Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts

Linking Heterogeneous Biodiversity Information Systems on the GRID: the GRAB Prototype

In the field of biodiversity informatics a wide range of diverse databases and tools already exists. The challenge is to integrate such resources in order to support scientists wishing to explore complex problems of relevance to biodiversity, and to create new resources where necessary. In this paper we outline the relevance of biodiversity informatics requirements to the future development of the GRID, identifying the main issues that need to be addressed in this area. We present GRAB (GRid And Biodiversity), which is a prototype demonstrator illustrating how one particular biodiversity-related task, namely bioclimatic modelling, can be supported in a Globus-based environment. We also describe a much larger-scale GRID application project that is just commencing (BiodiversityWorld) in which a flexible problem-solving environment is to be built for full-scale investigations by scientists working in a number of biodiversity research areas

The Prometheus Taxonomic Model: a practical approach to representing multiple classification.

A model for representing taxonomic data in a flexible and dynamic system capable of handling and comparing multiple simultaneous classifications is presented. The Prometheus Taxonomic Model takes as its basis the idea that a taxon can be circumscribed by the specimens or taxa of a lower rank which are said to belong to it. In this model alternative taxon concepts are therefore represented in terms of differing circumscriptions. This provides a more objective way of expressing taxonomic concepts than purely descriptive circumscriptions have been published. Using specimens as the fundamental elements of taxon circumscription also allows for the automatic naming of taxa based upon the distribution and priority of types within each circumscription, and by application of the International Code of Botanical Nomenclature. This approach effectively separates the process of naming taxa (nomenclature) from that of classification, and therefore enables the system to store multiple classifications. The derivation of the model, how it compares with other models, and the implications for the construction of global data sets and taxonomic working practice are discussed

A methodology for composing well-defined character descriptions.

Taxonomy has been described as “the science of documenting biodiversity”, which involves collecting, naming, describing, identifying and classifying specimens of organisms (Keogh, 1995). Descriptions are the fundamental information units used in the process of constructing classifications and communicating taxonomic concepts. The quality of stored description data is limited by the lack of a formal model and methodology for composing specimen descriptions, and by the absence of an agreed defined terminology. This impedes the communication, interpretation and reuse of original descriptions. This paper describes a novel approach to composing and recording taxonomic descriptions of botanical specimens. An underlying model for creating character descriptions is presented together with a process for creating an ontology of defined terms, which will be used to compose these description elements. It is hoped that these developments will facilitate the unambiguous interpretation of descriptions and enhance the taxonomic process

A methodology for composing well-defined character descriptions.

Taxonomy has been described as “the science of documenting biodiversity”, which involves collecting, naming, describing, identifying and classifying specimens of organisms (Keogh, 1995). Descriptions are the fundamental information units used in the process of constructing classifications and communicating taxonomic concepts. The quality of stored description data is limited by the lack of a formal model and methodology for composing specimen descriptions, and by the absence of an agreed defined terminology. This impedes the communication, interpretation and reuse of original descriptions. This paper describes a novel approach to composing and recording taxonomic descriptions of botanical specimens. An underlying model for creating character descriptions is presented together with a process for creating an ontology of defined terms, which will be used to compose these description elements. It is hoped that these developments will facilitate the unambiguous interpretation of descriptions and enhance the taxonomic process

Supporting taxonomic names in cell and molecular biology databases.

Groups of organisms require labels or names to refer to them, however the idea of a single static name index, although tempting for its simplicity, is both impractical and unadvisable as a basis for referring to organisms for which data has been collected and stored for analyses and sharing. The relevant issues are described and some of the challenges facing database researchers are discussed

Interactive visualisation tools for supporting taxonomists working practice.

The necessity for scientists and others to use consistent terminology has recently beenregarded as fundamental to advancing scientific research, particularly where data fromdisparate sources must be shared, compared or integrated. One area where there aresignificant difficulties with the quality of collected data is the field of taxonomicdescription. Taxonomic description lies at the heart of the classification of organismsand communication of ideas of biodiversity. As part of their working practice,taxonomists need to gather descriptive data about a number of specimens on aconsistent basis for individual projects. Collecting semantically well-defined structureddata could improve the clarity and comparability of such data. No tools howevercurrently exist to allow taxonomists to do so within their working practice.Ontologies are increasingly used to describe and define complex domain data. As a partof related research an ontology of descriptive terminology for controlling the storageand use of flowering plant description data was developed.This work has applied and extended model-based user interface developmentenvironments to utilise such an ontology for the automatic generation of appropriatedata entry interfaces that support semantically well defined and structured descriptivedata. The approach taken maps the ontology to a system domain model, which ataxonomist can then specialise using their domain expertise, for their data entry needs asrequired for individual projects. Based on this specialised domain knowledge, thesystem automatically generates appropriate data entry interfaces that capture dataconsistent with the original ontology. Compared with traditional model-based userautomatic interface development environments, this approach also has the potential toreduce the labour requirements for the expert developer.The approach has also been successfully tested to generate data entry interfaces basedon an XML schema for the exchange of biodiversity datasets