Analysis of a diverse assemblage of diazotrophic bacteria from Spartina alterniflora using DGGE and clone library screening

Journal of Microbiological Methods
C R LovellGeorge Y Matsui

Abstract

Methods to assess the diversity of the diazotroph assemblage in the rhizosphere of the salt marsh cordgrass, Spartina alterniflora were examined. The effectiveness of nifH PCR-denaturing gradient gel electrophoresis (DGGE) was compared to that of nifH clone library analysis. Seventeen DGGE gel bands were sequenced and yielded 58 nonidentical nifH sequences from a total of 67 sequences determined. A clone library constructed using the GC-clamp nifH primers that were employed in the PCR-DGGE (designated the GC-Library) yielded 83 nonidentical sequences from a total of 257 nifH sequences. A second library constructed using an alternate set of nifH primers (N-Library) yielded 83 nonidentical sequences from a total of 138 nifH sequences. Rarefaction curves for the libraries did not reach saturation, although the GC-Library curve was substantially dampened and appeared to be closer to saturation than the N-Library curve. Phylogenetic analyses showed that DGGE gel band sequencing recovered nifH sequences that were frequently sampled in the GC-Library, as well as sequences that were infrequently sampled, and provided a species composition assessment that was robust, efficient, and relatively inexpensive to obtain. Further, the DGGE met...Continue Reading

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Citations

Feb 17, 2009·Applied and Environmental Microbiology·Casandra K GutierrezCharles R Lovell
Feb 15, 2016·World Journal of Microbiology & Biotechnology·Zhiqing HuangLi Ni
Jun 1, 2010·International Journal of Systematic and Evolutionary Microbiology·Melissa J CramerCharles R Lovell
Mar 16, 2018·Microorganisms·Debra A DavisCharles R Lovell

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