scholarly journals Distribution of bacterial populations in a stratified fjord (mariager fjord, denmark) quantified by in situ hybridization and related to chemical gradients in the water column

1996 ◽  
Vol 62 (10) ◽  
pp. 3914-3914
Author(s):  
N B Ramsing ◽  
H Fossing ◽  
T G Ferdelman ◽  
F Andersen ◽  
B Thamdrup
Keyword(s):  
In Situ Hybridization ◽  
Aluminum Oxide ◽  
Pore Size ◽  
Water Column ◽  
Bacterial Populations ◽  
Chemical Gradients

Volumn 62, no. 4, p. 1392, lines 37 and 38: "Aluminum oxide filters (0.2 mm pore size; Anopore; Millipore GmbH, Eschborn, Germany)" should read "Aluminum oxide filters (0.2 (mu)m pore size; Anopore; Whatman, Inc., Clifton, N.J.)." Page 1403, reference 15: "Fenchel, T." should read "Fenchel, T., L. D. Kristensen, and L. Rasmussen." [This corrects the article on p. 1391 in vol. 62.].

scholarly journals Distribution of bacterial populations in a stratified fjord (mariager fjord, denmark) quantified by in situ hybridization and related to chemical gradients in the water column

1996 ◽  
Vol 62 (10) ◽  
pp. 3915-3915
Author(s):  
N B Ramsing ◽  
H Fossing ◽  
T G Ferdelman ◽  
F Andersen ◽  
B Thamdrup
Keyword(s):  
In Situ Hybridization ◽  
Vertical Distribution ◽  
Water Column ◽  
Recent Article ◽  
Bacterial Populations ◽  
Chemical Gradients ◽  
The Vertical Distribution

Volume 62, no. 4, p. 1391-1404: after publication of this article, it was brought to the attention of the authors that a more extensive treatment of the hydrodynamics of Mariager Fjord and the vertical distribution of bacteria and protozoa therein was published in a recent article by Fenchel et al. This work contains important information about the studied ecosystem, but unfortunately, the existence of this work was realized only after publication of our article. Thus, the following reference should have been cited in our article: [This corrects the article on p. 1391 in vol. 62.].

Influence of phosphate and disinfection on the composition of biofilms produced from drinking water, as measured by fluorescence in situ hybridization

2003 ◽  
Vol 49 (12) ◽  
pp. 741-753 ◽  
Author(s):  
M Batté ◽  
L Mathieu ◽  
P Laurent ◽  
M Prévost
Keyword(s):  
Drinking Water ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Bacterial Populations ◽  
Health Related ◽  
Phosphate Treatment ◽  
The Stability ◽  
Eub338 Probe ◽  
Direct Counts

Biofilms were grown in annular reactors supplied with drinking water enriched with 235 µg C/L. Changes in the biofilms with ageing, disinfection, and phosphate treatment were monitored using fluorescence in situ hybridization. EUB338, BET42a, GAM42a, and ALF1b probes were used to target most bacteria and the alpha (α), beta (β), and gamma (γ) subclasses of Proteobacteria, respectively. The stability of biofilm composition was checked after the onset of colonization between T = 42 days and T = 113 days. From 56.0% to 75.9% of the cells detected through total direct counts with DAPI (4'-6-diamidino-2-phenylindole) were also detected with the EUB338 probe, which targets the 16S rRNA of most bacteria. Among these cells, 16.9%–24.7% were targeted with the BET42a probe, 1.8%–18.3% with the ALF1b probe, and <2.5% with the GAM42a probe. Phosphate treatment induced a significant enhancement to the proportion of γ-Proteobacteria (detected with the GAM42a probe), a group that contains many health-related bacteria. Disinfection with monochloramine for 1 month or chlorine for 3 days induced a reduction in the percentage of DAPI-stained cells that hybridized with the EUB338 probe (as expressed by percentages of EUB338 counts/DAPI) and with any of the ALF1b, BET42a, and GAM42a probes. The percentage of cells detected by any of the three probes (ALF1b+BET42a+GAM42a) tended to decrease, and reached in total less than 30% of the EUB338-hybridized cells. Disinfection with chlorine for 7 days induced a reverse shift; an increase in the percentage of EUB338 counts targeted by any of these three probes was noted, which reached up to 87%. However, it should be noted that the global bacterial densities (heterotrophic plate counts and total direct counts) tended to decrease over the duration of the experiment. Therefore, those bacteria that could be considered to resist 7 days of chlorination constituted a small part of the initial biofilm community, up to the point at which the other bacterial groups were destroyed by chlorination. The results suggest that there were variations in the kinetics of inactivation by disinfectant, depending on the bacterial populations involved.Key words: biofilm, phosphate, chlorine, monochloramine, FISH, drinking water.

Structure and function of nitrifying biofilms as determined by molecular techniques and the use of microelectrodes

2002 ◽  
Vol 46 (1-2) ◽  
pp. 233-241 ◽  
Author(s):  
S. Okabe ◽  
H. Naitoh ◽  
H. Satoh ◽  
Y. Watanabe
Keyword(s):  
In Situ Hybridization ◽  
Bacterial Community ◽  
Spatial Organization ◽  
Domestic Wastewater ◽  
Rotating Disk ◽  
Molecular Techniques ◽  
Bacterial Populations ◽  
Steady State Condition ◽  
Synthetic Media

