Use of substrate responsive-direct viable counts to visualize naphthalene degrading bacteria in a coal tar-contaminated groundwater microbial community

Combination of Direct Viable Count and Fluorescent In Situ Hybridization (DVC-FISH) as a Potential Method for Identifying Viable Vibrio parahaemolyticus in Oysters and Mussels

Vibrio parahaemolyticus is a human food-borne pathogen with the ability to enter the food chain. It is able to acquire a viable, non-cultivable state (VBNC), which is not detected by traditional methods. The combination of the direct viable count method and a fluorescent in situ hybridization technique (DVC-FISH) makes it possible to detect microorganisms that can present VBNC forms in complex samples The optimization of the in vitro DVC-FISH technique for V. parahaemolyticus was carried out. The selected antibiotic was ciprofloxacin at a concentration of 0.75 μg/mL with an incubation time in DVC broth of 5 h. The DVC-FISH technique and the traditional plate culture were applied to detect and quantify the viable cells of the affected pathogen in artificially contaminated food matrices at different temperatures. The results obtained showed that low temperatures produced an important logarithmic decrease of V. parahaemolyticus, while at 22 °C, it proliferated rapidly. The DVC-FISH technique proved to be a useful tool for the detection and quantification of V. parahaemolyticus in the two seafood matrices of oysters and mussels. This is the first study in which this technique has been developed to detect viable cells for this microorganism.

Direct viable count combined with fluorescence in situ hybridization (DVC-FISH) for specific enumeration of viable escherichia coli in cow manure

A direct viable count procedure combined with fluorescence in situ hybridization (DVC-FISH) was developed for the specific detection and enumeration of viable Escherichia coli in cow manure. The DVC method was performed by trapping bacterial cells, extracted from cow manure samples, onto Nucleopore filters followed by incubation on a DVC medium containing yeast extract and four gyrase inhibitors. E. coli cells were identified by using the probe ES445. The DVC method efficiently promoted the elongation of E. coli cells and allowed for the recognition of individual cell division events, by observing microcolonies. Cell recovery by DVC-FISH together with bacterial extraction, was 53% with an inoculum of 10(7) to 10(10) cells g(-1) dry weight, when the manure samples were inoculated with a fresh culture of E. coli and determinations were made immediately. An examination of the survival of E. coli in a cow manure microcosm showed that an increasing fraction of E. coli became non-culturable but were still detectable by DVC-FISH. All these results suggest that DVC-FISH is useful for enumerating viable, even non-culturable, E. coli in cow manure.

Isolation of functional single cells from environments using a micromanipulator: application to study denitrifying bacteria

We developed a novel method to isolate functionally active single cells from environmental samples and named it the functional single-cell (FSC) isolation method. This method is based on a combination of substrate-responsive direct viable counts, live-cell staining with 5-carboxyfluorescein diacetate acetoxymethyl ester, and micromanipulation followed by cultivation in a medium. To evaluate this method, we applied it to study a denitrifying community in rice paddy soil. Similar denitrifier counts were obtained by the conventional most probable number analysis and our FSC isolation method. Using the FSC isolation method, 37 denitrifying bacteria were isolated, some of which harbored copper-containing nitrite reductase gene (nirK). The 16S rRNA gene analysis showed that members belonging to the genera Azospirillum and Ochrobactrum may be the major denitrifiers in the rice paddy soil. These results indicate that the FSC isolation method is a useful tool to obtain functionally active single cells from environmental samples.

