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The structure of archael community of the rumen is discussed. One of the results concluded that most of rumen archaea use hydrogen and formate as their energy sources.

An assay based on transcription-mediated amplification (TMA) technology is used for quantitative Enterococcus fecal indicator bacteria in environmental water samples. The results have shown sensitive and rapid detection and quantitation of Enterococcus bacteria when compared to the results with the growth-based methods.

A culture-independent multiplex real-time reverse transcriptase-PCR (RT-PCR) protocol for the simultaneous quantification of all four subgroups of [F.sup.+]-specific RNA coliphages using novel primer sets and molecular beacons is presented.

Wells designated as groundwater under the direct influence (GUDI) of surface water have caused an ongoing boil‐water advisory afflicting the island of Tutuila, American Samoa for almost a decade. Regulatory testing at these wells found turbidity and indicator bacteria spikes correlated with heavy rainfall events. However, the mechanism of this contamination has, until now, remained unknown. Surface water may reach wells through improperly sealed well casings, or through the aquifer matrix itself. In this study, three independent surface water tracers, turbidity, indicator bacteria, and water isotopes were used to assess recharge timing and determine contamination mechanisms. Results from each method were reasonably consistent, revealing average GUDI well breakthrough times of 37 ± 21 h for turbidity, 18 to 63 h for bacteria, and 1 to 5 days for water isotopes. These times match well with estimated subsurface flow rates through highly permeable aquifer materials. In contrast, where one well casing was found to be compromised, turbidity breakthrough was observed at 3 to 4 h. These results support local management decisions and show repairing or replacing wells will likely result in continued GUDI contamination. Additionally, differences in observed rainfall response for each tracer provide insight into the recharge dynamics and subsurface flow characteristics of this and other highly conductive young‐basaltic aquifers. [ABSTRACT FROM AUTHOR]

It is well documented that microbial contamination of coastal waters poses a significant risk to human health through recreational exposure and consumption of shellfish. Identifying the source of microbial contamination (microbial source tracking) plays a dominant role in enabling effective management and remediation strategies. One method used to determine the source of the contamination is quantification of the ratio of the four subgroups of F+-specific RNA coliphages (family Leviviridae) in impacted water samples. Because of typically low concentrations in the environment, enrichment assays are performed prior to detection, even though differential replication rates have been reported. These assays are also compromised by differential loss of phage infectivity among subgroups after release into the environment, thus obscuring the initial ratio. Here, a culture-independent multiplex real-time reverse transcriptase-PCR (RT-PCR) protocol for the simultaneous quantification of all four subgroups of F+-specific RNA coliphages using novel primer sets and molecular beacons is presented. This assay is extremely sensitive, achieving detection with as few as 10 copies of isolated coliphage RNA, and is linear for a minimum of six orders of magnitude. During survival experiments, the real-time RT-PCR technique was able to quantify coliphages in seawater when culture-based double agar layer assay failed. While infectivity was lost at different rates at the subgroup level, decay constants in seawater, calculated using the real-time RT-PCR estimates, did not vary among subgroups. The accurate determination of the in situ concentration of F+-specific RNA coliphages using this method will facilitate more effective remediation strategies for impacted environments. [ABSTRACT FROM AUTHOR]