Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Empirical leucine-to-carbon conversion factors in north-eastern Atlantic waters (50-2000 m) shaped by bacterial community composition and optical signature of DOM.

ABSTRACT: Microbial heterotrophic activity is a major process regulating the flux of dissolved organic matter (DOM) in the ocean, while the characteristics of this DOM strongly influence its microbial utilization and fate in the ocean. In order to broaden the vertical resolution of leucine-to-carbon conversion factors (CFs), needed for converting substrate incorporation into biomass production by heterotrophic bacteria, 20 dilution experiments were performed in the North Atlantic Ocean. We found a depth-stratification in empirical CFs values from epipelagic to bathypelagic waters (4.00 ± 1.09 to 0.10 ± 0.00 kg C mol Leu^-1). Our results demonstrated that the customarily used theoretical CF of 1.55 kg C mol Leu^-1 in oceanic samples can lead to an underestimation of prokaryotic heterotrophic production in epi- and mesopelagic waters, while it can overestimate it in the bathypelagic ocean. Pearson correlations showed that CFs were related not only to hydrographic variables such as temperature, but also to specific phylogenetic groups and DOM quality and quantity indices. Furthermore, a multiple linear regression model predicting CFs from relatively simple hydrographic and optical spectroscopic measurements was attempted. Taken together, our results suggest that differences in CFs throughout the water column are significantly connected to DOM, and also reflect differences linked to specific prokaryotic groups.

SUBMITTER: Orta-Ponce CP

PROVIDER: S-EPMC8692456 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Nitrogen fixation and nitrogenase (nifH) expression in tropical waters of the eastern North Atlantic.

Project description:Expression of nifH in 28 surface water samples collected during fall 2007 from six stations in the vicinity of the Cape Verde Islands (north-east Atlantic) was examined using reverse transcription-polymerase chain reaction (RT-PCR)-based clone libraries and quantitative RT-PCR (RT-qPCR) analysis of seven diazotrophic phylotypes. Biological nitrogen fixation (BNF) rates and nutrient concentrations were determined for these stations, which were selected based on a range in surface chlorophyll concentrations to target a gradient of primary productivity. BNF rates greater than 6?nmolN?l(-1)?h(-1) were measured at two of the near-shore stations where high concentrations of Fe and PO(4)(3-) were also measured. Six hundred and five nifH transcripts were amplified by RT-PCR, of which 76% are described by six operational taxonomic units, including Trichodesmium and the uncultivated UCYN-A, and four non-cyanobacterial diazotrophs that clustered with uncultivated Proteobacteria. Although all five cyanobacterial phylotypes quantified in RT-qPCR assays were detected at different stations in this study, UCYN-A contributed most significantly to the pool of nifH transcripts in both coastal and oligotrophic waters. A comparison of results from RT-PCR clone libraries and RT-qPCR indicated that a ?-proteobacterial phylotype was preferentially amplified in clone libraries, which underscores the need to use caution interpreting clone-library-based nifH studies, especially when considering the importance of uncultivated proteobacterial diazotrophs.

| S-EPMC3146282 | biostudies-literature

Microbial methanol uptake in northeast Atlantic waters.

Project description:Methanol is the predominant oxygenated volatile organic compound in the troposphere, where it can significantly influence the oxidising capacity of the atmosphere. However, we do not understand which processes control oceanic concentrations, and hence, whether the oceans are a source or a sink to the atmosphere. We report the first methanol loss rates in seawater by demonstrating that (14)C-labelled methanol can be used to determine microbial uptake into particulate biomass, and oxidation to (14)CO(2). We have found that methanol is used predominantly as a microbial energy source, but also demonstrated its use as a carbon source. We report biological methanol oxidation rates between 2.1 and 8.4 nmol l(-1) day(-1) in surface seawater of the northeast Atlantic. Kinetic experiments predict a V(max) of up to 29 nmol l(-1) day(-1), with a high affinity K(m) constant of 9.3 nM in more productive coastal waters. We report surface concentrations of methanol in the western English channel of 97±8 nM (n=4) between May and June 2010, and for the wider temperate North Atlantic waters of 70±13 nM (n=6). The biological turnover time of methanol has been estimated between 7 and 33 days, although kinetic experiments suggest a 7-day turnover in more productive shelf waters. Methanol uptake rates into microbial particles significantly correlated with bacterial and phytoplankton parameters, suggesting that it could be used as a carbon source by some bacteria and possibly some mixotrophic eukaryotes. Our results provide the first methanol loss rates from seawater, which will improve the understanding of the global methanol budget.

