Diversity of Burkholderia isolates from woodland rhizosphere environments

Aims: Determination of genetic diversity among UK Burkholderia cepacia isolates from various environmental niches, principally woodland tree rhizospheres and onions. Methods and Results: Genus determination was made using polymerase chain reaction (PCR) amplification and fatty acid methyl ester profiling. Genetic diversity was investigated by repetitive sequence genetic PCR fingerprinting. Several onion isolates were similar to clinical isolates but others were diverse. Some environmental isolates were possibly synonymous with B. cepacia and B. gladioli but most from woodland rhizospheres were distinct and clustered together. The 16S rRNA genes of representatives from these clusters were PCR amplified, sequenced and phylogenetically compared with all known Burkholderia and related species. This revealed that the rhizospheric isolates had closest affinity with Burkholderia spp. with known bioremediative and biocontrol capabilities and were unrelated to taxa comprising plant or human pathogenic strains. Conclusions: All of the analyses investigated revealed that environmental and onion isolates of B. cepacia complex bacteria are genetically diverse but that woodland rhizospheric isolates are related to each other and unrelated to plant or human pathogenic strains. Significance and Impact of the Study: Woodland rhizospheric isolates of B. cepacia are potentially good candidates for use in bioremediation and biocontrol, as they appear distinct from plant or human pathogenic strains.Peer reviewe

Preserving accuracy in GenBank

GenBank, the public repository for nucleotide and protein sequences, is a critical resource for molecular biology, evolutionary biology, and ecology. While some attention has been drawn to sequence errors, common annotation errors also reduce the value of this database. In fact, for organisms such as fungi, which are notoriously difficult to identify, up to 20% of DNA sequence records may have erroneous lineage designations in GenBank. Gene function annotation in protein sequence databases is similarly error-prone. Because identity and function of new sequences are often determined by bioinformatic analyses, both types of errors are propagated into new accessions, leading to long-term degradation of the quality of the database. Currently, primary sequence data are annotated by the authors of those data, and can only be reannotated by the same authors. This is inefficient and unsustainable over the long term as authors eventually leave the field. Although it is possible to link third-party databases to GenBank records, this is a short-term solution that has little guarantee of permanence. Similarly, the current third-party annotation option in GenBank (TPA) complicates rather than solves the problem by creating an identical record with a new annotation, while leaving the original record unflagged and unlinked to the new record. Since the origin of public zoological and botanical specimen collections, an open system of cumulative annotation has evolved, whereby the original name is retained, but additional opinion is directly appended and used for filing and retrieval. This was needed as new specimens and analyses allowed for reevaluation of older specimens and the original depositors became unavailable. The time has come for the public sequence database to incorporate a community-curated, cumulative annotation process that allows third parties to improve the annotations of sequences when warranted by published peer-reviewed analyses.Fil: Bidartondo, Martin I.. Imperial College London; Reino Unido. Royal Botanic Gardens; Reino UnidoFil: Bruns, Thomas D.. University of California at Berkeley; Estados UnidosFil: Blackwell, Meredith. Louisiana State University; Estados UnidosFil: Edwards, Ivan. University of Michigan; Estados UnidosFil: Taylor, Andy F. S.. Swedish University of Agricultural Sciences; SueciaFil: Bianchinotti, Maria Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur; ArgentinaFil: Padamsee, Mahajabeen. University of Minnesota; Estados UnidosFil: Callac, Philippe. Institut National de la Recherche Agronomique; FranciaFil: Lima, Nelson. Universidade do Minho; PortugalFil: White, Merlin M.. Boise State University; Estados UnidosFil: Barreau Daly, Camila. Centre National de la Recherche Scientifique; Francia. Institut National de la Recherche Agronomique; FranciaFil: Juncai, M. A.. Chinese Academy of Sciences; República de ChinaFil: Buyck, Bart. Museum National d'Histoire Naturelle; FranciaFil: Rabeler, Richard K.. University of Michigan; Estados UnidosFil: Liles, Mark R.. Auburn University; Estados UnidosFil: Estes, Dwayne. Austin Peay State University; Estados UnidosFil: Carter, Richard. Valdosta State University; Estados UnidosFil: Herr Jr., J. M.. University of South Carolina; Estados UnidosFil: Chandler, Gregory. University of North Carolina; Estados UnidosFil: Kerekes, Jennifer. University of California at Berkeley; Estados UnidosFil: Cruse Sanders, Jennifer. Salem College Herbarium; Estados UnidosFil: Galán Marquez, R.. Universidad de Alcalá; EspañaFil: Horak, Egon. Zurich Herbarium; SuizaFil: Fitzsimons, Michael. University of Chicago; Estados UnidosFil: Döering, Heidi. Royal Botanic Gardens; Reino UnidoFil: Yao, Su. China Center of Industrial Culture Collection; ChinaFil: Hynson, Nicole. University of California at Berkeley; Estados UnidosFil: Ryberg, Martin. University Goteborg; SueciaFil: Arnold, A. E.. University of Arizona; Estados UnidosFil: Hughes, Karen. University of Tennessee; Estados Unido