The easiest way of detecting specific nucleic acid sequences or genes of interest is through direct hybridization of a probe to microbial nucleic acid extracts. Whole-cell DNA or RNA is extracted from the environmental sample and fixed to a positively charged membrane, e.g. nylon or nitrocellulose. Bacterial colonies can also be replica-plated from agar plates to membranes and their nucleic acids exposed in situ following lysis for subsequent hybridization. Probes may be used to detect genes in the bacterial genome (Southern blots) or to detect mRNA or rRNA (Northern blots). For the in situ identification of individual whole cells it is necessary to make the cells permeable to oligonucleotide probes hybridizing with rRNA. These hybridization techniques rely on the specific binding of nucleic acid probes to complementary DNA or RNA (target nucleic acid). The probes are single strands of nucleic acid with the potential of carrying detectable marker molecules highly specifically to complementary target sequences, even if these sequences account for only a small fraction of the target nucleic acid. Either DNA or RNA can serve as a nucleic acid probe, but for a number of reasons (e.g. ease of synthesis and stability), most studies have employed DNA probes (Holben and Hedje 1988). Two general types of probes that have been developed are DNA probes complementary to a single gene or a small region of a gene and DNA probes complementary to genus- or species-specific regions of 16S rRNA for use in whole cell in situ hybridization (FISH).

DOI link for The easiest way of detecting specific nucleic acid sequences or genes of interest is through direct hybridization of a probe to microbial nucleic acid extracts. Whole-cell DNA or RNA is extracted from the environmental sample and fixed to a positively charged membrane, e.g. nylon or nitrocellulose. Bacterial colonies can also be replica-plated from agar plates to membranes and their nucleic acids exposed in situ following lysis for subsequent hybridization. Probes may be used to detect genes in the bacterial genome (Southern blots) or to detect mRNA or rRNA (Northern blots). For the in situ identification of individual whole cells it is necessary to make the cells permeable to oligonucleotide probes hybridizing with rRNA. These hybridization techniques rely on the specific binding of nucleic acid probes to complementary DNA or RNA (target nucleic acid). The probes are single strands of nucleic acid with the potential of carrying detectable marker molecules highly specifically to complementary target sequences, even if these sequences account for only a small fraction of the target nucleic acid. Either DNA or RNA can serve as a nucleic acid probe, but for a number of reasons (e.g. ease of synthesis and stability), most studies have employed DNA probes (Holben and Hedje 1988). Two general types of probes that have been developed are DNA probes complementary to a single gene or a small region of a gene and DNA probes complementary to genus- or species-specific regions of 16S rRNA for use in whole cell in situ hybridization (FISH).

The easiest way of detecting specific nucleic acid sequences or genes of interest is through direct hybridization of a probe to microbial nucleic acid extracts. Whole-cell DNA or RNA is extracted from the environmental sample and fixed to a positively charged membrane, e.g. nylon or nitrocellulose. Bacterial colonies can also be replica-plated from agar plates to membranes and their nucleic acids exposed in situ following lysis for subsequent hybridization. Probes may be used to detect genes in the bacterial genome (Southern blots) or to detect mRNA or rRNA (Northern blots). For the in situ identification of individual whole cells it is necessary to make the cells permeable to oligonucleotide probes hybridizing with rRNA. These hybridization techniques rely on the specific binding of nucleic acid probes to complementary DNA or RNA (target nucleic acid). The probes are single strands of nucleic acid with the potential of carrying detectable marker molecules highly specifically to complementary target sequences, even if these sequences account for only a small fraction of the target nucleic acid. Either DNA or RNA can serve as a nucleic acid probe, but for a number of reasons (e.g. ease of synthesis and stability), most studies have employed DNA probes (Holben and Hedje 1988). Two general types of probes that have been developed are DNA probes complementary to a single gene or a small region of a gene and DNA probes complementary to genus- or species-specific regions of 16S rRNA for use in whole cell in situ hybridization (FISH).