| S-EPMC3105731 | biostudies-other

+50 Years of Terrestrial Hydroclimatic Variability in Africa's Transboundary Waters.

Project description:GRACE Terrestrial Water Storage (TWS) provides unique and unprecedented perspectives about freshwater availability and change globally. However, GRACE-TWS records are relatively short for long-term hydroclimatic variability studies, dating back to April 2002. In this paper, we made use of Noah Land Surface Model (LSM), and El Niño-Southern Oscillation (ENSO) data in an autoregressive model with exogenous variables (ARX) to reconstruct a 66-year record of TWS for nine major transboundary river basins (TRBs) in Africa. Model performance was evaluated using standard indicators, including the Nash Sutcliffe Efficiency criteria, cumulative density frequency, standardized residuals plots, and model uncertainty bounds. Temporally, the reconstruction results were evaluated for trend, cycles, and mode of variability against ancillary data from the WaterGAP Model (WGHM-TWS) and GPCC-based precipitation anomalies. The temporal pattern reveals good agreement between the reconstructed TWS, WGHM-TWS, and GPCC, (p-value?<?0.0001). The reconstructed TWS suggests a significant declining trend across the northern and central TRBs since 1951, while the southern basins show an insignificant trend. The mode of variability analysis indicates short storage periodicity of four to sixteen-month in the northern basins, while strong intra-annual variability in the central and southern basins. The long-term TWS records provide additional support to Africa's water resources research on hydroclimatic variability and change in shared transboundary water basins.

| S-EPMC6707189 | biostudies-literature

Caligus madeirensis sp. nov. (Copepoda: Caligidae) Parasitic on Pompano, Trachinotus ovatus (Linnaeus, 1758), from Eastern Atlantic Waters, Surrounding the Madeira Archipelago, Portugal

Project description:Introduction A new species of the genus Caligus is described based on specimens collected from pompano, Trachinotus ovatus (Linnaeus), caught in eastern Atlantic waters, near the Madeira archipelago. Methods Pompano (n?=?21) were purchased from the local fish market and examined for parasitic copepods. Morphological features of the copepods were examined and drawn using an Olympus BX51 equipped with a drawing tube. Key diagnostic characters were scanned using a confocal laser scanning microscope and a scanning electron microscope. Results Caligus madeirensis sp. nov., can be distinguished from all congeners (270 spp.) by the combination of the following characters: (i) an accessory process on the 3 outer terminal spines located on the distal exopodal segment of leg 1, (ii) a mandible with 14 teeth, (iii) a sternal furca with parallel, spatulate tines, (iv) a maxilliped with 2 simple setae at base of a claw, (v) a leg 3 with second endopodal segment with 5 pinnate setae, (vi) a 2-segmented leg 4 exopod with I; III spine formula, (vii) a male antenna with 4 overlapping plates on the distal segment, (viii) a male maxilliped corpus bearing a prominent myxal process ornamented with dense corrugations along inner margin. Conclusion Together with Caligus madeirensis sp. nov., the Caligus fauna of Portugal consists of 13 species reported from 17 Portuguese marine fishes. Considering the large number of marine fish species (510 spp.) currently recorded from Portuguese waters it seems that only 3.3% of the Portuguese marine fishes have been found to be infested with species of the genus Caligus O.F. Müller, 1758, the result of which, however, might be due to limited sampling. Electronic supplementary material The online version of this article (10.1007/s11686-020-00290-3) contains supplementary material, which is available to authorized users.

| S-EPMC7526516 | biostudies-literature

Endoparasitic Insights of Free-Living Fin (Balaenoptera physalus), Humpback (Megaptera novaeangliae) and North Atlantic Right Whales (Eubalaena glacialis) from Eastern Canadian Waters.

