Pier Luigi Buttigieg

Helmholtz Metadata Collaboration · Earth and Environment

This paper captures perspectives and recommendations from many of the repositories that are members of the Earth Science Information Partners (ESIPFed, n.d.) in conjunction with members of the Collaboratory for Indigenous Data Governance (Collaboratory for Indigenous Data Governance n.d.) and GIDA, defines and prioritizes the set of activities Eart...

This paper presents the specific process used by members of the Earth Science Information Partners (ESIP) Semantic Harmonization Cluster, to harmonize cryospheric terms gathered by the Global Cryosphere Watch (GCW) with two leading semantic resources used in the Earth and Environmental science communities—the Semantic Web for Earth and Environmenta...

EuropaBON EBV workflow templates The information provided here represents the EBV workflow templates collected during the EuropaBON online workshop on Essential Biodiversity Variable (EBV) workflows from 22–24 February 2023. The templates were designed to capture comprehensive descriptions about the three workflow components (data collection and s...

The presented pilot for the Synthesis Product for Ocean Time Series (SPOTS) includes data from 12 fixed ship-based time-series programs. The related stations represent unique open-ocean and coastal marine environments within the Atlantic Ocean, Pacific Ocean, Mediterranean Sea, Nordic Seas, and Caribbean Sea. The focus of the pilot has been placed...

Climate change is opening the Arctic Ocean to increasing human impact and ecosystem changes. Arctic fjords, the region’s most productive ecosystems, are sustained by a diverse microbial community at the base of the food web. Here we show that Arctic fjords become more prokaryotic in the picoplankton (0.2–3 µm) with increasing water temperatures. Ac...

Seamounts are abundant features on the seafloor that serve as hotspots and barriers for the dispersal of benthic organisms. The primary focus of seamount ecology has typically been on the composition and distribution of faunal communities, with far less attention given to microbial communities. Here, we investigated the microbial communities in the...

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizatio...

The presented pilot for the “Synthesis Product for Ocean Time-Series” (SPOTS) includes data from 12 fixed ship-based time-series programs. The related stations represent unique marine environments within the Atlantic Ocean, Pacific Ocean, Mediterranean Sea, Nordic Seas, and Caribbean Sea. The focus of the pilot has been placed on biogeochemical ess...

Aim We aimed to apply ontological techniques to address semantic ambiguities in protected area and conservation informatics. By doing so, we aimed to create a coherent, machine‐actionable semantic representation of the biogeographic areas (which often overlap protected areas) to support more efficient and standardized informatics, supporting resear...

Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on...

Indigenous knowledge is often disregarded and opportunities for positive change are lost. To protect the Ocean, a “two-eyed seeing” approach combining Indigenous and western knowledge systems can create advancements while empowering coastal Indigenous Peoples.

Ocean life—from viruses to whales—is built from “biomolecules.” Biomolecules such as DNA infuse each drop of ocean water, grain of sediment, and breath of ocean air. The Ocean Biomolecular Observing Network (OBON) is developing a global collaboration that will allow science and society to understand ocean life like never before. The program will tr...

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 int...

In the marine realm, microorganisms are responsible for the bulk of primary production, thereby sustaining marine life across all trophic levels. Longhurst provinces have distinct microbial fingerprints; however, little is known about how microbial diversity and primary productivity change at finer spatial scales. Here, we sampled the Atlantic Ocea...

Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontolog...

Maintaining healthy, productive ecosystems in the face of pervasive and accelerating human impacts including climate change requires globally coordinated and sustained observations of marine biodiversity. Global coordination is predicated on an understanding of the scope and capacity of existing monitoring programs, and the extent to which they use...

Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over time and space. It is an especially effective approach for investigating the marine microbiome. To mature marine microbiome rese...

Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over time and space. To achieve a global ocean biomolecular observing network (OBON) for the UN Decade of Ocean Science for Sustainab...

