Monitoring microbial communities

Design of Hybridization Probes and their Application to Monitoring Microbial Communities... 

Dot blot hybridization has been used to monitor the alkB gene in n-alkane-degrading bacterial isolates [126]. The gene was shown to be widely spread among short-chain alkane degraders. Dot blot hybridization is also suitable for monitoring microbial communities after a bioremediation process [127]. 

Telang AJ, S Ebert, LM Focht, DW Westlake, GE Jenneman, D Gevertz, G Voordouw (1997) Effect of nitrate injection on the microbial community in an oil field monitored by reverse sample genome probing. Appl Environ Microbiol 63 1785-1793. 

The performance of a biotreatment system ultimately depends on optimization of the activity of microbes and the ability to control the process parameters of the treatment system [157]. In this respect, the ability to monitor gene copy numbers and gene expression is highly useful for real time optimization of the efficiency of a biotreatment system. Advanced molecular techniques as well as low cost methods (e.g., antibody detection of enzymes based on color reaction strips fluorescence i.e., GFP marked organisms with UV light detection) can also be applied to monitor the microbial community structure, persistence of the added bacteria, and their interactions with indigenous populations. 

Dabert P, Fleurat-Lessard A, Mounier E et al (2001) Monitoring of the microbial community of a sequencing batch reactor bioaugmented to improve its phosphorus removal capabilities. Wat Sci Technol 43 1-3... 

Kandeler E, Kampichler C, Horak O (1996) Influence of heavy metals on the functional diversity of soil microbial communities. Biol Fertil Soils 23 299-306 Kandeler E, Tscherko D, Spiegel H (1999) Long-term monitoring of microbial biomass, N mineralisation and enzyme activities of a Chernozem under different tillage management. Biol Fertil Soils 28 343-351... 

Again, the absence of monitoring data does not necessarily indicate a lack of cresols in the environment. Cresols are widely occurring natural and anthropogenic products. However, biodegradation is probably the dominant mechanism responsible for the rapid removal of cresols from surface waters (see Section 5.3.2.2). Nevertheless, cresols may persist in extremely oligotrophic waters, in waters with limited microbial communities, and/or under anaerobic conditions such as in some sediments and groundwater aquifers. 

J.G. Bundy, G.L. Paton, and C.D. Campbell, Combined Microbial Community Level and Single Species Biosensor Responses to Monitor Recovery of Oil Polluted Soil, Soil Biol. Biochem. 36(7), 1149-1159, July (2004). 

Although qPCR can be used to detect and evaluate from one to five types of microorganisms (limits of available fluorescence probes and detector), microarray analysis can be used to evaluate a microbial community consisting of multiple species. Microarrays are conventionally used to monitor intracellular gene expression under different conditions. Recently, microarray analyses have been developed to evaluate the microbial community by targeting 16S rDNA and some functional genes [40, 41]. 

Comparing Microbial Communities and Monitoring Their Changes... 

Dennis P, Edwards EA, Liss SN, Fulthorpe R (2003) Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl Environ Microbiol... 

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