ORCID Profile
0000-0002-4366-3088
Current Organisation
Alfred Wegener Institute for Polar and Marine Research
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Copernicus GmbH
Date: 31-07-2023
Publisher: Oxford University Press (OUP)
Date: 28-12-2022
DOI: 10.1093/GIGASCIENCE/GIAD068
Abstract: Omic BON is a thematic Bio ersity Observation Network under the Group on Earth Observations Bio ersity 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 organizations and data and s le management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.
Publisher: Copernicus GmbH
Date: 31-07-2023
Abstract: Abstract. 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 essential ocean variables: dissolved oxygen, dissolved inorganic nutrients, inorganic carbon (pH, total alkalinity, dissolved inorganic carbon, and partial pressure of CO2), particulate matter, and dissolved organic carbon. The time-series used include a variety of temporal resolutions (monthly, seasonal, or irregular), time ranges (10 – 36 years), and bottom depths (80 – 6000 m), with the oldest s les dating back to 1983 and the most recent one corresponding to 2021. Besides having been harmonized into the same format (semantics, ancillary data, units), the data were subjected to a qualitative assessment in which the applied methods were evaluated and categorized. The most recently applied methods of the time-series programs usually follow the recommendations outlined by the Bermuda Time-Series Workshop report (Lorenzoni and Benway, 2013) which is used as the main reference for “biogeochemical best-practices”. However, measurements of dissolved oxygen and pH in particular, still show room for improvement. Additional data-quality descriptors include precision and accuracy estimates, indicators for data variability, and offsets compared to a reference and widely recognized data product for the global ocean: the “GLobal Ocean Data Analysis Project”. Generally, these descriptors indicate a high level of continuity in measurement quality within time-series programs and a good consistency with the GLobal Interior Ocean Carbon Data, even though robust comparisons to the latter are limited. The data are available as (i) a merged comma-separated file that is compliant with the World Ocean Circulation Experiment (WOCE) exchange format and ii) a format dependent on user queries via the ERDDAP server of the Global Ocean Observing System (GOOS). The pilot increases the data utility, findability, accessibility, interoperability, and reusability following the FAIR philosophy, enhancing the readiness of biogeochemical time-series. It facilitates a variety of applications that benefit from the collective value of biogeochemical time-series observations and forms the basis for a sustained time-series living data product, SPOTS, complementing relevant products for the global interior ocean carbon data (GLobal Ocean Data Analysis Project), global surface ocean carbon data (Surface Ocean CO2 Atlas SOCAT), and global interior and surface methane and nitrous oxide data (MarinE MethanE and NiTrous Oxide product). Aside from the actual data compilation, the pilot project produced suggestions for reporting metadata, implementing quality control measures, and making estimations about uncertainty. These recommendations aim at encouraging the community to adopt more consistent and uniform practices for analysis and reporting and at updating these practices regularly. The detailed recommendations, links to the original time-series programs, the original data, their documentation, and related efforts are available on the SPOTS website. This site also provides access to the data product (DOI: 10.26008/1912/bco-dmo.896862.1, Lange et al., 2023) and ancillary data.
Publisher: Copernicus GmbH
Date: 22-09-2023
Publisher: Elsevier BV
Date: 2019
Publisher: eLife Sciences Publications, Ltd
Date: 31-03-2022
DOI: 10.7554/ELIFE.67667
Abstract: 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 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its ersity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally erse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M 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.
Publisher: Wiley
Date: 11-11-2021
Abstract: 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 ersity and primary productivity change at finer spatial scales. Here, we s led the Atlantic Ocean from south to north (~50°S–50°N), every ~0.5° latitude. We conducted measurements of primary productivity, chlorophyll‐ a and relative abundance of 16S and 18S rRNA genes, alongside analyses of the physicochemical and hydrographic environment. We analysed the ersity of autotrophs, mixotrophs and heterotrophs, and noted distinct patterns among these guilds across provinces with high and low chlorophyll‐ a conditions. Eukaryotic autotrophs and prokaryotic heterotrophs showed a shared inter‐province ersity pattern, distinct from the ersity pattern shared by mixotrophs, cyanobacteria and eukaryotic heterotrophs. Additionally, we calculated s lewise productivity‐specific length scales, the potential horizontal displacement of microbial communities by surface currents to an intrinsic biological rate (here, specific primary productivity). This scale provides key context for our trophically disaggregated ersity analysis that we could relate to underlying oceanographic features. We integrate this element to provide more nuanced insights into the mosaic‐like nature of microbial provincialism, linking ersity patterns to oceanographic transport through primary production.
Publisher: Pensoft Publishers
Date: 03-10-2023
Publisher: Frontiers Media SA
Date: 18-10-2019
Publisher: Frontiers Media SA
Date: 09-2019
Publisher: Frontiers Media SA
Date: 23-07-2019
Publisher: Frontiers Media SA
Date: 28-02-2019
Publisher: Frontiers Media SA
Date: 17-07-2019
Publisher: PeerJ
Date: 03-12-2018
DOI: 10.7717/PEERJ.5984
Abstract: 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), an upwelling site at Bolivar Channel (BoC) subjected to a weak El Niño event at the time of s ling in October 2014, as well as a site without volcanic or upwelling influence at Cowley Islet (CoI). We recorded physico-chemical parameters, and quantified particulate and dissolved organic carbon, transparent exopolymeric particles, and the potential of the water to form larger marine aggregates. Free-living and particle-attached bacterial communities were assessed via 16S rRNA gene sequencing. Both RoR and BoC exhibited temperatures elevated by 1–1.5 °C compared to CoI. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools at each of the three sites, with highest dissolved organic carbon concentrations at BoC and RoR, and highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton communities at BoC were dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter , known to thrive in phytoplankton blooms, as opposed to oligotrophic taxa dominating at CoI, such as members of the SAR11 clade. Therefore, we propose that bacterial communities were mainly influenced by the availability of organic carbon at the investigated sites. Our study provides a comprehensive characterization of organic carbon pools and bacterioplankton communities, highlighting the high heterogeneity of various components of the marine carbon cycle around the Galapagos Archipelago.
Publisher: Cold Spring Harbor Laboratory
Date: 07-2020
DOI: 10.1101/2020.06.30.180448
Abstract: 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 propose a conceptual framework and a computational workflow that bridge the known-unknown gap in genomes and metagenomes. We showcase our approach by exploring 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 ersity, and its relevance across multiple biomes. Furthermore, we provide a collection of 283,874 lineage-specific genes of unknown function for Cand . Patescibacteria, being 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.
Location: Brazil
Location: Germany
Location: Germany
Location: Germany
Location: Germany
Location: No location found
No related grants have been discovered for Pier Luigi Buttigieg.