Biogeochemical cycling of carbon (C) and nitrogen (N) in the ocean depends on both the composition and activity of underlying biological communities and on abiotic factors. The Southern Ocean is encircled by a series of strong currents and fronts, providing a barrier to microbial dispersion into adjacent oligotrophic gyres. Our study region straddl...

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontolo...

The UN Decade of Ocean Science for Sustainable Development (Ocean Decade) challenges marine science to better inform and stimulate social and economic development while conserving marine ecosystems. To achieve these objectives, we must make our diverse methodologies more comparable and interoperable, expanding global participation and foster capaci...

Biogeochemical cycling of carbon (C) and nitrogen (N) in the ocean depends on both the composition and activity of underlying biological communities and on abiotic factors. The Southern Ocean is encircled by a series of strong currents and fronts, providing a barrier to microbial dispersion into adjacent oligotrophic gyres. Our study region straddl...

Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh environmental conditions, such as near-freezing tempe...

This perspective outlines how authors of ocean methods, guides, and standards can harmonize their work across the scientific community. We reflect on how documentation practices can be linked to modern information technologies to improve discoverability, interlinkages, and thus the evolution of distributed methods into common best practices within...

Microorganisms produce an immense variety of natural products through the expression of Biosynthetic Gene Clusters (BGCs): physically clustered genes that encode the enzymes of a specialized metabolic pathway. These natural products cover a wide range of chemical classes (e.g., aminoglycosides, lantibiotics, nonribosomal peptides, oligosaccharides,...

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heter...

Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture and agrifood systems requires quality data labeling or annotation in order to be interoperable. As recommended by the FAIR principles, data, labels, and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain an...

In order to advance ongoing efforts in the (still emerging) field of marine restoration, different forms of knowledge must be combined: not only the biological and technical aspects, but also the social and cultural dimensions of marine restoration efforts. This calls for a newly combined array of methods that allows for a bridging of these differe...

Bridging the gap between the known and the unknown coding sequence space is one of the biggest challenges in molecular biology today. This challenge is especially extreme in microbiome analyses where between 40% to 60% of the coding sequences detected are of unknown function, and ignoring this fraction limits our understanding of microbial systems....

In this document, we provide details on how to best use the Ocean Best Practices System (OBPS) templates, thus allowing greater discovery, machine readability, sharing and understandability of methods and best practices (Buttigieg et al. 2019). This document clarifies how to optimally populate the different sections of an OBPS template. We describe...

We are on the threshold of a new and exciting era of discovery in the oceans that will shape the development of human endeavours for decades to come. New insights on the significance of the microscopic scale of ocean life have shown this level affects almost every aspect of our lives (health, food, industry, ecosystems). For society’s future, we ne...

This Vision Statement, or Roadmap, of marine microbiome research is conducted within work package 6 of the Atlantic Ocean Research Alliance (AORA) between Canada, the European Union and the United States of America. We are on the threshold of a new and exciting era of discovery in the oceans that will shape the development of human endeavours for...

Surveys of 16S rRNA gene sequences derived from marine sediments have indicated that a widely distributed group of Gammaproteobacteria, named "JTB255-Marine Benthic Group" (now the candidate order Woeseiales), accounts for 1-22% of the retrieved sequences. Despite their ubiquity in seafloor communities, little is known about their distribution and...

This report presents the outcome of the joint work of PhD students and senior researchers working with DNA-based biodiversity assessment approaches with the goal to facilitate others the access to definitions and explanations about novel DNA-based methods. The work was performed during a PhD course (SLU PNS0169) at the Swedish University of Agricul...

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 acti...

Development of global ocean observing capacity for the biological EOVs is on the cusp of a step-change. Current capacity to automate data collection and processing and to integrate the resulting data streams with complementary data, openly available as FAIR data, is certain to dramatically increase the amount and quality of information and knowledg...

For the last 15 years, Biodiversity Information Standards (TDWG) has recognized two competing standards for organism occurrence data, ABCD (Access to Biological Collections Data; Holetschek et al. 2012) and DarwinCore (Wieczorek et al. 2012). These two representations emerged from contrasting strategies for mobilizing information about organism occ...

