Best practice data standards for discrete chemical oceanographic observations

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Jiang, L.-Q., Pierrot, D., Wanninkhof, R., Feely, R. A., Tilbrook, B., Alin, S., Barbero, L., Byrne, R. H., Carter, B. R., Dickson, A. G., Gattuso, J.-P., Greeley, D., Hoppema, M., Humphreys, M. P., Karstensen, J., Lange, N., Lauvset, S. K., Lewis, E. R., Olsen, A., Pérez, F. F., Sabine, C., Sharp, J. D., Tanhua, T., Trull, T. W., Velo, A., Allegra, A. J., Barker, P., Burger, E., Cai, W-J., Chen, C-T. A., Cross, J., Garcia, H., Hernandez-Ayon J. M., Hu, X., Kozyr, A., Langdon, C., Lee., K, Salisbury, J., Wang, Z. A., & Xue, L. Best practice data standards for discrete chemical oceanographic observations. Frontiers in Marine Science, 8, (2022): 705638, https://doi.org/10.3389/fmars.2021.705638.Effective data management plays a key role in oceanographic research as cruise-based data, collected from different laboratories and expeditions, are commonly compiled to investigate regional to global oceanographic processes. Here we describe new and updated best practice data standards for discrete chemical oceanographic observations, specifically those dealing with column header abbreviations, quality control flags, missing value indicators, and standardized calculation of certain properties. These data standards have been developed with the goals of improving the current practices of the scientific community and promoting their international usage. These guidelines are intended to standardize data files for data sharing and submission into permanent archives. They will facilitate future quality control and synthesis efforts and lead to better data interpretation. In turn, this will promote research in ocean biogeochemistry, such as studies of carbon cycling and ocean acidification, on regional to global scales. These best practice standards are not mandatory. Agencies, institutes, universities, or research vessels can continue using different data standards if it is important for them to maintain historical consistency. However, it is hoped that they will be adopted as widely as possible to facilitate consistency and to achieve the goals stated above.Funding for L-QJ and AK was from NOAA Ocean Acidification Program (OAP, Project ID: 21047) and NOAA National Centers for Environmental Information (NCEI) through NOAA grant NA19NES4320002 [Cooperative Institute for Satellite Earth System Studies (CISESS)] at the University of Maryland/ESSIC. BT was in part supported by the Australia’s Integrated Marine Observing System (IMOS), enabled through the National Collaborative Research Infrastructure Strategy (NCRIS). AD was supported in part by the United States National Science Foundation. AV and FP were supported by BOCATS2 Project (PID2019-104279GB-C21/AEI/10.13039/501100011033) funded by the Spanish Research Agency and contributing to WATER:iOS CSIC interdisciplinary thematic platform. MH was partly funded by the European Union’s Horizon 2020 Research and Innovation Program under grant agreement N°821001 (SO-CHIC)

Atlantic Ocean CO2 uptake reduced by weakening of the meridional overturning circulation

7 páginas, 4 figuras.-- Proyecto CarbochangeUptake of atmospheric carbon dioxide in the subpolar North Atlantic Ocean declined rapidly between 1990 and 2006. This reduction in carbon dioxide uptake was related to warming at the sea surface, which—according to model simulations—coincided with a reduction in the Atlantic meridional overturning circulation. The extent to which the slowdown of this circulation system—which transports warm surface waters to the northern high latitudes, and cool deep waters south—contributed to the reduction in carbon uptake has remained uncertain. Here, we use data on the oceanic transport of volume, heat and carbon dioxide to track carbon dioxide uptake in the subtropical and subpolar regions of the North Atlantic Ocean over the past two decades. We separate anthropogenic carbon from natural carbon by assuming that the latter corresponds to a pre-industrial atmosphere, whereas the remaining is anthropogenic. We find that the uptake of anthropogenic carbon dioxide—released by human activities—occurred almost exclusively in the subtropical gyre. In contrast, natural carbon dioxide uptake—which results from natural Earth system processes—dominated in the subpolar gyre. We attribute the weakening of contemporary carbon dioxide uptake in the subpolar North Atlantic to a reduction in the natural component. We show that the slowdown of the meridional overturning circulation was largely responsible for the reduction in carbon uptake, through a reduction of oceanic heat loss to the atmosphere, and for the concomitant decline in anthropogenic CO2 storage in subpolar waters.This work was supported by the Spanish Ministry of Sciences and Innovation and co-funded by the Fondo Europeo de Desarrollo Regional 2007 2012 (FEDER) through the CATARINA project (CTM2010-17141) and through EU FP7 project CARBOCHANGE `Changes in carbon uptake and emissions by oceans in a changing climate', which received funding from the European Commission's seventh Framework Programme EU under grant agreement no. 264879. The OVIDE research projectPeer reviewe

