Neal Phillip R.

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Phillip R.

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  • Preprint
    Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure
    ( 2008-07) Huber, Julie A. ; Morrison, Hilary G. ; Huse, Susan M. ; Neal, Phillip R. ; Sogin, Mitchell L. ; Mark Welch, David B.
    PCR-based surveys of microbial communities commonly use regions of the small subunit ribosomal RNA (SSU rRNA) gene to determine taxonomic membership and estimate total diversity. Here we show that the length of the target amplicon has a significant effect on assessments of microbial richness and community membership. Using OTU- and taxonomy-based tools, we compared the V6 hypervariable region of the bacterial SSU rRNA gene of three amplicon libraries of ca. 100 base pair (bp), 400bp, and 1000bp from each of two hydrothermal vent fluid samples. We found that the smallest amplicon libraries contained more unique sequences, higher diversity estimates, and a different community structure than the other two libraries from each sample. We hypothesize that a combination of polymerase dissociation, cloning bias, and mis-priming due to secondary structure accounts for the differences. While this relationship is not linear, it is clear that the smallest amplicon libraries contained more different types of sequences, and accordingly, more diverse members of the community. Because divergent and lower abundant taxa can be more readily detected with smaller amplicons, they may provide better assessments of total community diversity and taxonomic membership than longer amplicons in molecular studies of microbial communities.
  • Article
    Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA
    (Inter-Research, 2010-12-30) Pommier, Thomas ; Neal, Phillip R. ; Gasol, Josep M. ; Coll, Montserrat ; Acinas, Silvia G. ; Pedros-Alio, Carlos
    Due to analytical limitations, patterns of richness and evenness of microbes are scarce in the current literature. The newest and powerful pyrosequencing technology may solve this issue by sampling thousands of sequences from the same community. We conducted a study of diversity along a horizontal transect (ca. 120 km) and a depth profile (surface to bottom at ca. 2000 m) in the northwestern Mediterranean Sea, using this technology on the V6 region of the 16S rDNA gene and analyzed patterns of richness and evenness of marine free-living bacterial communities. A total of 201605 tag sequences were obtained from the 10 samples considered and clustered according to their similarity in 1200 operational taxonomic units (OTUs) per sample on average. We found a parallel decrease in richness and evenness from coast to offshore and from bottom to surface. We also observed a predominance of a few OTUs in each sample, while ca. 50% of all OTUs were found as singletons, which indicated that the community structures differed dramatically between sites despite the relative proximity and the physical connectivity between the samples. Despite these differences, using the 300 most abundant OTUs only was sufficient to obtain the same clustering of samples as with the complete dataset. Finally, both richness and evenness were negatively correlated with bacterial biomass and heterotrophic production.