scholarly journals Quantitative Distributions of Epsilonproteobacteria and a Sulfurimonas Subgroup in Pelagic Redoxclines of the Central Baltic Sea

2007 ◽  
Vol 73 (22) ◽  
pp. 7155-7161 ◽  
Author(s):  
Jana Grote ◽  
Matthias Labrenz ◽  
Birgit Pfeiffer ◽  
Günter Jost ◽  
Klaus Jürgens
Keyword(s):  
Baltic Sea ◽  
The Black Sea ◽  
Specific Gene ◽  
Gene Probe ◽  
Appl Environ ◽  
The Baltic ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
Total Bacteria

ABSTRACT Members of the class Epsilonproteobacteria are known to be of major importance in biogeochemical processes at oxic-anoxic interfaces. In pelagic redoxclines of the central Baltic Sea, an uncultured epsilonproteobacterium related to Sulfurimonas denitrificans was proposed to play a key role in chemolithotrophic denitrification (I. Brettar, M. Labrenz, S. Flavier, J. Bötel, H. Kuosa, R. Christen, and M. G. Höfle, Appl. Environ. Microbiol. 72:1364-1372, 2006). In order to determine the abundance, activity, and vertical distribution of this bacterium in high-resolution profiles, 16S rRNA cloning and catalyzed reporter deposition and fluorescence in situ hybridization (CARD-FISH) and quantitative PCR measurements were carried out. The results showed that 21% of the derived clone sequences, which in the present study were grouped together under the name GD17, had >99% similarity to the uncultured epsilonproteobacterium. A specific gene probe against GD17 (S-*-Sul-0090-a-A-18) was developed and used for enumeration by CARD-FISH. In different pelagic redoxclines sampled during August 2003, May 2005, and February 2006, GD17 cells were always detected from the lower oxic area to the sulfidic area. Maximal abundance was detected around the chemocline, where sulfide and nitrate concentrations were close to the detection limit. The highest GD17 numbers (2 × 105 cells ml−1), representing up to 15% of the total bacteria, were comparable to those reported for Epsilonproteobacteria in pelagic redoxclines of the Black Sea and the Cariaco Trench (X. Lin, S. G. Wakeham, I. F. Putnam, Y. M. Astor, M. I. Scranton, A. Y. Chistoserdov, and G. T. Taylor, Appl. Environ. Microbiol. 72:2679-2690, 2006). However, in the Baltic Sea redoxclines, Epsilonproteobacteria consisted nearly entirely of cells belonging to the distinct GD17 group. This suggested that GD17 was the best-adapted epsilonproteobacterium within this ecological niche.

scholarly journals Epsilonproteobacteria Represent the Major Portion of Chemoautotrophic Bacteria in Sulfidic Waters of Pelagic Redoxclines of the Baltic and Black Seas

2008 ◽  
Vol 74 (24) ◽  
pp. 7546-7551 ◽  
Author(s):  
Jana Grote ◽  
Günter Jost ◽  
Matthias Labrenz ◽  
Gerhard J. Herndl ◽  
Klaus Jürgens
Keyword(s):  
Baltic Sea ◽  
Black Sea ◽  
Total Cell ◽  
The Black Sea ◽  
Autotrophic Denitrification ◽  
The Baltic Sea ◽  
The Baltic ◽  
Catalyzed Reporter Deposition ◽  
Chemoautotrophic Bacteria

