophilic, terrestrial Thaumarchaeota . This suggests that while phylogeny has a strong influence on GDGT distribution, the environmental niche that a thaumarchaeote inhabits also shapes its GDGT composition.

La presencia de sistemas flagelares es común en muchas bacterias de vida libre, sin embargo, estos han sido considerados ausentes en bacterias del orden Rickettsiales. Candidatus Hepatobacter penaei es una bacteria Rickettsial de origen marino descrita como un microorganismo con motilidad, propulsada por un sistema flagelar, el cual también facilita la infección. Siendo esta bacteria uno de los principales riesgos de infección en granjas camaronícolas. El objetivo de este trabajo fue determinar la presencia de genes que codifiquen proteínas del sistema flagelar de la bacteria Candidatus Hepatobacter penaei. Para el análisis se utilizó la secuencia genómica la base de datos del GenBank con número de acceso NZ_JQAJ00000000.1, una vez detectados los genes, se dedujeron las secuencias de aminoácidos. Las secuencias de aminoácidos del sistema flagelar se identificaron mediante BlastP, por medio de un alineamiento múltiple de dominios conservados. Posteriormente, se realizó un modelado de la proteína FlhA y se comparó con la proteína reportada para Oceanibaculum indicum para la conformación hojas  y  hélices. Los resultados mostraron la presencia de algunas secuencias de aminoácidos relacionadas con los genes del sistema flagelar de la bacteria como MotA, FliG, FliN, FliL FlhA, FlhB, FliQ, FliR y FliF. Finalmente, estos resultados sugieren que Candidatus Hepatobacter penaei es una bacteria tipo Rickettsia que posee un sistema flagelar, el cual posiblemente le confiere motilidad y forma parte del proceso de infección en hospederos como crustáceos marinos.