Nucleic Acid Probes and Their Application in Environmental Microbiology

Abstract

Microbiology has entered the molecular age. It is now routine to start the classification of a newly isolated microorganism with the determination and comparative analysis of at least one nucleic acid sequence. Clearly, the most commonly used molecule for this purpose is the ribonucleic acid of the small subunit of the ribosome, the 16S rRNA of Bacteria and Archaea . Nucleic acid hybridization techniques, such as DNA–DNA reassociation or DNA–rRNA hybridization, have been used by bacterial taxonomists at times when nucleic acid sequencing was still difficult and available only to specialists. The increasing availability of nucleic acid sequences in databases, the ease of synthesizing oligonucleotide probes, and numerous other methodological advances in molecular biology, such as the polymerase chain reaction (PCR), have made nucleic acid probes a routinely used tool in microbiological laboratories.

Changing Microspatial Patterns of Sulfate-Reducing Microorganisms (SRM) during Cycling of Marine Stromatolite Mats

“…DAPI (4′6′-diamidino-2- phenylindole) and PI (Molecular Probes, Eugene, OR, USA) were also used for general bacteria (DNA) staining [58,59]. FISH-probing was conducted according general methods modified from [60–62]. After fixation, intact mat samples were gently washed in phosphate-buffered saline (PBS) and stored in ethanol:PBS (1:1) at −20 ºC.…”