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

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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Spreading of brine in the Puck Bay in view of in-situ measurements

E3S Web of Conferences ◽

10.1051/e3sconf/20185400029 ◽

2018 ◽

Vol 54 ◽

pp. 00029

Author(s):

Małgorzata Robakiewicz

Keyword(s):

Coastal Waters ◽

Near Field ◽

Mixing Conditions ◽

The North ◽

North Eastern ◽

Using Data ◽

Under Construction ◽

North Eastern Part ◽

Puck Bay

Since autumn of 2010 in the north-eastern part of Poland underground gas stores are under construction by diluting salt deposits. A by-product of the technology applied is brine, which is discharged into the coastal waters of the Puck Bay (south Baltic Sea). In the pre-investment study a theoretical analysis of the mixing conditions in the near-field and far-field of the proposed installation was conducted. An extensive monitoring programme carried out since 2010 shows a good mixing of brine with the surrounding waters. Excess salinity due to the continuous discharge of brine estimated using data measured in situ is generally lower than permitted, i.e. not exceeding 0.5 psu in the near-field of installation.

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Combining Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization and Microautoradiography To Detect Substrate Utilization by Bacteria and Archaea in the Deep Ocean

Applied and Environmental Microbiology ◽

10.1128/aem.70.7.4411-4414.2004 ◽

2004 ◽

Vol 70 (7) ◽

pp. 4411-4414 ◽

Cited By ~ 234

Author(s):

Eva Teira ◽

Thomas Reinthaler ◽

Annelie Pernthaler ◽

Jakob Pernthaler ◽

Gerhard J. Herndl

Keyword(s):

North Atlantic ◽

Deep Ocean ◽

Proteinase K ◽

Detection Rates ◽

The North ◽

Deep Waters ◽

The North Atlantic ◽

Catalyzed Reporter Deposition ◽

Card Fish

ABSTRACT The recently developed CARD-FISH protocol was refined for the detection of marine Archaea by replacing the lysozyme permeabilization treatment with proteinase K. This modification resulted in about twofold-higher detection rates for Archaea in deep waters. Using this method in combination with microautoradiography, we found that Archaea are more abundant than Bacteria (42% versus 32% of 4′,6′-diamidino-2-phenylindole counts) in the deep waters of the North Atlantic and that a larger fraction of Archaea than of Bacteria takes up l-aspartic acid (19% versus 10%).

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

Microorganisms ◽

10.3390/microorganisms8060936 ◽

2020 ◽

Vol 8 (6) ◽

pp. 936 ◽

Cited By ~ 2

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.

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

Journal of Microbiological Methods ◽

10.1016/j.mimet.2008.01.012 ◽

2008 ◽

Vol 73 (2) ◽

pp. 142-147 ◽

Cited By ~ 15

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

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Spatial separation of ribosomes and DNA in Asgard archaeal cells

The ISME Journal ◽

10.1038/s41396-021-01098-3 ◽

2021 ◽

Cited By ~ 1

Author(s):

Burak Avcı ◽

Jakob Brandt ◽

Dikla Nachmias ◽

Natalie Elia ◽

Mads Albertsen ◽

...

Keyword(s):

Super Resolution ◽

Spatial Separation ◽

Eukaryotic Cell ◽

Catalyzed Reporter Deposition ◽

Card Fish ◽

Open Question ◽

Super Resolution Microscopy ◽

Rrna Sequences ◽

Genomic Material

AbstractThe origin of the eukaryotic cell is a major open question in biology. Asgard archaea are the closest known prokaryotic relatives of eukaryotes, and their genomes encode various eukaryotic signature proteins, indicating some elements of cellular complexity prior to the emergence of the first eukaryotic cell. Yet, microscopic evidence to demonstrate the cellular structure of uncultivated Asgard archaea in the environment is thus far lacking. We used primer-free sequencing to retrieve 715 almost full-length Loki- and Heimdallarchaeota 16S rRNA sequences and designed novel oligonucleotide probes to visualize their cells in marine sediments (Aarhus Bay, Denmark) using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Super-resolution microscopy revealed 1–2 µm large, coccoid cells, sometimes occurring as aggregates. Remarkably, the DNA staining was spatially separated from ribosome-originated FISH signals by 50–280 nm. This suggests that the genomic material is condensed and spatially distinct in a particular location and could indicate compartmentalization or membrane invagination in Asgard archaeal cells.

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Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition (CARD-FISH)

mSphere ◽

10.1128/msphere.00686-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Michaela M. Salcher ◽

Adrian-Ştefan Andrei ◽

Paul-Adrian Bulzu ◽

Zsolt G. Keresztes ◽

Horia L. Banciu ◽

...