Mitochondrial phylogeography of European pond turtles (Emys orbicularis, Emys trinacris) - an update

Based on more than 1100 samples of Emys orbicularis and E. trinacris, data on mtDNA diversity and distribution of haplotypes are provided, including for the first time data for Armenia, Georgia, Iran, and the Volga, Ural and Turgay River Basins of Russia and Kazakhstan. Eight mitochondrial lineages comprising 51 individual haplotypes occur in E. orbicularis, a ninth lineage with five haplotypes corresponds to E. trinacris. A high diversity of distinct mtDNA lineages and haplotypes occurs in the south, in the regions where putative glacial refuges were located. More northerly parts of Europe and adjacent Asia, which were recolonized by E. orbicularis in the Holocene, display distinctly less variation; most refuges did not contribute to northern recolonizations. Also in certain southern European lineages a decrease of haplotype diversity is observed with increasing latitude, suggestive of Holocene range expansions on a smaller scale.nul

Mitochondrial phylogeography of European pond turtles (Emys orbicularis, Emys trinacris) - an update

Based on more than 1100 samples of Emys orbicularis and E. trinacris, data on mtDNA diversity and distribution of haplotypes are provided, including for the first time data for Armenia, Georgia, Iran, and the Volga, Ural and Turgay River Basins of Russia and Kazakhstan. Eight mitochondrial lineages comprising 51 individual haplotypes occur in E. orbicularis, a ninth lineage with five haplotypes corresponds to E. trinacris. A high diversity of distinct mtDNA lineages and haplotypes occurs in the south, in the regions where putative glacial refuges were located. More northerly parts of Europe and adjacent Asia, which were recolonized by E. orbicularis in the Holocene, display distinctly less variation; most refuges did not contribute to northern recolonizations. Also in certain southern European lineages a decrease of haplotype diversity is observed with increasing latitude, suggestive of Holocene range expansions on a smaller scale.nul

There is no evidence for a temporal link between pathogen arrival and frog extinctions in North-Eastern Australia

Pathogen spread can cause population declines and even species extinctions. Nonetheless, in the absence of tailored\ud monitoring schemes, documenting pathogen spread can be difficult. In the case of worldwide amphibian declines the best\ud present understanding is that the chytrid fungus Batrachochytrium dendrobatidis (Bd) has recently spread, causing\ud amphibian declines and extinction in the process. However, good evidence demonstrating pathogen arrival followed by\ud amphibian decline is rare, and analysis of putative evidence is often inadequate. Here we attempt to examine the\ud relationship between Bd arrival and amphibian decline across north-eastern Australia, using sites where a wave-like pattern\ud of amphibian decline was first noticed and at which intensive research has since been conducted. We develop an analytical\ud framework that allows rigorous estimation of pathogen arrival date, which can then be used to test for a correlation\ud between the time of pathogen arrival and amphibian decline across sites. Our results show that, with the current dataset,\ud the earliest possible arrival date of Bd in north-eastern Australia is completely unresolved; Bd could have arrived\ud immediately before sampling commenced or may have arrived thousands of years earlier, the present data simply cannot\ud say. The currently available data are thus insufficient to assess the link between timing of pathogen arrival and population\ud decline in this part of the world. This data insufficiency is surprising given that there have been decades of research on\ud chytridiomycosis in Australia and that there is a general belief that the link between Bd arrival and population decline is well\ud resolved in this region. The lack of data on Bd arrival currently acts as a major impediment to determining the role of\ud environmental factors in driving the global amphibian declines, and should be a major focus of future research

Best Practice Data Standards for Discrete Chemical Oceanographic Observations

Effective data management plays a key role in oceanographic research as cruise-based data, collected from different laboratories and expeditions, are commonly compiled to investigate regional to global oceanographic processes. Here we describe new and updated best practice data standards for discrete chemical oceanographic observations, specifically those dealing with column header abbreviations, quality control flags, missing value indicators, and standardized calculation of certain properties. These data standards have been developed with the goals of improving the current practices of the scientific community and promoting their international usage. These guidelines are intended to standardize data files for data sharing and submission into permanent archives. They will facilitate future quality control and synthesis efforts and lead to better data interpretation. In turn, this will promote research in ocean biogeochemistry, such as studies of carbon cycling and ocean acidification, on regional to global scales. These best practice standards are not mandatory. Agencies, institutes, universities, or research vessels can continue using different data standards if it is important for them to maintain historical consistency. However, it is hoped that they will be adopted as widely as possible to facilitate consistency and to achieve the goals stated above