In-situ enumeration and probing of pyrene-degrading soil bacteria

Inferences about which microorganisms degrade polycyclic aromatic hydrocarbons in contaminated soils have largely been obtained using culture-based techniques, despite the low percentage of microorganisms in soil that are believed to be culturable. We used a substrate-responsive direct viable count method to identify and quantify potential polycyclic aromatic hydrocarbon-degrading bacteria in a soil containing petroleum wastes. Bacteria were extracted and their response to substrates determined in the presence of DNA gyrase inhibitors, which cause viable and active cells to elongate. When yeast extract, a widely used carbon source, was added as a growth substrate, together with nalidixic acid, piromidic acid and ciprofloxacin, a significant increase in elongated cells to 47%, 37% and 22%, respectively, was observed within 24 h. With pyrene as the main substrate, 10 mg L(-1) of nalidixic acid or piromidic acid caused 18-22% and 8-12%, respectively, of the cells to elongate within 24 h; whereas the effect of 0.5 mg L(-1) ciprofloxacin was not significant until 53 h later. Enlarged cells were identified and enumerated by fluorescent in situ hybridization, using Alpha-, Beta- and Gammaproteobacteria, and domain Bacteria-specific probes. The Bacteria-specific probe detected 35-71% of the total microorganisms detected by the DNA-binding dye 4,6-diamidino-2-phenylindole. Initially, 44%, 13% and 5% of the total bacteria in the soil extract were Alpha-, Beta- and Gammaproteobacteria, respectively. Without pyrene or a gyrase inhibitor, these subgroups decreased to 30% of the total population but were predominant with piromidic acid or unchanged with ciprofloxacin when pyrene was the main substrate. The proportion of elongated Alpha- and Betaproteobacteria (potential pyrene degraders) increased significantly (P<0.05). This approach links phylogenetic information with physiological function in situ without the conventional cultivation of bacteria and can be used to probe and enumerate degradative groups at even a finer level of discrimination.

Detection in coal tar waste-contaminated groundwater of mRNA transcripts related to naphthalene dioxygenase by fluorescent in situ hybridization with tyramide signal amplification

The ideal ecological metabolic activity assay would be applied to naturally occurring microbial populations immediately fixed in the field, and the assay would focus upon intracellular parameters indicative of a dynamic biogeochemical process. In this study, fluorescent in situ hybridization (FISH) with tyramide signal amplification (TSA) detected intracellular mRNA in bacteria. Detection sensitivity was enhanced by using a Hamamatsu color chilled CCD camera and extended exposure times. Pseudomonas putida NCIB 9816-4, a model naphthalene degrading bacterium, was used to refine the protocol. Probe Ac627BR was developed for detecting naphthalene dioxygenase (nahAc) mRNA transcripts. Only induced cells showed positive hybridization to probe Ac627BR. Results were verified by RNase A or DNase I digestion of samples prior to hybridization. When applied to field-fixed groundwater samples, the naphthalene dioxygenase mRNA probe conferred fluorescence on a subset (approximately 1%) of the cells present in the contaminated groundwater. This methodology represents progress towards achieving one of the longstanding goals of environmental microbiology: to simultaneously ascertain the identity, activity, and biogeochemical impact of individual microorganisms in situ-in soil, water, or sediment where they dwell.

Further biogeochemical characterization of a trichloroethene-contaminated fractured dolomite aquifer: electron source and microbial communities involved in reductive dechlorination

A recent article presented geochemical and microbial evidence establishing metabolic adaptation to and in-situ reductive dechlorination of trichloroethene (TCE) in a fractured dolomite aquifer. This study was designed to further explore site conditions and microbial populations and to explain previously reported enhancement of reductive dechlorination by the addition of pulverized dolomite to laboratory microcosms. A survey of groundwater geochemical parameters (chlorinated ethenes, ethene, H2, CH4, DIC, DOC, and delta13C values for CH4, DIC, and DOC) indicated that in situ reductive dechlorination was ongoing and that an unidentified pool of organic carbon was contributing, likely via microbial respiration, to the large and relatively light on-site DIC pool. Petroleum hydrocarbons associated with the dolomite rock were analyzed by GC/MS and featured a characteristically low delta13C value. Straight chain hydrocarbons were extracted from the dolomite previously found to stimulate reductive dechlorination; these were particularly depleted in hexadecane (HD). Thus, we hypothesized that HD and related hydrocarbons might be anaerobically respired and serve both as the source of on-site DIC and support reductive dechlorination of TCE. Microcosms amended with pulverized dolomite demonstrated reductive dechlorination, whereas a combusted dolomite amendment did not. HD-amended microcosms were also inactive. Therefore, the stimulatory factor in the pulverized dolomite was heat labile, but that component was not HD. Amplified Ribosomal DNA Restriction Analysis (ARDRA) of the microbial populations in well waters indicated that a relatively low diversity, sulfur-transforming community outside the plume was shifted toward a high diversity community including Dehalococcoides ethenogenes-type microorganisms inside the zone of contamination. These observations illustrate biogeochemical intricacies of in situ reductive dechlorination reactions.