ABSTRACT Recent studies have indicated that chemoautotrophic Epsilonproteobacteria might play an important role, especially as anaerobic or microaerophilic dark CO2-fixing organisms, in marine pelagic redoxclines. However, knowledge of their distribution and abundance as actively CO2-fixing microorganisms in pelagic redoxclines is still deficient. We determined the contribution of Epsilonproteobacteria to dark CO2 fixation in the sulfidic areas of central Baltic Sea and Black Sea redoxclines by combining catalyzed reporter deposition-fluorescence in situ hybridization with microautoradiography using [14C]bicarbonate and compared it to the total prokaryotic chemoautotrophic activity. In absolute numbers, up to 3 × 105 14CO2-fixing prokaryotic cells ml−1 were enumerated in the redoxcline of the central Baltic Sea and up to 9 × 104 14CO2-fixing cells ml−1 were enumerated in the Black Sea redoxcline, corresponding to 29% and 12%, respectively, of total cell abundance. 14CO2-incorporating cells belonged exclusively to the domain Bacteria. Among these, members of the Epsilonproteobacteria were approximately 70% of the cells in the central Baltic Sea and up to 100% in the Black Sea. For the Baltic Sea, the Sulfurimonas subgroup GD17, previously assumed to be involved in autotrophic denitrification, was the most dominant CO2-fixing group. In conclusion, Epsilonproteobacteria were found to be mainly responsible for chemoautotrophic activity in the dark CO2 fixation maxima of the Black Sea and central Baltic Sea redoxclines. These Epsilonproteobacteria might be relevant in similar habitats of the world's oceans, where high dark CO2 fixation rates have been measured.

scholarly journals SUP05 Dominates the Gammaproteobacterial Sulfur Oxidizer Assemblages in Pelagic Redoxclines of the Central Baltic and Black Seas

2013 ◽  
Vol 79 (8) ◽  
pp. 2767-2776 ◽  
Author(s):  
Sabine Glaubitz ◽  
Katrin Kießlich ◽  
Christian Meeske ◽  
Matthias Labrenz ◽  
Klaus Jürgens
Keyword(s):  
Baltic Sea ◽  
Phylogenetic Analyses ◽  
The Black Sea ◽  
Rrna Gene ◽  
Gene Transcript ◽  
Oligonucleotide Probes ◽  
Bisphosphate Carboxylase ◽  
Prokaryotic Abundance ◽  
Card Fish

ABSTRACTGammaproteobacterial sulfur oxidizers (GSOs), particularly SUP05-related sequences, have been found worldwide in numerous oxygen-deficient marine environments. However, knowledge regarding their abundance, distribution, and ecological role is scarce. In this study, on the basis of phylogenetic analyses of 16S rRNA gene sequences originating from a Baltic Sea pelagic redoxcline, thein situabundances of different GSO subgroups were quantified by CARD-FISH (catalyzed reporter fluorescencein situhybridization) with oligonucleotide probes developed specifically for this purpose. Additionally, ribulose bisphosphate carboxylase/oxygenase form II (cbbM) gene transcript clone libraries were used to detect potential active chemolithoautotrophic GSOs in the Baltic Sea. Taken together, the results obtained by these two approaches demonstrated the existence of two major phylogenetic subclusters embedded within the GSO, one of them affiliated with sequences of the previously described SUP05 subgroup. CARD-FISH analyses revealed that only SUP05 occurred in relatively high numbers, reaching 10 to 30% of the total prokaryotes around the oxic-anoxic interface, where oxygen and sulfide concentrations are minimal. The applicability of the oligonucleotide probes was confirmed with samples from the Black Sea redoxcline, in which the SUP05 subgroup accounted for 10 to 13% of the total prokaryotic abundance. ThecbbMtranscripts presumably originating from SUP05 cells support previous evidence for the chemolithoautotrophic activity of this phylogenetic group. Our findings on the vertical distribution and high abundance of SUP05 suggest that this group plays an important role in marine redoxcline biogeochemistry, probably as anaerobic or aerobic sulfur oxidizers.

scholarly journals A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

2020 ◽  
Vol 8 (6) ◽  
pp. 936 ◽  
Author(s):  
Claudia Leoni ◽  
Mariateresa Volpicella ◽  
Bruno Fosso ◽  
Caterina Manzari ◽  
Elisabetta Piancone ◽  
...  
Keyword(s):  
Ecological Model ◽  
Salinity Range ◽  
Rrna Gene ◽  
Hypervariable Regions ◽  
Cell Counts ◽  
Precious Resource ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
The 16S Rrna Gene

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.