Project description:PurposeTo date, little is still known on parasite infections affecting free-living large whale populations worldwide. Data presented should be considered as a baseline study for future monitoring surveys on endoparasites affecting whales, thereby enhancing investigations on impacts of zoonotic parasitoses not only on vulnerable or endangered baleen whale population health but also on public health.MethodsThe presented study is a first report on gastrointestinal parasites infecting different free-living baleen whales inhabiting East Canadian waters using non-invasive methods. Individual faecal samples from fin (n = 3; Balaenoptera physalus), humpback (n = 4; Megaptera novaeangliae) and North Atlantic right whales (n = 1; Eubalaena glacialis) were collected without animal disturbance, within their natural habitats on an ecological expedition during annual surveys in summer 2017. Faecal samples were assessed by standardized diagnostic methods, such as sodium acetate acetic formalin (SAF) technique, carbol fuchsin-stained faecal smears, Giardia/Cryptosporidium coproantigen ELISAs and were applied for further identification.ResultsParasitological infections included three different potentially zoonotic parasite species, one protozoa (Entamoeba spp.) and two metazoans (Diphyllobothriidae gen. sp., Ascaridida indet.). No positive Giardia/Cryptosporidium coproantigen ELISA could be found in the studied whales.ConclusionThis study adds to the current knowledge of intestinal and zoonotic parasite infections of vulnerable to partly endangered free-ranging baleen whales. Only few or no parasitological studies exist for these whale species, usually dealing with only one dead specimen. We call for more research in this field especially for the importance of conservation of free-living marine mammals using non-invasive methods.

| S-EPMC8166656 | biostudies-literature

Hydrocarbon-Degrading Bacteria Found Tightly Associated with the 50-70 ?m Cell-Size Population of Eukaryotic Phytoplankton in Surface Waters of a Northeast Atlantic Region.

Project description:The surface of marine eukaryotic phytoplankton can harbour communities of hydrocarbon-degrading bacteria; however, this algal-bacterial association has, hitherto, been only examined with non-axenic laboratory cultures of micro-algae. In this study, we isolated an operationally-defined community of phytoplankton, of cell size 50-70 ?m, from a natural community in sea surface waters of a subarctic region in the northeast Atlantic. Using MiSeq 16S rRNA sequencing, we identified several recognized (Alcanivorax, Marinobacter, Oleispira, Porticoccus, Thalassospira) and putative hydrocarbon degraders (Colwelliaceae, Vibrionaceae) tightly associated with the phytoplankton population. We combined fluorescence in situ hybridisation with flow-cytometry (FISH-Flow) to examine the association of Marinobacter with this natural eukaryotic phytoplankton population. About 1.5% of the phytoplankton population contained tightly associated Marinobacter. The remaining Marinobacter population were loosely associated with either eukaryotic phytoplankton cells or non-chlorophyll particulate material. This work is the first to show the presence of obligate, generalist and putative hydrocarbonoclastic bacteria associated with natural populations of eukaryotic phytoplankton directly from sea surface water samples. It also highlights the suitability of FISH-Flow for future studies to examine the spatial and temporal structure and dynamics of these and other algal-bacterial associations in natural seawater samples.

| S-EPMC7763645 | biostudies-literature

Return of naturally sourced Pb to Atlantic surface waters.

