Application of phenotypic microarrays to environmental microbiology.
Environmental organisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. This review describes applications of phenotype arrays to anaerobic and thermophilic microorganisms, use of the plates in stress response studies, in development of culture media for newly discovered strains, and for assessment of phenotype of environmental communities. Also discussed are considerations and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting.
Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, MS 70A-3317, Berkeley, CA 94720, USA.
Sharon
S
Borglin
Dominique
D
Joyner
Kristen M
KM
DeAngelis
Jane
J
Khudyakov
Patrik
P
D'haeseleer
Marcin P
MP
Joachimiak
Terry
T
Hazen
D001105:Archaea / Q000254:growth & development* / Q000302:isolation & purification / Q000378:metabolism; D001419:Bacteria / Q000254:growth & development* / Q000302:isolation & purification / Q000378:metabolism; D003470:Culture Media; D004783:Environmental Microbiology; D045302:Geobacter / Q000254:growth & development / Q000302:isolation & purification / Q000378:metabolism; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D059392:Petroleum Pollution; D010641:Phenotype; D010802:Phylogeny; D016944:Sulfolobus / Q000254:growth & development / Q000302:isolation & purification / Q000378:metabolism
D003470:Culture Media