scholarly journals Haloacetic acid-degrading bacterial communities in drinking water systems as determined by cultivation and by terminal restriction fragment length polymorphism of PCR-amplified haloacid dehalogenase gene fragments

2012 ◽  
Vol 112 (4) ◽  
pp. 809-822 ◽  
Author(s):  
A.S. Grigorescu ◽  
R.M. Hozalski ◽  
T.M. LaPara
Holzforschung ◽  
2012 ◽  
Vol 66 (4) ◽  
Author(s):  
Grant T. Kirker ◽  
M. Lynn Prewitt ◽  
Walter J. Diehl ◽  
Susan V. Diehl

Abstract The effects of wood preservatives on the bacterial community in southern yellow pine were assessed by the molecular method ‘terminal restriction fragment length polymorphism’ (T-RFLP). Stakes, treated with 0.25% and 0.37% ammoniacal copper quat (ACQ-C), 0.1% and 0.25% chlorothalonil (CTN), 0.1% and 0.25% CTN with 2% butylated hydroxytoluene (BHT), and 2% BHT were installed with untreated controls in two field test sites in Mississippi and sampled every 90 days. Bacterial DNA was amplified by means of general 16S rDNA primers. Community data were analyzed to determine the effects of test site, exposure (above or below ground), treatment concentrations, and exposure time on the bacterial communities inhabiting the field stakes. Wood preservatives altered the bacterial communities, which fluctuated in numbers and composition over time. Initial exposure to CTN changed the pattern of species that colonized the stakes, and the bacterial communities did not become more similar to controls after CTN depletion. Bacterial communities on untreated controls were the most similar to each other and changed the least over time. Preservative treatment led to greater population turnover and increased diversity by creating a more unstable bacterial environment, which prevented these communities from reaching equilibrium. Although preservative treatment led to changes over time, there were still many shared species within and between the untreated controls and the different preservative treatments.


2006 ◽  
Vol 72 (2) ◽  
pp. 1270-1278 ◽  
Author(s):  
Catherine A. Osborne ◽  
Gavin N. Rees ◽  
Yaniv Bernstein ◽  
Peter H. Janssen

ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) analysis has the potential to be useful for comparisons of complex bacterial communities, especially to detect changes in community structure in response to different variables. To do this successfully, systematic variations have to be detected above method-associated noise, by standardizing data sets and assigning confidence estimates to relationships detected. We investigated the use of different standardizing methods in T-RFLP analysis of PCR-amplified 16S rRNA genes to elucidate the similarities between the bacterial communities in 17 soil and sediment samples. We developed a robust method for standardizing data sets that appeared to allow detection of similarities between complex bacterial communities. We term this the variable percentage threshold method. We found that making conclusions about the similarities of complex bacterial communities from T-RFLP profiles generated by a single restriction enzyme (RE) may lead to erroneous conclusions. Instead, the use of multiple REs, each individually, to generate multiple data sets allowed us to determine a confidence estimate for groupings of apparently similar communities and at the same time minimized the effects of RE selection. In conjunction with the variable percentage threshold method, this allowed us to make confident conclusions about the similarities of the complex bacterial communities in the 17 different samples.


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