Project description:Anthropogenic emissions completely overwhelmed natural marine lead (Pb) sources during the past century, predominantly due to leaded petrol usage. Here, based on Pb isotope measurements, we reassess the importance of natural and anthropogenic Pb sources to the tropical North Atlantic following the nearly complete global cessation of leaded petrol use. Significant proportions of up to 30-50% of natural Pb, derived from mineral dust, are observed in Atlantic surface waters, reflecting the success of the global effort to reduce anthropogenic Pb emissions. The observation of mineral dust derived Pb in surface waters is governed by the elevated atmospheric mineral dust concentration of the North African dust plume and the dominance of dry deposition for the atmospheric aerosol flux to surface waters. Given these specific regional conditions, emissions from anthropogenic activities will remain the dominant global marine Pb source, even in the absence of leaded petrol combustion.

| S-EPMC5052796 | biostudies-literature

Phytoplankton communities in Eastern Mediterranean coastal waters

Project description:Nitrate-enrichment structures phytoplankton communities in the shallow eastern Mediterranean coastal waters

| PRJEB40572 | ENA

Incidence of Hepatocellular Carcinoma in All 50 United States, From 2000 Through 2012.

Project description:Background & aimsThe incidence and mortality of hepatocellular carcinoma (HCC) have been reported to be plateauing in the United States. The United States has large racial, ethnic, and regional variation; we collected data from all 50 states to better analyze changes in HCC incidence in the entire United States.MethodsWe collected data from the US Cancer Statistics registry, which covers 97% of the population, and calculated adjusted incidence rates. We assessed annual trends among sociodemographic and geographic subgroups using joinpoint analysis.ResultsHCC incidence increased from 4.4/100,000 in 2000 to 6.7/100,000 in 2012, increasing by 4.5% (95% confidence interval [CI], 4.3%-4.7%) annually between 2000 and 2009, but only by 0.7% annually (95% CI, -0.2% to 1.6%) from 2010 through 2012. The average annual percentage change (AAPC) between 2000 and 2012 was higher in men (increase, 3.7%) than in women (increase, 2.7%), and highest in 55- to 59-year-old individuals (AAPC, 8.9%; 95% CI, 7.1%-10.7%) and 60- to 64-year-old individuals (AAPC, 6.4%; 95% CI, 4.7%-8.2%). By 2012, rates in Hispanics surpassed those in Asians, and rates in Texas surpassed those in Hawaii (9.71/100,000 vs 9.68/100,000). Geographic variation within individual race and ethnic groups was observed, but rates were highest in all major race and ethnic groups in Texas.ConclusionsIn an analysis of the incidence of HCC in all 50 US states, we found the rate of increase in HCC to have slowed from 2010 through 2012. However, incidence is increasing in subgroups such as men ages 55 to 64 years old-especially those born in the peak era of hepatitis C virus infection and among whites/Caucasians. Rates in Hispanics have surpassed those in Asian Americans. We observed geographic differences, with Texas having the highest age-adjusted HCC rates nationwide.

| S-EPMC5346030 | biostudies-literature

Bryozoans are Major Modern Builders of South Atlantic Oddly Shaped Reefs.

Project description:In major modern reef regions, either in the Indo-Pacific or the Caribbean, scleractinian corals are described as the main reef framework builders, often associated with crustose coralline algae. We used underwater cores to investigate Late Holocene reef growth and characterise the main framework builders in the Abrolhos Shelf, the largest and richest modern tropical reef complex in the South Western Atlantic, a scientifically underexplored reef province. Rather than a typical coralgal reef, our results show a complex framework building system dominated by bryozoans. Bryozoans were major components in all cores and age intervals (2,000 yrs BP), accounting for up to 44% of the reef framework, while crustose coralline algae and coral accounted for less than 28 and 23%, respectively. Reef accretion rates varied from 2.7 to 0.9 mm yr-1, which are similar to typical coralgal reefs. Bryozoan functional groups encompassed 20 taxa and Celleporaria atlantica (Busk, 1884) dominated the framework at all cores. While the prevalent mesotrophic conditions may have driven suspension-feeders' dominance over photoautotrophs and mixotrophs, we propose that a combination of historical factors with the low storm-disturbance regime of the tropical South Atlantic also contributed to the region's low diversity, and underlies the unique mushroom shape of the Abrolhos pinnacles.

| S-EPMC6018419 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data