The phylogenetic diversity of a nitrifying bacterial community of two types of nitrifying biofilms, a domestic wastewater biofilm and an autotrophic nitrifying biofilm grown on rotating disk reactors (RDR), was characterized by 16S ribosomal DNA (rDNA)-cloning analysis. Thereafter, successional development of nitrifying the bacterial community within both biofilms was visualized in situ by fluorescent in situ hybridization (FISH) with a set of fluorescently labeled 16S rRNA-targeted DNA probes. In situ hybridization revealed that Nitrosomonas ureae was the numerically dominant species of the ammonia-oxidizing population in the domestic wastewater biofilm and that a population shift from N. urea to N. europaea and N. eutropha occurred when the culture medium was switched to the synthetic media from the domestic wastewater. After reaching the steady-state condition, microprofiles of NH4+, NO2−, NO3−, and O2 in the biofilms were measured by use of microsensors, and the spatial distributions of in situ nitrifying activities were determined. The relationship between the spatial organization of nitrifying bacterial populations and the in situ activity of these populations within the biofilms was discussed. Microelectrode measurements revealed that the active ammonia-oxidizing zone was vertically separated from the active nitrite-oxidizing zone. This vertical separation became more evident with increase of the substrate C/N ratio, leading to deterioration of nitrification efficiency. The combined use of these techniques made it possible to relate in situ nitrifying activity directly to the occurrence of nitrifying bacterial populations.

Structure and function of nitrifying biofilms as determined by in situ hybridization and the use of microelectrodes

2000 ◽  
Vol 42 (12) ◽  
pp. 21-32 ◽  
Author(s):  
S. Okabe ◽  
Y. Watanabe
Keyword(s):  
In Situ Hybridization ◽  
Spatial Organization ◽  
Settling Tank ◽  
Outer Part ◽  
Domestic Wastewater ◽  
Nitrifying Bacteria ◽  
Ammonia Oxidizing Bacteria ◽  
Bacterial Populations ◽  
Nitrite Oxidizing Bacteria

Time dependent development of the spatial organization of NH4+- and NO2−-oxidizing bacterial populations in a domestic wastewater biofilm and in an autotrophic nitrifying biofilm were investigated by fluorescent in situ hybridization (FISH) with a set of 16S rRNA-targeted oligonucleotide probes. Population dynamics of nitrifying bacteria in the biofilms were correlated with the biofilm performance. In situ hybridization indicated that Nitrosomonas spp. (excluding probe NEU stained NH4+-oxidizing bacteria: i.e., N. marina-lineage, N. europaea-lineage, N. eutropha, and N. halophila) and Nitrospira-like bacteria were the numerically dominant nitrifying species in the domestic wastewater biofilm. However, probe NEU stained NH4+-inoxidizing bacteria became dominant populations in the autotrophic nitrifying biofilm (which were initially cultured with the primary settling tank effluent) after switching to the synthetic media. This population shift might be attributed to the effect of NO2−-–N accumulation and higher growth rates of N. europaea-lineage and N. eutropha, outcompeting other Nitrosomonas spp. in the synthetic medium. This evidence indirectly supports that N. europhaea has been most commonly isolated and studied in most of the previous researches. For the spatial organization of NH4+- and NO2−-oxidizing bacterial populations, bacteria of the genus Nitrobacter could not be detected, instead Nitrospira-like bacteria were found as the main nitrite-oxidizing bacteria in both biofilms. Whereas most of the ammonia-oxidizing bacteria were found throughout the biofilms, the location of nitrite-oxidizing bacteria was restricted to the active nitrite-oxidizing zone, which was detected in the inner part of the biofilms. Microelectrode measurements showed that the active ammonia-oxidizing zone was located in the outer part of a biofilm, whereas the active nitrite-oxidizing zone was located just below the ammonia-oxidizing zone and overlapped the location of NO2−-oxidizing bacteria, as determined with FISH. These observations have considerable significance to our understanding of microbial nitrification occurring in wastewater treatment processes and in the natural environment.

scholarly journals Flow Sorting of Marine Bacterioplankton after Fluorescence In Situ Hybridization

2004 ◽  
Vol 70 (10) ◽  
pp. 6210-6219 ◽  
Author(s):  
Raju Sekar ◽  
Bernhard M. Fuchs ◽  
Rudolf Amann ◽  
Jakob Pernthaler
Keyword(s):  
Flow Cytometry ◽  
In Situ Hybridization ◽  
Rrna Gene ◽  
Fluorescent Reporter ◽  
Bacterial Populations ◽  
Flow Sorting ◽  
Powerful Approach ◽  
Card Fish ◽  
Sequence Types

ABSTRACT We describe an approach to sort cells from coastal North Sea bacterioplankton by flow cytometry after in situ hybridization with rRNA-targeted horseradish peroxidase-labeled oligonucleotide probes and catalyzed fluorescent reporter deposition (CARD-FISH). In a sample from spring 2003 >90% of the cells were detected by CARD-FISH with a bacterial probe (EUB338). Approximately 30% of the microbial assemblage was affiliated with the Cytophaga-Flavobacterium lineage of the Bacteroidetes (CFB group) (probe CF319a), and almost 10% was targeted by a probe for the β-proteobacteria (probe BET42a). A protocol was optimized to detach cells hybridized with EUB338, BET42a, and CF319a from membrane filters (recovery rate, 70%) and to sort the cells by flow cytometry. The purity of sorted cells was >95%. 16S rRNA gene clone libraries were constructed from hybridized and sorted cells (S-EUB, S-BET, and S-CF libraries) and from unhybridized and unsorted cells (UNHYB library). Sequences related to the CFB group were significantly more frequent in the S-CF library (66%) than in the UNHYB library (13%). No enrichment of β-proteobacterial sequence types was found in the S-BET library, but novel sequences related to Nitrosospira were found exclusively in this library. These bacteria, together with members of marine clade OM43, represented >90% of the β-proteobacteria in the water sample, as determined by CARD-FISH with specific probes. This illustrates that a combination of CARD-FISH and flow sorting might be a powerful approach to study the diversity and potentially the activity and the genomes of different bacterial populations in aquatic habitats.

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