Editing Hybridization probe (section)

== Uses in microbial ecology ==
Within the field of [[microbial ecology]], oligonucleotide probes are used in order to determine the presence of microbial species, genera, or microorganisms classified on a more broad level, such as [[bacteria]], [[archaea]], and [[eukaryotes]] via [[fluorescence in situ hybridization]] (FISH).<ref>{{cite journal |vauthors=Amann R, Ludwig W | year = 2000 | title = Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology | journal = FEMS Microbiology Reviews | volume = 24 | issue = 5 | pages = 555–565 | doi=10.1111/j.1574-6976.2000.tb00557.x| pmid = 11077149 | doi-access = free }}</ref> rRNA probes have enabled scientists to visualize microorganisms, yet to be cultured in laboratory settings, by retrieval of rRNA sequences directly from the environment.<ref>{{cite journal | author = Amann, R. |author2=Ludwig, W.  |author3=Schleifer, K.-H. | year = 1995 | title = Phylogenetic identification and in situ detection of individual microbial cells without cultivation | journal = Microbiological Reviews | volume = 59 |issue=1 | pages = 143–169 |doi=10.1128/MMBR.59.1.143-169.1995 |pmid=7535888 |pmc=239358 | doi-access = free }}</ref> Examples of these types of microorganisms include:

*''[[Nevskia ramosa]]'': ''N. ramosa'' is a neuston bacterium that forms typical, dichotomically-branching rosettes on the surface of shallow freshwater habitats.<ref>{{cite journal | author = Glöckner, F.O. |author2=Babenzien H.D.| author3=Amann R. | year = 1998 | title = Phylogeny and identification in situ of ''Nevskia ramosa'' | journal = Appl. Environ. Microbiol. | volume = 64 |issue=5| pages = 1895–1901 |doi=10.1128/AEM.64.5.1895-1901.1998|pmid=9572969|pmc=106248|bibcode=1998ApEnM..64.1895G| doi-access = free }}</ref>
*''[[Achromatium oxaliferum]]'': This huge bacterium (cell length up to >100&nbsp;μm, diameter up to 50&nbsp;μm) contains sulfur globules and massive calcite inclusions and inhabits the upper layers of freshwater sediments. It is visible to the naked eye and has, by its resistance to cultivation, puzzled generations of microbiologists.<ref>{{cite journal | author = Glöckner, F.O. |author2= Babenzien H.D.| author3=Amann R. | year = 1999 | title = Phylogeny and diversity of ''Achromatium oxaliferum'' | journal = Syst. Appl. Microbiol. | volume = 22 |issue= 1| pages = 28–38 | doi=10.1016/s0723-2020(99)80025-3|pmid= 10188276}}</ref>

=== Limitations ===
In some instances, differentiation between species may be problematic when using [[16S ribosomal RNA|16S rRNA]] sequences due to similarity. In such instances, [[23S rRNA]] may be a better alternative.<ref>{{cite journal | author1 = Fox, G.E. |author2= Wisotzkey, J.D. | author3=Jurtshuk Jr., P. | year = 1992 | title = How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. | journal = Int. J. Syst. Bacteriol. | volume = 42 |issue= 1 | pages = 166–170 | doi=10.1099/00207713-42-1-166|pmid= 1371061 | doi-access = free }}</ref> The global standard library of rRNA sequences is constantly becoming larger and continuously being updated, and thus the possibility of a random hybridization event between a specifically-designed probe (based on complete and current data from a range of test organisms) and an undesired/unknown target organism cannot be easily dismissed.<ref>{{cite journal | author = Olsen, G.J. |author2=Lane, D.J. |author3=Giovannoni, S.J. |author4= Pace, N.R.  |author5= Stahl, D.A. | year = 1986 | title = Microbial ecology and evolution: a ribosomal RNA approach | journal = Annu. Rev. Microbiol. | volume = 40 | pages = 337–365 | doi=10.1146/annurev.mi.40.100186.002005|pmid=2430518 }}</ref> On the contrary, it is plausible that there exist microorganisms, yet to be identified, which are phylogenetically members of a probe target group, but have partial or near-perfect target sites, usually applies when designing group-specific probes.

Probably the greatest practical limitation to this technique is the lack of available automation.<ref>{{cite journal |vauthors=Amann R, Ludwig W | year = 2000 | title = Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology | journal = FEMS Microbiology Reviews | volume = 24 | issue = 5 | pages = 555–565 | doi=10.1111/j.1574-6976.2000.tb00557.x| pmid = 11077149 | doi-access = free }}</ref>