Comparative Genomic Study of Vinyl Chloride Cluster and Description of Novel Species, Mycolicibacterium vinylchloridicum sp. nov.

Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato. These results also revealed the presence of an additional xcbF1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4, M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato. Mycolicibacterium aurum L1T (CECT 8761T = DSM 6695T) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027T. Phenotypic, chemotaxonomic and genomic data considering strain L1T (CECT 8761T = DSM 6695T) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov

Mycolicibacterium stellerae sp. nov., a rapidly growing scotochromogenic strain isolated from Stellera chamaejasme

A polyphasic study was undertaken to establish the taxonomic provenance of a rapidly growing Mycolicibacterium strain, CECT 8783T, recovered from the plant Stellera chamaejasme L. in Yunnan Province, China. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the strain formed a distinct branch within the evolutionary radiation of the genus Mycolicibacterium . The strain was most closely related to Mycolicibacterium moriokaense DSM 44221T with 98.4 % 16S rRNA gene sequence similarity, but was distinguished readily from this taxon by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity and digital DNA–DNA hybridization values of 79.5 and 21.1 %, respectively. Consequently, the strain is considered, to represent a novel species of Mycolicibacterium for which the name Mycolicibacterium stellerae sp. nov is proposed; the type strain is I10A-01893T (=CECT 8783T=KCTC 19843T=DSM 45590T)

Cutting the Gordian knot : early and complete amino acid sequence confirmation of class II lasso peptides by HCD fragmentation

SAJ would like to thank the University of Aberdeen for an Elphinstone Scholarship. CC-A thanks CONICYT PFCHA/DOCTORADO BECAS CHILE/2016 (#21160585) fellowship and CONICYT Basal Centre Grant for the Centre for Biotechnology and Bioengineering, CeBiB (FB0001). JFC also thanks CONICYT for a National PhD Scholarship (#21110356) and a Visiting Student Scholarship.Peer reviewedPostprin

Bioprospection and peptidogenomics of novel Streptomyces species from Salar de Huasco

Tesis para optar al grado de Doctor en Ciencias de la Ingeniería, Mención Ingeniería Química y BiotecnologíaDurante la ultima década, el Desierto de Atacama se ha convertido en uno de los mas estudiados biomas de la extremobiósfera para la bioprospección microbiana enfocada en nuevas especies de actinobacterias. Muchos de estos hábitats encontrados en el Desierto de Atacama, incluyendo aquellos definidos como híper-áridos e híper-salinos han demostrado una dominancia de actinobacterias, de las cuales muchas han sido fuente de una nueva quimiodiversidad de productos naturales y clusters de genes biosintéticos de metabolitos especializados de gran interés farmacéutico. El Salar de Huasco es un humedal de altura, atalasohalino y poliextremo en el altiplano Chileno del Desierto de Atacama, caracterizado por sus altos niveles de radiación solar, aridez y alta salinidad de sus suelos. Nuestro primer estudio dependiente de cultivo llevado a cabo en este ecosistema, para el aislamiento selectivo de nuevas especies de Streptomyces, desde muestras de suelo áridas de la orilla del Salar de Huasco, mostró la presencia de una alto número de cepas de Streptomyces fenotípica y genotípicamente diferentes. Algunas de ellas inhibieron exitosamente el crecimiento de patógenos Gram-positivos y negativos, patógenos fúngicos y mostraron citotoxicidad contra líneas celulares de carcinoma hepatocelular (HepG2) y fibroblastos de ratón (NIH-3T3). Dos de las cepas de Streptomyces mas prometedoras demostraron características fenotípicas, genéticas y quimiotaxonómicas que las distinguieron de sus cepas tipo mas cercanas y fueron válidamente descritas como las nuevas especies álcali-tolerantes Streptomyces altiplanensis HST21T y Streptomyces huasconensis HST28T. Un análisis de minería de genomas centrado en proteínas, de estas nuevas especies, reveló un alto número de clusters de genes biosintéticos (CGBs) incluyendo péptidos lazo y lantipéptidos. Streptomyces huasconensis HST28T mostró 4 CGBs de péptidos lazo, de las clases II y IV, de los cuales un nuevo péptido lazo clase II fue exitosamente detectado in vitro por medio de una aproximación peptidogenómica. Este nuevo péptido lazo, denominado huascopeptina, mostró el primer motivo estructural de anillo macrolactámico de siete miembros, el anillo mas pequeño actualmente descrito en un péptido lazo. Nuestros hallazgos sugieren que los ambientes poliextremos como el Salar de Huasco son fuentes prometedoras para explorar nuevos y valiosos productores de productos naturales con potencial farmacéutico.PFCHA / DOCTORADO BECAS CHILE / 2016 2116058

Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia

This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis

The Polyextreme Ecosystem, Salar de Huasco at the Chilean Altiplano of the Atacama Desert Houses Diverse <i>Streptomyces</i> spp. with Promising Pharmaceutical Potentials

Salar de Huasco at the Chilean Altiplano of the Atacama Desert is considered a polyextreme environment, where solar radiation, salinity and aridity are extremely high and occur simultaneously. In this study, a total of 76 bacterial isolates were discovered from soil samples collected at two different sites in the east shoreline of Salar de Huasco, including H0 (base camp next to freshwater stream in the north part) and H6 (saline soils in the south part). All isolated bacteria were preliminarily identified using some of their phenotypic and genotypic data into the genera Streptomyces (86%), Nocardiopsis (9%), Micromonospora (3%), Bacillus (1%), and Pseudomonas (1%). Streptomyces was found dominantly in both sites (H0 = 19 isolates and H6 = 46 isolates), while the other genera were found only in site H0 (11 isolates). Based on the genotypic and phylogenetic analyses using the 16S rRNA gene sequences of all Streptomyces isolates, 18% (12 isolates) revealed &lt;98.7% identity of the gene sequences compared to those in the publicly available databases and were determined as highly possibly novel species. Further studies suggested that many Streptomyces isolates possess the nonribosomal peptide synthetases-coding gene, and some of which could inhibit growth of at least two test microbes (i.e., Gram-positive and Gram-negative bacteria and fungi) and showed also the cytotoxicity against hepatocellular carcinoma and or mouse fibroblast cell lines. The antimicrobial activity and cytotoxicity of these Streptomyces isolates were highly dependent upon the nutrients used for their cultivation. Moreover, the HPLC-UV-MS profiles of metabolites produced by the selected Streptomyces isolates unveiled apparent differences when compared to the public database of existing natural products. With our findings, the polyextreme environments like Salar de Huasco are promising sources for exploring novel and valuable bacteria with pharmaceutical potentials

Downsizing Class II Lasso Peptides:Genome Mining-Guided Isolation of Huascopeptin Containing the First Gly1-Asp7 Macrocycle

This work was financially supported by the CONICYT PFCHA/DOCTORADO BECAS CHILE/2016-21160585 fellowship and CONICYT Basal Centre Grant for the Centre for Biotechnology and Bioengineering, CeBiB (FB0001). S.A.J. thanks the University of Aberdeen for providing an Elphinstone Scholarship. We thank the Scottish High-Field NMR (SHF NMR) Centre at the University of Edinburgh for NMR experiments. We also thank Dr. Paul Herron (Strathclyde Institute of Pharmacy and Biomedical Sciences) for genome sequencing. Additionally, we thank Kirsti Helland, Marte Albrigsten, and Jeanette Andersen (University of Tromsø - The Arctic University of Norway) for conducting biologicalassays. Finally, we thank Dr. Imen Nouioui and Dr. Cristina Dorador for their feedback during manuscript preparation.Peer reviewedPostprin

Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases

Strains 335427T and 234509T, isolated from two 76-year-old patients with chronic pulmonary diseases, were the subject of polyphasic taxonomic studies and comparative genomic analyses for virulence factors. The 16 rRNA gene sequence similarity between strains 335427T and 234509T and their closest phylogenetic neighbors Nocardia asiatica NBRC 100129T and Nocardia abscessus NBRC 100374T were 99.5% and 100%, respectively. Digital DNA&ndash;DNA hybridization values between the aforementioned studied strains were well below the 70% threshold for assigning prokaryotic strains to a novel species. Strains 335427T and 234509T have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427T has C16:0, C18:1 &omega;9c, C18:0 and C18:0 10 methyl as major fatty acids (&gt;15%) and mycolic acids formed of 52&ndash;54 carbon atoms. However, only C18:1 &omega;9c was detected for isolate 234509T, which had mycolic acids with 44&ndash;56 carbon. Based on phenotypic and genetic data, strains 335427T (DSM 109819T = CECT 9924T) and 234509T (DSM 111366T = CECT 30129T) merit recognition as novel species, which are named Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in M. tuberculosis, including experimentally verified virulence genes in humans related to tuberculosis. The narGHIJ (nitrate reduction pathway) and gvpAFGOJLMK (gas vesicles) genetic maps of strains 335427T, 234509T, NBRC 100129T and NBRC 100374T showed the same syntenic block and raise the question of whether their functions are interlinked during the infection of the human host. However, further research is required to decipher the role of the gas vesicle in the pathogenicity mechanism of Nocardia spp