Abstract
BackgroundThe adaptation of pyrosequencing technologies for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems.Methodology/Principal FindingsWe examined the patterns of fine scale Beta diversity in four adjacent sediment samples (1mm apart) from the source of an anaerobic sulfide and sulfur rich spring (Zodletone spring) in southwestern Oklahoma, USA. Using pyrosequencing, a total of 292,130 16S rRNA gene sequences were obtained. The beta diversity patterns within the four datasets were examined using various qualitative and quantitative similarity indices. Low levels of Beta diversity (high similarity indices) were observed between the four samples at the phylum-level. However, at a putative species (OTU0.03) level, higher levels of beta diversity (lower similarity indices) were observed. Further examination of beta diversity patterns within dominant and rare members of the community indicated that at the putative species level, beta diversity is much higher within rare members of the community. Finally, sub-classification of rare members of Zodletone spring community based on patterns of novelty and uniqueness, and further examination of fine scale beta diversity of each of these subgroups indicated that members of the community that are unique, but non novel showed the highest beta diversity within these subgroups of the rare biosphere.Conclusions/SignificanceThe results demonstrate the occurrence of high inter-sample diversity within seemingly identical samples from a complex habitat. We reason that such unexpected diversity should be taken into consideration when exploring gamma diversity of various ecosystems, as well as planning for sequencing-intensive metagenomic surveys of highly complex ecosystems.
Highlights
The adaptation of pyrosequencing technologies [1] for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest
We examined the bacterial diversity in an anaerobic sulfur- and sulfide-rich spring in southwestern Oklahoma
While comparative diversity between multiple communities has been extensively studied using culture-based [39,40,41,42], and culture independent [6,7,12, 14,18] surveys, most of these studies have focused on elucidating the effect of specific measurable factor(s) on microbial community structure e.g. along gradients of various length scales, from cm [43] to global [44,45] scales
Summary
The adaptation of pyrosequencing technologies [1] for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. Replica fine scale sampling from such sediments could be regarded as a true measure of spatial difference between samples exposed to identical geochemical and environmental parameters, rather than an exploration of the effect of environmental variations on microbial communities. We used these replica samples to demonstrate that significant levels of beta diversity exist on a mm-scale in Zodletone spring, that these changes are truly spatial and could not be explained by sample size inadequacy, and that rare members of the microbial community are primarily responsible for such levels of diversity. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems
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