The presence of methanogenic bacteria was assessed in peat and soil cores taken from upland moors. The sampling area was largely covered by blanket bog peat together with small areas of red-brown limestone and peaty gley. A 30-cm-deep core of each soil type was taken, and DNA was extracted from 5-cm transverse sections. Purified DNA was subjected to PCR amplification with primers 1Af and 1100Ar, which specifically amplify 1.1 kb of the archaeal 16S rRNA gene, and ME1 and ME2, which were designed to amplify a 0.75-kb region of the ␣-subunit gene for methyl coenzyme M reductase (MCR). Amplification with both primer pairs was obtained only with DNA extracted from the two deepest sections of the blanket bog peat core. This is consistent with the notion that anaerobiosis is required for activity and survival of the methanogen population. PCR products from both amplifications were cloned, and the resulting transformants were screened with specific oligonucleotide probes internal to the MCR or archaeal 16S rRNA PCR product. Plasmid DNA was extracted from probe-positive clones of both types and the insert was sequenced. The DNA sequences of 8 MCR clones were identical, as were those of 16 of the 17 16S rRNA clones. One clone showed marked variation from the remainder in specific regions of the sequence. From a comparison of these two different 16S rRNA sequences, an oligonucleotide was synthesized that was 100% homologous to a sequence region of the first 16 clones but had six mismatches with the variant. This probe was used to screen primary populations of PCR clones, and all of those that were probe negative were checked for the presence of inserts, which were then sequenced. By using this strategy, further novel methanogen 16S rRNA variants were identified and analyzed. The sequences recovered from the peat formed two clusters on the end of long branches within the methanogen radiation that are distinct from each other. These cannot be placed directly with sequences from any cultured taxa for which sequence information is available.

The ability of a flow cytometer to rapidly assess microbial viability was investigated using three vital stains: rhodamine 123 (Rh123); 3,3'-dihexyloxacarbocyanine iodide [DiOC6(3)] and fluorescein diacetate (FDA). Rh123 was found to clearly differentiate viable from non-viable bacteria. The methodology for staining bacteria with this dye was optimised. Rh123 was shown to stain and discriminate several different species of viable bacteria although this was not universal. Viable cells of Bacillus subtilis were found to stain better with FDA than with Rh123. The results demonstrate the ability of flow cytometry to rapidly detect and estimate the viability of bacterial populations.

It is demonstrated using reflection anisotropy spectroscopy that the adsorption of cytosine and cytidine -monophosphate at the Au(110) 1 x 2/electrolyte interface gives rise to ordered structures in which the base is oriented vertical to the surface and parallel to the [110] axis of the Au(110) plane.

The ability of flow cytometry (FCM) to detect viable bacteria after staining with a range of fluorogenic esters was investigated with several bacterial species. The dyes studied were the fluorescein diacetate (FDA) derivatives carboxyfluorescein diacetate, 2′,7′‐bis‐(2‐carboxyethyl)‐5(6)‐carboxyfluorescein acetoxymethyl ester and calcein acetoxymethyl ester, as well as ChemChrome B, a commercially‐available stain for the detection of viable bacteria in suspension. No one dye was found to be universal but ChemChrome B dye stained the widest number of Gram‐positive and Gram‐negative species, whereas the FDA derivatives preferentially stained Gram‐positive bacteria. The use of ChemChrome B to detect viable bacteria in environmental samples was investigated further by studying the survival of Klebsiella pneumoniae in lakewater. During survival studies, a higher number of viable bacteria were detected both by direct viable counts and FCM after staining with rhodamine 123 and ChemChrome B than by colony‐forming units, suggesting the presence of viable but nonculturable cells. These results demonstrate the potential use of FCM to enumerate viable bacteria in natural waters.

Reflection anisotropy spectroscopy (RAS) has been used to show that at saturation coverage adenine adsorbs on the Au(110)/electrolyte interface in a base-stacking configuration with the plane of the bases orientated vertically on the surface and with the long axis of the molecules parallel to the [110] direction. Changes in the RAS observed from adsorbed adenine as a result of changes in the potential applied to the Au(110) electrode could arise from slight changes in the orientation of the molecules in the vertical plane.

Recent trends in flow cytometry have established new techniques in bacteriology. Advances in fluorescent dye technology complement these improvements, offering probes for a variety of cellular functions. Bacterial ecology requires the application of new techniques to help answer questions unanswerable by traditional methods alone. Here we review some aspects of how coupling the two technologies has enabled researchers to directly study individual bacterial cells, and revealed the complexity and heterogeneity present in both laboratory cultures and in environmental samples. Results are discussed with respect to viability analysis, stress induced changes, specific cell detection and cell sorting. © 1996 Wiley‐Liss, Inc.

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The effect of short-chain fatty acids (SCFAs) on the contractile activity and fluid output of the large bowel of the rat was studied using an isolated segment of cecum and colon, mounted in vitro. The rate of contractile activity per minute in the proximal, mid, and distal regions of the colon was depressed by luminal infusion of associated SCFAs either as a mixture (acetic, propionic, and butyric) or individually (100 mM/pH = 4.1, in each case). Dose responses were observed for the individual fatty acids, with the 100 mM solutions eliciting a more prominent reduction in colonic motor activity than that induced by 10 mM. Neither the Na salt of the fatty acids nor an acidified Krebs solution (pH = 4.1) inhibited contractile activity or fluid output. No reduction in the rate of contractile activity was observed in the cecum with any test solutions, except 100 mM butyric acid. The data suggest that SCFAs inhibit smooth muscle contractility and resultant fluid transit.