Identification of rhizobial strains nodulating Egyptian grain legumes

The presence of apothecia in mixed species (vegetatively reproducing lichens, occasionally producing ascomata) has been interpreted as a mechanism to increase genetic variability in mostly clonal populations. However, spore viability from these apothecia has not been studied. We asked whether ascospores of the mixed species Physconia grisea are viable and thereby contribute to increasing the genetic diversity within populations of this species. An ontogenetic study of spores in cultures of P. grisea and a related sexual species (P. distorta), showed that although mature apothecia from both species produced and discharged meiospores capable of germination, spores from P. grisea were only rarely (0.43 %) able to continue development whereas those from P. distorta germinated and developed successfully. The strongly reduced viability of P. grisea spores suggested that they do not have a strong reproductive function, at least in the two local populations analyzed. Additionally, we show that the segregation of Physconia grisea ssp. lilacina does not have molecular support. [Int Microbiol 2013; 16(3):145-155]Keywords: Physconia spp. · apothecia · sexual reproduction · germination · ontogenetic development · mixed specie

The ocean sampling day consortium.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

The Ocean Sampling Day Consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

Diversity of Bradyrhizobium strains isolated from root nodules of the shrubby legume Cytisus villosus growing in the Moroccan Rif

The genotypic and phenotypic diversity of nineteen bradyrhizobial strains isolated from the root nodules of wild-grown Cytisus villosus in the central-western region of the Moroccan Rif were carried out. PCR-based RFLP (restriction fragment length polymorphism) of the 16S rDNA (ARDRA) of 19 strains using the restriction enzymes AluI, CfoI, DdeI, HinfI, MspI and RsaI showed that they grouped in 3 clusters. The cluster I includes the type strain Bradyrhizobium canariense BTA-1, the cluster II the type strain Bradyrhizobium japonicum USDA6 and the cluster III the type strains Bradyrhizobium cytisi CTAW11 and Bradyrhizobium rifense CTAW71. The results from 63 physiological and biochemical tests confirmed the existence of the B. canariense and the B. japonicum groups but also allowed the separation of the B. cytisi and B. rifense strains in two groups. The phenotypic characteristics analysed permitted description of a wide physiological and biochemical diversity among the strains, and showed that the heavy metals resistance test was the most discriminating characteristic.This study was supported by the ERDF-cofinanced grants PEAGR2012-1968 from Consejería de Economía, Innovación y Ciencia (Junta de Andalucía, Spain), and AGL2015-64582-C3-3-R from MINECO. Authors thank to AECID for the PCI-Mediterráneo grant A/017685/08 and to CNRST (Morocco) and CSIC (Spain) for cooperation grant 2009MA0013.Peer Reviewe

DataSheet1_Adjustment of p-value expression to ontology using machine learning for genetic prediction, prioritization, interaction, and its validation in glomerular disease.PDF

The results of gene expression analysis based on p-value can be extracted and sorted by their absolute statistical significance and then applied to multiple similarity scores of their gene ontology (GO) terms to promote the combination and adjustment of these scores as essential predictive tasks for understanding biological/clinical pathways. The latter allows the possibility to assess whether certain aspects of gene function may be associated with other varieties of genes, to evaluate regulation, and to link them into networks that prioritize candidate genes for classification by applying machine learning techniques. We then detect significant genetic interactions based on our algorithm to validate the results. Finally, based on specifically selected tissues according to their normalized gene expression and frequencies of occurrence from their different biological and clinical inputs, a reported classification of genes under the subject category has validated the abstract (glomerular diseases) as a case study.</p

Bradyrhizobium centrosemae (symbiovar centrosemae) sp. nov., Bradyrhizobium americanum (symbiovar phaseolarum) sp. nov. and a new symbiovar (tropici) of Bradyrhizobium viridifuturi establish symbiosis with Centrosema species native to America

17 páginas, 2 figuras, 1 tabla. -- The definitive version is available at http://www.elsevier.comIn this work we analyze through a polyphasic approach several Bradyrhizobium strains isolated in Venezuela from root nodules of Centrosema species. The analysis of the 16S rRNA gene showed that the strains belong to three clusters within genus Bradyrhizobium which have 100% similarity with Bradyrhizobium daqingense CCBAU 15774TBradyrhizobium guangxiense CCBAU 53363T and Bradyrhizobium viridifuturi SEMIA 690T. The results of recA and glnII gene analysis confirmed the identification of the strains CMVU02 and CMVU30 as Bradyrhizobium viridifuturi but the nodC gene analysis showed that they belong to a new symbiovar for which we propose the name tropici. Nevertheless, the concatenated recA and glnII gene phylogenetic analysis, DNA–DNA hybridization and phenotypic characterization showed that the strains A9T, CMVU44T and CMVU04 belong to two novel Bradyrhizobium species. The analysis of the nodC gene showed that these strains also represent two new symbiovars. Based on these results we propose the classification of the strain A9T isolated from Centrosema molle into the novel species Bradyrhizobium centrosemae (sv. centrosemae) sp. nov. (type strain A9T = LMG 29515T = CECT 9095T). and the classification of the strains CMVU44T and CMVU04 isolated from C. macrocarpum into the novel species Bradyrhizobium americanum (sv. phaseolarum) sp. nov. (type strain CMVU44T = LMG 29514T = CECT 9096T).This research was funded by the AECID Spanish-Venezuelan projects ref. A/021330/08 and A/023939/09 from Spanish Ministry of External Affairs and Cooperation (MAEC).Peer reviewe