A quantitative assay for linking microbial community function and structure of a naphthalene-degrading microbial consortium.
A comprehensive culture-independent assay, called Q-FAST, was developed for concurrent identification and quantification of active microorganisms involved a specific function in a given microbial community. The development of Q-FAST was achieved by integrating the concept of stable isotope probing technique into a new quantitative fingerprinting assay called real-time-t-RFLP for microbial community structure analysis. The Q-FAST was successfully validated by using a three-member artificial microbial community containing a known naphthalene-utilizing bacterium (Pseudomonas putida G7) and two nonnaphthalene-degrading bacteria (Escherichia coli and Bacillus thuringiensis). The application of Q-FAST to identify and quantify a guild of naphthalene-utilizing microorganisms in soils revealed the involvement of eight members, with six members relating to several phylogenetic groups of eubacteria (three in beta-proteobacteria, two in gamma-proteobacteria, and one in genera Intrasporangium of Gram-positive bacteria) and two members showing no close phylogenetic affiliation to any known bacterial sequences deposited in GenBank. The quantity of three members belonging to beta-proteobacteria accounted for 34% of total 16S rDNA copies measured from the "heavier" fraction of DNA that was contributed from the DNA of microorganisms capable of incorporating 13C-labeled naphthalene into their genetic biomarkers. The other five members composed 66% of total 16S rDNA copies of active naphthalene-utilizing populations measured. Offering a powerful tool for studying microbial ecology, Q-FAST thus opens a new avenue for deeper exploration of microbial-mediated processes, mainly the quantitative relationship between microbial diversity and microbial activity in a given environment.
Yu
Chang-Ping
CP
Zachry Department of Civil Engineering, Texas A&M University, College Station, Texas 77843-3136, USA.
Chu
Kung-Hui
KH
D001413:Bacillus thuringiensis / Q000302:isolation & purification / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000378:metabolism*; D001673:Biodegradation, Environmental; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004784:Environmental Monitoring / Q000379:methods; D004926:Escherichia coli / Q000302:isolation & purification / Q000378:metabolism; D007553:Isotope Labeling / Q000379:methods; D009281:Naphthalenes / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics; D012988:Soil Microbiology; D014871:Water Microbiology
D009281:Naphthalenes; D012336:RNA, Ribosomal, 16S; C031721:naphthalene; D004247:DNA