Global observational needs and resources for marine biodiversity

Otros autores: Best, B., Brandt, A., Goodwin, K., Iken, A., Marques, A., Miloslavich, P., Ostrowski, M., Turner, W., Achterberg, E., Barry, T., Bigatti, G., Henry, L.A., Ramiro-Sánchez, B., Durán, P., Morato, T., Murray Roberts, J., García-Alegre, A., Cuadrado, M., Murton, B.The diversity of life in the sea is critical to the health of ocean ecosystems that support living resources and therefore essential to the economic, nutritional, recreational, and health needs of billions of people. Yet there is evidence that the biodiversity of many marine habitats is being altered in response to a changing climate and human activity. Understanding this change, and forecasting where changes are likely to occur, requires monitoring of organism diversity, distribution, abundance, and health. It requires a minimum of measurements including productivity and ecosystem function, species composition, allelic diversity, and genetic expression. These observations need to be complemented with metrics of environmental change and socio-economic drivers. However, existing global ocean observing infrastructure and programs often do not explicitly consider observations of marine biodiversity and associated processes. Much effort has focused on physical, chemical and some biogeochemical measurements. Broad partnerships, shared approaches, and best practices are now being organized to implement an integrated observing system that serves information to resource managers and decision-makers, scientists and educators, from local to global scales. This integrated observing system of ocean life is now possible due to recent developments among satellite, airborne, and in situ sensors in conjunction with increases in information system capability and capacity, along with an improved understanding of marine processes represented in new physical, biogeochemical, and biological models

A core ontology of macroscopic stuff

Domain ontologies contain representations of types of stuff (matter, mass, or substance), such as milk, alcohol, and mud, which are represented in a myriad of ways that are neither compatible with each other nor do they follow a structured approach within the domain ontology. Foundational ontologies and Ontology distinguish between pure stuff and mixtures only, if it contains stuff. We aim to fill this gap between foundational and domain ontologies by applying the notion of a `bridging' core ontology, being an ontology of categories of stuff that is formalised in OWL. This core ontology both refines the DOLCE and BFO foundational ontologies and resolves the main type of interoperability issues with stuffs in domain ontologies, thereby also contributing to better ontology quality. Modelling guidelines are provided to facilitate the Stuff Ontology's use

Evolving and sustaining ocean best practices and standards for the next decade

The oceans play a key role in global issues such as climate change, food security, and human health. Given their vast dimensions and internal complexity, efficient monitoring and predicting of the planet's ocean must be a collaborative effort of both regional and global scale. A first and foremost requirement for such collaborative ocean observing is the need to follow well-defined and reproducible methods across activities: from strategies for structuring observing systems, sensor deployment and usage, and the generation of data and information products, to ethical and governance aspects when executing ocean observing. To meet the urgent, planet-wide challenges we face, methods across all aspects of ocean observing should be broadly adopted by the ocean community and, where appropriate, should evolve into "Ocean Best Practices." While many groups have created best practices, they are scattered across the Web or buried in local repositories and many have yet to be digitized. To reduce this fragmentation, we introduce a new open access, permanent, digital repository of best practices documentation (oceanbestpractices.org) that is part of the Ocean Best Practices System (OBPS). The new OBPS provides an opportunity space for the centralized and coordinated improvement of ocean observing methods. The OBPS repository employs user-friendly software to significantly improve discovery and access to methods. The software includes advanced semantic technologies for search capabilities to enhance repository operations. In addition to the repository, the OBPS also includes a peer reviewed journal research topic, a forum for community discussion and a training activity for use of best practices. Together, these components serve to realize a core objective of the OBPS, which is to enable the ocean community to create superior methods for every activity in ocean observing from research to operations to applications that are agreed upon and broadly adopted across communities. Using selected ocean observing examples, we show how the OBPS supports this objective. This paper lays out a future vision of ocean best practices and how OBPS will contribute to improving ocean observing in the decade to come

Marine microbes in 4D - using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health

Microbial observation is of high relevance in assessing marine phenomena of scientific and societal concern including ocean productivity, harmful algal blooms, and pathogen exposure. However, we have yet to realise its potential to coherently and comprehensively report on global ocean status. The ability of satellites to monitor the distribution of phytoplankton has transformed our appreciation of microbes as the foundation of key ecosystem services; however, more in-depth understanding of microbial dynamics is needed to fully assess natural and anthropogenically induced variation in ocean ecosystems. While this first synthesis shows that notable efforts exist, vast regions such as the ocean depths, the open ocean, the polar oceans, and most of the Southern Hemisphere lack consistent observation. To secure a coordinated future for a global microbial observing system, existing long-term efforts must be better networked to generate shared bioindicators of the Global Ocean's state and health

Unifying the known and unknown microbial coding sequence space

Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40%-60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1,749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data. © 2022, eLife Sciences Publications Ltd. All rights reserved.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]