A method or detecting the presence of living or dead microorganisms and viruses in a sample comprises adding to a pre-determined volume of a sample comprising nucleic acid-containing microbe (s) and/or virus (es), known amounts of a pair of primers binding to sequences up-stream and down-stream to a universal or specific microbial and/or viral nucleic acid sequence and polymerase chain reaction (PCR) reagents, cycling the mixture to amplify the universal or specific microbial and/or viral nucleic acid sequence; adding a polynucleotide comprising a DNA internal segment that is hybridizably complementary to at least a portion of the universal or specific nucleic acid sequence; and a first and a second DNA arm segment adjoining the DNA internal segment, the first DNA arm segment ending in a 5' terminus and the second DNA arm segment ending in a 3' terminus, the arms segments comprising nucleotide sequences such that they are hybridizably complementary to one another. Optionally, the terminus of one arm segment is operatively connected to a fluorogen and the terminus of the other arm segment is operatively connected to a quencher, such that the polynucleotide comprises a "fluorescent beacon."
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