Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

Abstract

Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87-80 1C) and Site B (79 1C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 ( p ¼ 36.1%), Aeropyrum ( p ¼ 16.6%), the archaeal lineage pSL4 ( p ¼ 15.9%), the archaeal lineage NAG1 ( p ¼ 10.6%) and Thermocrinis ( p ¼ 7.6%). The ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus' was relatively abundant in all sediment samples o82 1C ( p ¼ 9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles.

Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments

“…Singletons remained in the analysis, and these studies are therefore compared with our unfiltered data containing singletons. Hou et al (2013) denoised their data set, whereas Cole et al (2013) did not, however our analyses suggest that denoising has a minimal effect on the Shannon index (on average a 15.7% decline; Supplementary Table S2). Alpha diversities for these two studies were rarefied to depths of 978 and 5325, both of which are above the 700-sequence depth at which our samples leveled off.…”

“…To further verify the temperature-diversity relationship, Shannon diversity index data from two recent pyrotag sequencing studies of neutralalkaline hot springs in China and the US (Cole et al, 2013;Hou et al, 2013) were included in Figure 3b. To conform with our sample set, only sediment and biomat samples were included, whereas water samples were ignored.…”

“…Although the analysis pipelines were not identical among the different studies, they were similar. Primers used by Cole et al (2013) are the same primers used in the current study and amplified the V6-V8 region of the 16S rRNA gene. Primers from Hou et al (2013) amplified the V4-V8 region.…”

“…However, studies comparing diversity across geothermal systems remain few in number and consistent trends remain unresolved. Although some studies have noted a lack of correlation (Yim et al, 2006;Huang et al, 2011;Hou et al, 2013;Wang et al, 2013) or even a slight increase in diversity with increasing temperature (Purcell et al, 2007), others have noted a decrease in diversity with increasing temperature (Miller et al, 2009;Tobler and Benning, 2011;Everroad et al, 2012;Cole et al, 2013). Although these studies hint at underlying general patterns, they are all limited by at least one of several shortcomings: restricted methodologies that detect only the few most abundant operational taxonomic units (OTUs), such as construction of clone libraries (Yim et al, 2006;Purcell et al, 2007;Miller et al, 2009;Huang et al, 2011;Tobler and Benning, 2011;Everroad et al, 2012); low numbers of samples (o10) (Yim et al, 2006;Purcell et al, 2007;Miller et al, 2009;Tobler and Benning, 2011;Everroad et al, 2012); samples taken from a single geothermal field and therefore possibly showing site-specific trends (Yim et al, 2006;Miller et al, 2009;Everroad et al, 2012;Cole et al, 2013); or a limited temperature range (o30 1C total range) (Purcell et al, 2007;Miller et al, 2009;Everroad et al, 2012;Cole et al, 2013).…”

“…Two recent studies based on 16S rRNA gene pyrotag sequencing, the technique that assesses microbial diversity to the most depth, support the notion that extreme temperatures may restrict microbial diversity (Everroad et al, 2012;Cole et al, 2013), but other pyrotag sequencing studies with a larger number of samples and a broader temperature range do not Wang et al, 2013). The relative importance of pH versus temperature is also unknown as few studies cover wide-ranges of both temperature and pH.…”