Catalyzed reporter deposition-fluorescent in situ hybridization (CARD-FISH) detection of Dehalococcoides

2008 ◽  
Vol 73 (2) ◽  
pp. 142-147 ◽  
Author(s):  
J.A. Dijk ◽  
P. Breugelmans ◽  
J. Philips ◽  
P.J. Haest ◽  
E. Smolders ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
Fish Detection ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

scholarly journals In-Situ Evaluation of the Protectivity of Coatings Applied to Metal Cultural Artefacts Using Non-Destructive Electrochemical Measurements

2021 ◽  
Vol 2 (1) ◽  
pp. 120-132
Author(s):  
Douglas J. Mills ◽  
Katarzyna Schaefer ◽  
Tomasz Wityk
Keyword(s):  
Baltic Sea ◽  
Electrochemical Noise ◽  
Organic Coating ◽  
Noise Measurement ◽  
The Baltic Sea ◽  
Coating Type ◽  
The Baltic ◽  
Non Destructive ◽  
Electrolytic Resistance

Electrochemical Noise Measurement (ENM) and DC electrolytic resistance measurement (ERM) can be used to assess the level of protectiveness provided by an organic coating (paint or varnish) to the underlying metal. These techniques also have applicability to the thinner, transparent type of coatings used to protect archaeological artefacts. Two studies are presented here demonstrating how ERM and ENM techniques can be applied in artefact preservation. The similarity of the techniques, both of which are a measure of resistance, means results can be considered to be analogous. The first study investigated the use of ERM to determine the protection levels provided by typical coatings in order to develop a database of coating type and application for objects, for specific environments. The second study used ENM to evaluate coatings which had been applied to historic artefacts recovered from shipwrecks in the Baltic Sea and displayed inside the museum or kept in the museum store area. The studies showed the usefulness of both techniques for determining the level of protection of a coating and how a better performing coating can be specified if a pre-existing coating on an artefact has been found to be unsuitable.

scholarly journals Characteristics of natural radiation background at the Callio Lab (Finland) performed within the BSUIN project

2020 ◽  
Author(s):  
Jan Kisiel ◽  
Kinga Polaczek-Grelik ◽  
Katarzyna Szkliniarz ◽  
Agata Walencik-Łata ◽  
Jari Joutsenvaara ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Gamma Ray ◽  
Background Radiation ◽  
Gamma Ray Spectrometry ◽  
Radiation Background ◽  
Rock Samples ◽  
Baltic Sea Region ◽  
Semiconductor Spectrometer ◽  
The Baltic

<p>The BSUIN (Baltic Sea Underground Innovation Network) aims to enhance the accessibility of the underground laboratories in the Baltic Sea region for innovation, business and science. One of the BSUIN project activities is characterization of natural background radiation (NBR) in underground facilities. In this talk results from NBR measurements performed in Callio Lab, Pyhäsalmi, Finland, at the depth of 4100 m w.e. will be presented. The in-situ gamma spectra were collected with the use of  HPGe semiconductor spectrometer, whereas the  concentration of radon were measured with RAD7 electronic detector. In addition, the water and rock samples were taken for laboratory analysis in Institute of Physics, University of Silesia, Poland. The concentration radioisotopes in water samples were performed by using a liquid scintillation α/β counter (LSC) and α-particle spectrometry, while the concentration of radioisotopes in rock samples were performed by using laboratory gamma ray spectrometry and also α-particle spectrometry.</p>

scholarly journals Evaluation of Sentinel-3A OLCI Products Derived Using the Case-2 Regional CoastColour Processor over the Baltic Sea

Sensors ◽  
2019 ◽  
Vol 19 (16) ◽  
pp. 3609 ◽  
Author(s):  
Kyryliuk ◽  
Kratzer
Keyword(s):  
Remote Sensing ◽  
Baltic Sea ◽  
Attenuation Coefficient ◽  
Secchi Depth ◽  
Local Algorithm ◽  
The Baltic Sea ◽  
In Situ Data ◽  
The Baltic ◽  
Level 2

