Terminal Restriction Fragment Length Polymorphism Data Analysis for Quantitative Comparison of Microbial Communities

Blackwood, Christopher B.; Marsh, Terence L.; Kim, Sang-Hoon; Paul, Eldor A.

doi:10.1128/aem.69.2.926-932.2003

Cited by 284 publications

(195 citation statements)

References 30 publications

Supporting

Mentioning

187

Contrasting

Unclassified

Order By: Relevance

“…We analyzed the microbial community structure using terminal restriction fragment length polymorphism analysis (TRFLP) [33][34][35]. To perform TRFLP, bacterial 16S rRNA genes were amplified using the universal primers Bac8f with a 5′ end 6-FAM label (5′-AGAGTTTGATCCTGGCTCAG-3′) and unlabelled primer Univ1492r (5′-GGTTACCTTGTTACGACTT-3′) [36].…”

Section: Dna Extraction Amplification Trflp and Quantitative Pcrmentioning

confidence: 99%

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

2013

View full text Add to dashboard Cite

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ( 13 C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 − as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.2

show abstract

Section: Dna Extraction Amplification Trflp and Quantitative Pcrmentioning

confidence: 99%

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

2013

View full text Add to dashboard Cite

show abstract

“…TRFLP is not a perfect method, and as with any PCRbased method there are potential limitations of primer binding bias (Leuders and Friedrich 2003), operon copy number heterogeneity (Crosby and Criddle 2003), and polymerase error (Osborn et al 2000), although many of these issues can be ameliorated by procedural modification (Polz andCavanaugh 1998, Osborn et al 2000). When conducted with appropriate methodological and statistical treatment, TRFLP has been shown to yield reliable, accurate, pseudo-quantitative representations of complex microbial community structure (Blackwood et al 2003, Leuders and Friedrich 2003, Liu et al 1997, Osborn et al 2000, Schutte et al 2008, Trotha et al 2002.…”

mentioning

confidence: 99%

Profiling the Yeast Communities of Wine Fermentations Using Terminal Restriction Fragment Length Polymorphism Analysis

Bokulich¹,

Hwang²,

Liu³

et al. 2011

Am. J. Enol. Vitic.

View full text Add to dashboard Cite

Abstract:Terminal restriction fragment length polymorphism (TRFLP), used most often to describe bacterial communities, presents a high-throughput, low-cost solution for analyzing mixed yeast communities in wine and other fermentations. In this study, a TRFLP approach was developed for the identification and discrimination of yeasts and used to construct a TRFLP database comprising 121 strains of yeast (representing 24 genera and 72 species) associated with wine and food fermentations. This database exhibits sensitive discrimination among species and robust intraspecific conservation of TRFLP profiles, enabling reliable characterization of mixed yeast communities. The yeast ecology of sweet, botrytized wine fermentations from two separate vintages was analyzed using this database, demonstrating the utility of this method for fast-paced, qualitative detection and identification of differences in yeast community structures over time in a complex, diverse fermentation system.

show abstract

“…Recently, in leaf decomposition studies, molecular methods have been employed to look at microbial diversity to circumvent inadequacies of culture-based methods (5,43). Denaturing gradient gel electrophoresis (DGGE) has been used extensively for examination of complex microbial community assemblages (6,20,30,46,52).…”

mentioning

confidence: 99%

Diversity of Fungi, Bacteria, and Actinomycetes on Leaves Decomposing in a Stream

Das

Royer

Leff

2007

Appl Environ Microbiol

189

137

View full text Add to dashboard Cite

Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCRdenaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycetespecific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality.

show abstract

Terminal Restriction Fragment Length Polymorphism Data Analysis for Quantitative Comparison of Microbial Communities

Cited by 284 publications

References 30 publications

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

Profiling the Yeast Communities of Wine Fermentations Using Terminal Restriction Fragment Length Polymorphism Analysis

Diversity of Fungi, Bacteria, and Actinomycetes on Leaves Decomposing in a Stream

Contact Info

Product

Resources

About