Efficiency and specificity of CARD‐FISH probes in detection of marine vibrios

2021 ◽  
Author(s):  
Elixabet Ogayar ◽  
Irene Larrañaga ◽  
Ana Lomba ◽  
Vladimir R. Kaberdin ◽  
Inés Arana ◽  
...  
Keyword(s):  
Marine Vibrios ◽  
Card Fish

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 Marine vibrios isolated from water along the dutch coast

1975 ◽  
Vol 9 (3-4) ◽  
pp. 351-364 ◽  
Author(s):  
Carol Golten ◽  
W.A. Scheffers
Keyword(s):  
Dutch Coast ◽  
Marine Vibrios

Evaluation of enzymatic cell treatments for application of CARD-FISH to methanogens

2008 ◽  
Vol 72 (1) ◽  
pp. 54-59 ◽  
Author(s):  
Kengo Kubota ◽  
Hiroyuki Imachi ◽  
Shuji Kawakami ◽  
Kohei Nakamura ◽  
Hideki Harada ◽  
...  
Keyword(s):  
Card Fish

Inhibition of filtration in bivalves by marine vibrios

Aquaculture ◽  
1987 ◽  
Vol 67 (1-2) ◽  
pp. 247-248 ◽  
Author(s):  
T.H Birkbeck ◽  
J.G McHenery ◽  
A.S Nottage
Keyword(s):  
Marine Vibrios

scholarly journals Biochemical characteristics and bacterial community structure of the sea surface microlayer in the South Pacific Ocean

2007 ◽  
Vol 4 (4) ◽  
pp. 2809-2844 ◽  
Author(s):  
I. Obernosterer ◽  
P. Catala ◽  
R. Lami ◽  
J. Caparros ◽  
J. Ras ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Pacific Ocean ◽  
Organic Carbon ◽  
South Pacific ◽  
Leucine Incorporation ◽  
Surface Microlayer ◽  
South Pacific Ocean ◽  
Subsurface Waters ◽  
Card Fish

Abstract. The chemical and biological characteristics of the surface microlayer were determined during a transect across the South Pacific Ocean in October-December 2004. Concentrations of particulate organic carbon (1.3 to 7.6-fold) and nitrogen (1.4 to 7), and POC:PON ratios were consistently higher in the surface microlayer as compared to subsurface waters (5 m). The large variability in particulate organic matter enrichment was negatively correlated to wind speed. No enhanced concentrations of dissolved organic carbon were detectable in the surface microlayer as compared to 5 m, but chromophoric dissolved organic matter was markedly enriched (by 2 to 4-fold) at all sites. Based on pigment analysis and cell counts, no consistent enrichment of any of the major components of the autotrophic and heterotrophic microbial community was detectable. CE-SSCP fingerprints and CARD FISH revealed that the bacterial communities present in the surface microlayer had close similarity (>76%) to those in subsurface waters. By contrast, bacterial heterotrophic production (3H-leucine incorporation) was consistently lower in the surface microlayer than in subsurface waters. By applying CARD-FISH and microautoradiography, we observed that Bacteroidetes and Gammaproteobacteria dominated leucine uptake in the surface microlayer, while in subsurface waters Bacteroidetes and Alphaproteobacteria were the major groups accounting for leucine incorporation. Our results demonstrate that the microbial community in the surface microlayer closely resembles that of the surface waters of the open ocean. However, even short time periods in the surface microlayer result in differences in bacterial groups accounting for leucine incorporation, probably as a response to the differences in the physical and chemical nature of the two layers.

scholarly journals Adaptation of Microbial Communities to Environmental Arsenic and Selection of Arsenite-Oxidizing Bacteria From Contaminated Groundwaters

2021 ◽  
Vol 12 ◽  
Author(s):  
Sarah Zecchin ◽  
Simona Crognale ◽  
Patrizia Zaccheo ◽  
Stefano Fazi ◽  
Stefano Amalfitano ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Inorganic Arsenic ◽  
16S Rrna Gene Sequencing ◽  
Northern Italy ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Main Driver ◽  
Rrna Gene Sequencing ◽  
Arsenite Oxidizing Bacteria ◽  
Card Fish

Arsenic mobilization in groundwater systems is driven by a variety of functionally diverse microorganisms and complex interconnections between different physicochemical factors. In order to unravel this great ecosystem complexity, groundwaters with varying background concentrations and speciation of arsenic were considered in the Po Plain (Northern Italy), one of the most populated areas in Europe affected by metalloid contamination. High-throughput Illumina 16S rRNA gene sequencing, CARD-FISH and enrichment of arsenic-transforming consortia showed that among the analyzed groundwaters, diverse microbial communities were present, both in terms of diversity and functionality. Oxidized inorganic arsenic [arsenite, As(III)] was the main driver that shaped each community. Several uncharacterized members of the genus Pseudomonas, putatively involved in metalloid transformation, were revealed in situ in the most contaminated samples. With a cultivation approach, arsenic metabolisms potentially active at the site were evidenced. In chemolithoautotrophic conditions, As(III) oxidation rate linearly correlated to As(III) concentration measured at the parental sites, suggesting that local As(III) concentration was a relevant factor that selected for As(III)-oxidizing bacterial populations. In view of the exploitation of these As(III)-oxidizing consortia in biotechnology-based arsenic bioremediation actions, these results suggest that contaminated aquifers in Northern Italy host unexplored microbial populations that provide essential ecosystem services.

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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