Over the past 20 years, immense progress has been made in enhancing the effectiveness, affordability, and deployability of molecular methods for biodiversity assessment and monitoring. From the micro- to macroscopic scale, methods such as amplicon sequencing of phylogenetic marker genes, metagenomics, and metatranscriptomics have greatly impacted b...

Founded in early 2018 through a collaboration between the EU Horizon 2020 AtlantOS project and Agriculture and Agri-Food Canada, the Global Omics Observatory Network (GLOMICON) is federating long-term ecological observatories employing "omic" (e.g. metagenomcis, metatranscriptomics, metabolomics) techniques to assess biodiversity across scales. GLO...

We would like to present FAIR Research Data: Semantic Knowledge Graph Infrastructure for the Life Sciences (in short, FAIR.ReD), a project initiative that is currently being evaluated for funding. FAIR.ReD is a software environment for developing data management solutions according to the FAIR (Findable, Accessible, Interoperable, R eusable; Wilkin...

The Earth system is enduring multiple, interacting stressors causing immense and irreversible change to its biosphere. The unprecedented magnitude of human influence on the planet is a cause for much concern, but also an opportunity to mitigate undesirable impact by instituting socio-ecological management strategies and monitoring their effectivene...

Climate change, habitat destruction, and myriad other ecological stressors will impact us all and have already contributed to what is being labeled the sixth wave of extinction (Ceballos et al. 2015, Régnier et al. 2015). As a countering force, conservation biology strives to identify those areas of the planet most worthy of protecting due to their...

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...

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...

In the next decade the pressures on ocean systems and the communities that rely on them will increase along with impacts from the multiple stressors of climate change and human activities. Our ability to manage and sustain our oceans will depend on the data we collect and the information and knowledge derived from it. Much of the uptake of this kno...

Open tabular data published as part of the open government initiatives typically contain a spatial dimension, a temporal dimension and the actual numeric data capturing information such as health indicators, pollution readings, sanitation status etc. "Semantic Harmonisation" of numeric data entails linking numeric data columns with web-accessible s...

Bacteria play a crucial role in the marine carbon cycle, contributing to the production and degradation of organic carbon. Here, we investigated organic carbon pools, aggregate formation, and bacterioplankton communities in three contrasting oceanographic settings in the Galapagos Archipelago. We studied a submarine CO 2 vent at Roca Redonda (RoR),...

The construction of high capacity data sharing networks to support increasing government and commercial data exchange has highlighted a key roadblock: the content of existing Internet-connected information remains siloed due to a multiplicity of local languages and data dictionaries. This lack of a digital lingua franca is obvious in the domain of...

Essential Biodiversity Variables (EBV) are fundamental variables that can be used for assessing biodiversity change over time, for determining adherence to biodiversity policy, for monitoring progress towards sustainable development goals, and for tracking biodiversity responses to disturbances and management interventions. Data from observations o...

Evolving and Sustaining Oceans Best Practices Workshop; Paris, France, 15–17 November 2017

Fig. S1. Phylogenetic affiliation of ANME and partner bacteria clades within Methanomicrobia and Deltaproteobacteria. In the E20 enrichment ANME‐2c forms consortia with Seep‐SRB2, in the G37 enrichment ANME‐1 forms consortia with Seep‐SRB2, and in the G60 enrichment ANME‐1 forms consortia with HotSeep‐1. The phylogenetic trees are modified from Weg...

Table S2. Classification of metagenomic and metatranscriptomic 16S rRNA gene fragments on different phylogenetic levels.

Table S5. Single copy genes identified in ANME draft genomes.

Table S7. Draft genomes and expression data generated in this study.

Table S8. Overview of c‐type cytochromes encoded in the ANME and SRB draft genomes.

The sulfate-dependent, anaerobic oxidation of methane (AOM) is an important sink for methane in marine environments. It is carried out between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) living in syntrophic partnership. In this study, we compared the genomes, gene expression patterns and ultrastructures of three phy...

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...