In this study, the Level-2 products of the Ocean and Land Colour Instrument (OLCI) data on Sentinel-3A are derived using the Case-2 Regional CoastColour (C2RCC) processor for the SentiNel Application Platform (SNAP) whilst adjusting the specific scatter of Total Suspended Matter (TSM) for the Baltic Sea in order to improve TSM retrieval. The remote sensing product “kd_z90max” (i.e., the depth of the water column from which 90% of the water-leaving irradiance are derived) from C2RCC-SNAP showed a good correlation with in situ Secchi depth (SD). Additionally, a regional in-water algorithm was applied to derive SD from the attenuation coefficient Kd(489) using a local algorithm. Furthermore, a regional in-water relationship between particle scatter and bench turbidity was applied to generate turbidity from the remote sensing product “iop_bpart” (i.e., the scattering coefficient of marine particles at 443 nm). The spectral shape of the remote sensing reflectance (Rrs) data extracted from match-up stations was evaluated against reflectance data measured in situ by a tethered Attenuation Coefficient Sensor (TACCS) radiometer. The L2 products were evaluated against in situ data from several dedicated validation campaigns (2016–2018) in the NW Baltic proper. All derived L2 in-water products were statistically compared to in situ data and the results were also compared to results for MERIS validation from the literature and the current S3 Level-2 Water (L2W) standard processor from EUMETSAT. The Chl-a product showed a substantial improvement (MNB 21%, RMSE 88%, APD 96%, n = 27) compared to concentrations derived from the Medium Resolution Imaging Spectrometer (MERIS), with a strong underestimation of higher values. TSM performed within an error comparable to MERIS data with a mean normalized bias (MNB) 25%, root-mean square error (RMSE) 73%, average absolute percentage difference (APD) 63% n = 23). Coloured Dissolved Organic Matter (CDOM) absorption retrieval has also improved substantially when using the product “iop_adg” (i.e., the sum of organic detritus and Gelbstoff absorption at 443 nm) as a proxy (MNB 8%, RMSE 56%, APD 54%, n = 18). The local SD (MNB 6%, RMSE 62%, APD 60%, n = 35) and turbidity (MNB 3%, RMSE 35%, APD 34%, n = 29) algorithms showed very good agreement with in situ data. We recommend the use of the SNAP C2RCC with regionally adjusted TSM-specific scatter for water product retrieval as well as the regional turbidity algorithm for Baltic Sea monitoring. Besides documenting the evaluation of the C2RCC processor, this paper may also act as a handbook on the validation of Ocean Colour data.

scholarly journals Prokaryotic Dynamics in the Meromictic Coastal Lake Faro (Sicily, Italy)

Diversity ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 37 ◽  
Author(s):  
Carmela Raffa ◽  
Carmen Rizzo ◽  
Marc Strous ◽  
Emilio De Domenico ◽  
Marilena Sanfilippo ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
Mixing Conditions ◽  
Coastal Lake ◽  
The North ◽  
Ribosomal Intergenic Spacer ◽  
North Eastern ◽  
Clear Identification ◽  
Catalyzed Reporter Deposition ◽  
Card Fish

Lake Faro, in the North-Eastern corner of Sicily (Italy), shows the typical stratification of a meromictic tempered basin, with a clear identification of the mixolimnion and the monimolimnion, separated by an interfacial chemocline. In this study, an annual-scaled study on the space-time distribution of the microbial communities in water samples of Lake Faro was performed by both ARISA (Amplified Ribosomal Intergenic Spacer Analysis) and CARD-FISH (Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization) approaches. A correlation between microbial parameters and both environmental variables (i.e., temperature, pH, dissolved oxygen, redox potential, salinity, chlorophyll-a) and mixing conditions was highlighted, with an evident seasonal variability. The most significative differences were detected by ARISA between the mixolimnion and the monimolimnion, and between Spring and Autumn, by considering layer and season as a factor, respectively.

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