Keyword(s):

Phylogenetic Diversity ◽

Cellular Morphology ◽

Epifluorescence Microscopy ◽

Environmental Distribution ◽

Sediment Samples ◽

Visual Evidence ◽

Cell Shapes ◽

Catalyzed Reporter Deposition ◽

Card Fish

ABSTRACT Metagenome-assembled genomes (MAGs) of Asgardarchaeota have been recovered from a variety of habitats, broadening their environmental distribution and providing access to the genetic makeup of this archaeal lineage. The recent success in cultivating the first representative of Lokiarchaeia was a breakthrough in science at large and gave rise to new hypotheses about the evolution of eukaryotes. Despite their singular phylogenetic position at the base of the eukaryotic tree of life, the morphology of these bewildering organisms remains a mystery, except for the report of an unusual morphology with long, branching protrusions of the cultivated Lokiarchaeion strain “Candidatus Prometheoarchaeum syntrophicum” MK-D1. In order to visualize this elusive group, we applied a combination of fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed CARD-FISH probes for Heimdallarchaeia and Lokiarchaeia lineages, and provide the first visual evidence for Heimdallarchaeia and new images of a lineage of Lokiarchaeia that is different from the cultured representative. Here, we show that while Heimdallarchaeia are characterized by a uniform cellular morphology typified by a centralized DNA localization, Lokiarchaeia display a plethora of shapes and sizes that likely reflect their broad phylogenetic diversity and ecological distribution. IMPORTANCE Asgardarchaeota are considered to be the closest relatives to modern eukaryotes. These enigmatic microbes have been mainly studied using metagenome-assembled genomes (MAGs). Only very recently, a first member of Lokiarchaeia was isolated and characterized in detail; it featured a striking morphology with long, branching protrusions. In order to visualize additional members of the phylum Asgardarchaeota, we applied a fluorescence in situ hybridization technique and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed probes for Heimdallarchaeia and Lokiarchaeia lineages. We provide the first visual evidence for Heimdallarchaeia that are characterized by a uniform cellular morphology typified by an apparently centralized DNA localization. Further, we provide new images of a lineage of Lokiarchaeia that is different from the cultured representative and with multiple morphologies, ranging from small ovoid cells to long filaments. This diversity in observed cell shapes is likely owing to the large phylogenetic diversity within Asgardarchaeota, the vast majority of which remain uncultured.

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Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean

Applied and Environmental Microbiology ◽

10.1128/aem.71.5.2303-2309.2005 ◽

2005 ◽

Vol 71 (5) ◽

pp. 2303-2309 ◽

Cited By ~ 391

Author(s):

Gerhard J. Herndl ◽

Thomas Reinthaler ◽

Eva Teira ◽

Hendrik van Aken ◽

Cornelius Veth ◽

...

Keyword(s):

North Atlantic ◽

Inorganic Carbon ◽

Sea Water ◽

Current System ◽

Deep Ocean ◽

Leucine Incorporation ◽

Lower Growth ◽

The North ◽

Catalyzed Reporter Deposition ◽

Card Fish

ABSTRACT Fluorescence in situ hybridization (FISH) in combination with polynucleotide probes revealed that the two major groups of planktonic Archaea (Crenarchaeota and Euryarchaeota) exhibit a different distribution pattern in the water column of the Pacific subtropical gyre and in the Antarctic Circumpolar Current system. While Euryarchaeota were found to be more dominant in nearsurface waters, Crenarchaeota were relatively more abundant in the mesopelagic and bathypelagic waters. We determined the abundance of archaea in the mesopelagic and bathypelagic North Atlantic along a south-north transect of more than 4,000 km. Using an improved catalyzed reporter deposition-FISH (CARD-FISH) method and specific oligonucleotide probes, we found that archaea were consistently more abundant than bacteria below a 100-m depth. Combining microautoradiography with CARD-FISH revealed a high fraction of metabolically active cells in the deep ocean. Even at a 3,000-m depth, about 16% of the bacteria were taking up leucine. The percentage of Euryarchaeota and Crenarchaeaota taking up leucine did not follow a specific trend, with depths ranging from 6 to 35% and 3 to 18%, respectively. The fraction of Crenarchaeota taking up inorganic carbon increased with depth, while Euryarchaeota taking up inorganic carbon decreased from 200 m to 3,000 m in depth. The ability of archaea to take up inorganic carbon was used as a proxy to estimate archaeal cell production and to compare this archaeal production with total prokaryotic production measured via leucine incorporation. We estimate that archaeal production in the mesopelagic and bathypelagic North Atlantic contributes between 13 to 27% to the total prokaryotic production in the oxygen minimum layer and 41 to 84% in the Labrador Sea Water, declining to 10 to 20% in the North Atlantic Deep Water. Thus, planktonic archaea are actively growing in the dark ocean although at lower growth rates than bacteria and might play a significant role in the oceanic carbon cycle.

