Characterisation and comparative genomics of three new Varanus-associated Borrelia spp. from Indonesia and Australia.

BACKGROUND: Borrelia are important disease-causing tick- and louse-borne spirochaetes than can infect a wide variety of vertebrates, including humans and reptiles. Reptile-associated (REP) Borrelia, once considered a peculiarity, are now recognised as a distinct and important evolutionary lineage, and are increasingly being discovered worldwide in association with novel hosts. Numerous novel Borrelia spp. associated with monitor lizards (Varanus spp.) have been recently identified throughout the Indo-Pacific region; however, there is a lack of genomic data on these Borrelia. METHODS: We used metagenomic techniques to sequence almost complete genomes of novel Borrelia spp. from Varanus varius and Varanus giganteus from Australia, and used long- and short-read technologies to sequence the complete genomes of two strains of a novel Borrelia sp. previously isolated from ticks infesting Varanus salvator from Indonesia. We investigated intra- and interspecies genomic diversity, including plasmid diversity and relatedness, among Varanus-associated Borrelia and other available REP Borrelia and, based on 712 whole genome orthologues, produced the most complete phylogenetic analysis, to the best of our knowledge, of REP Borrelia to date. RESULTS: The genomic architecture of Varanus-associated Borrelia spp. is similar to that of Borrelia spp. that cause relapsing fever (RF), and includes a highly conserved megaplasmid and numerous smaller linear and circular plasmids that lack structural consistency between species. Analysis of PF32 and PF57/62 plasmid partitioning genes indicated that REP Borrelia plasmids fall into at least six distinct plasmid families, some of which are related to previously defined Borrelia plasmid families, whereas the others appear to be unique. REP Borrelia contain immunogenic variable major proteins that are homologous to those found in Borrelia spp. that cause RF, although they are limited in copy number and variability and have low sequence identities to RF variable major proteins. Phylogenetic analyses based on single marker genes and 712 single copy orthologs also definitively demonstrated the monophyly of REP Borrelia as a unique lineage. CONCLUSIONS: In this work we present four new genomes from three novel Borrelia, and thus double the number of REP Borrelia genomes publicly available. The genomic characterisation of these Borrelia clearly demonstrates their distinctiveness as species, and we propose the names Borrelia salvatorii, 'Candidatus Borrelia undatumii', and 'Candidatus Borrelia rubricentralis' for them.

Integrating science into management of ecosystems in the Greater Blue Mountains.

Effective management of large protected conservation areas is challenged by political, institutional and environmental complexity and inconsistency. Knowledge generation and its uptake into management are crucial to address these challenges. We reflect on practice at the interface between science and management of the Greater Blue Mountains World Heritage Area (GBMWHA), which covers approximately 1 million hectares west of Sydney, Australia. Multiple government agencies and other stakeholders are involved in its management, and decision-making is confounded by numerous plans of management and competing values and goals, reflecting the different objectives and responsibilities of stakeholders. To highlight the complexities of the decision-making process for this large area, we draw on the outcomes of a recent collaborative research project and focus on fire regimes and wild-dog control as examples of how existing knowledge is integrated into management. The collaborative research project achieved the objectives of collating and synthesizing biological data for the region; however, transfer of the project's outcomes to management has proved problematic. Reasons attributed to this include lack of clearly defined management objectives to guide research directions and uptake, and scientific information not being made more understandable and accessible. A key role of a local bridging organisation (e.g., the Blue Mountains World Heritage Institute) in linking science and management is ensuring that research results with management significance can be effectively transmitted to agencies and that outcomes are explained for nonspecialists as well as more widely distributed. We conclude that improved links between science, policy, and management within an adaptive learning-by-doing framework for the GBMWHA would assist the usefulness and uptake of future research.