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Quantification of Target Molecules Needed To Detect Microorganisms by Fluorescence In Situ Hybridization (FISH) and Catalyzed Reporter Deposition-FISH

Applied and Environmental Microbiology ◽

10.1128/aem.00208-08 ◽

2008 ◽

Vol 74 (16) ◽

pp. 5068-5077 ◽

Cited By ~ 87

Author(s):

Tatsuhiko Hoshino ◽

L. Safak Yilmaz ◽

Daniel R. Noguera ◽

Holger Daims ◽

Michael Wagner

Keyword(s):

In Situ Hybridization ◽

16S Rrna ◽

Activated Sludge ◽

Fluorescence In Situ Hybridization ◽

Oligonucleotide Probes ◽

Pure Cultures ◽

Technical Modifications ◽

Catalyzed Reporter Deposition ◽

Card Fish

ABSTRACT Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a method that is widely used to detect and quantify microorganisms in environmental samples and medical specimens by fluorescence microscopy. Difficulties with FISH arise if the rRNA content of the probe target organisms is low, causing dim fluorescence signals that are not detectable against the background fluorescence. This limitation is ameliorated by technical modifications such as catalyzed reporter deposition (CARD)-FISH, but the minimal numbers of rRNA copies needed to obtain a visible signal of a microbial cell after FISH or CARD-FISH have not been determined previously. In this study, a novel competitive FISH approach was developed and used to determine, based on a thermodynamic model of probe competition, the numbers of 16S rRNA copies per cell required to detect bacteria by FISH and CARD-FISH with oligonucleotide probes in mixed pure cultures and in activated sludge. The detection limits of conventional FISH with Cy3-labeled probe EUB338-I were found to be 370 ± 45 16S rRNA molecules per cell for Escherichia coli hybridized on glass microscope slides and 1,400 ± 170 16S rRNA copies per E. coli cell in activated sludge. For CARD-FISH the values ranged from 8.9 ± 1.5 to 14 ± 2 and from 36 ± 6 to 54 ± 7 16S rRNA molecules per cell, respectively, indicating that the sensitivity of CARD-FISH was 26- to 41-fold higher than that of conventional FISH. These results suggest that optimized FISH protocols using oligonucleotide probes could be suitable for more recent applications of FISH (for example, to detect mRNA in situ in microbial cells).

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Catalyzed Reporter Deposition- Fluorescence In Situ Hybridization (CARD-FISH) and Abundance of Cycloclasticus

Handbook of Hydrocarbon and Lipid Microbiology ◽

10.1007/978-3-540-77587-4_318 ◽

2010 ◽

pp. 4085-4092

Author(s):

E. Teira

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Catalyzed Reporter Deposition ◽

Card Fish

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Coastal Sea Level Change from in the North Eastern Atlantic

10.5194/egusphere-egu2020-19345 ◽

2020 ◽

Author(s):

Luciana Fenoglio-Marc ◽

Bernd Uebbing ◽

Jürgen Kusche ◽

Salvatore Dinardo

Keyword(s):

Time Series ◽

Sea Level ◽

Sea Level Change ◽

Altimeter Data ◽

Level Change ◽

The North ◽

North Eastern ◽

Coastal Sea

A significant part of the World population lives in the coastal zone, which is affected by coastal sea level rise and extreme events. Our hypothesis is that the most accurate sea level height measurements are derived from the&#160;Synthetic Aperture Altimetry (SAR) mode. This study analyses the output of dedicated processing and assesses their impacts on the sea level change of the North-Eastern Atlantic.&#160;It will be shown that SAR altimetry reduces the minimum usable distance from five to three kilometres when the dedicated coastal retrackers SAMOSA+ and SAMOSA++ are applied to data processed in SAR mode. A similar performance is achieved with altimeter data processed in pseudo low resolution mode (PLRM) when the Spatio-Temporal Altimeter sub-waveform Retracker (STAR) is used. Instead the Adaptive Leading Edge Sub-waveform retracker (TALES) applied to PLRM is less performant.&#160;SAR processed altimetry can recover the sea level heights with 4 cm accuracy up to 3-4 km distance to coast. Thanks to the low noise of SAR mode data, the instantaneous SAR and in-situ data have the highest agreement, with the smallest standard deviation of differences and the highest correlation.&#160;A co-location of the altimeter data near the tide gauge is the best choice for merging in-situ and altimeter data. The r.m.s. (root mean squared) differences between altimetry and in-situ heights remain large in estuaries and in coastal zone with high tidal regimes, which are still challenging regions.&#160;The geophysical parameters derived from CryoSat-2 and Sentinel-3A measurements have similar accuracy, but the different repeat cycle of the two missions locally affects the constructed time-series.The impact of these new SAR observations in climate change studies is assessed by evaluating regional and local time series of sea level. At distances to coast smaller than 10 Kilometers the sea level change derived from SAR and LRM data is in good agreement. The long-term sea level variability derived from monthly time-series of LRM altimetry and of land motion-corrected tide gauges agrees within 1 mm/yr for half of in-situ German stations.&#160;The long-term sea level variability derived from SAR data show a similar behaviour with increasing length of the time series.&#160;

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