Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

Qian, Pei‐Yuan; Wang, Yong; Lee, On On; Lau, S. S.; Yang, Ji Hyun; Lafi, Feras F.; Al-Suwailem, Abdulaziz M.; Wong, Tim Y H

doi:10.1038/ismej.2010.112

Cited by 162 publications

(139 citation statements)

References 50 publications

(55 reference statements)

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“…We suggest that archaea in our ecosystem only comprised a minor part of the soil microbiota, as demonstrated in a recent metagenomics study of an alpine glacial system (Edwards et al, 2013a). Qian et al (2011) also observed poor classification success at the kingdom level of archaeal communities in the Red Sea and further suggested that this finding may arise from an underrepresentation of archaeal sequences in databases and unspecific primers. Our findings further suggest that this kingdom should be extensively investigated in future studies in order to document adequately changes in archaeal diversity.…”

Section: Origin Of Microbial Pioneers In Deglaciated Soilsmentioning

confidence: 81%

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier

2016

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Rapid disintegration of alpine glaciers has led to the formation of new terrain consisting of mineral debris colonized by microorganisms. Despite the importance of microbial pioneers in triggering the formation of terrestrial ecosystems, their sources (endogenous versus exogenous) and identities remain elusive. We used 454-pyrosequencing to characterize the bacterial and fungal communities in endogenous glacier habitats (ice, sub-, supraglacial sediments and glacier stream leaving the glacier forefront) and in atmospheric deposition (snow, rain and aeolian dust). We compared these microbial communities with those occurring in recently deglaciated barren soils before and after snow melt (snow-covered soil and barren soil). Atmospheric bacteria and fungi were dominated by plant-epiphytic organisms and differed from endogenous glacier habitats and soils indicating that atmospheric input of microorganisms is not a major source of microbial pioneers in newly formed soils. We found, however, that bacterial communities in newly exposed soils resembled those of endogenous habitats, which suggests that bacterial pioneers originating from sub-and supraglacial sediments contributed to the colonization of newly exposed soils. Conversely, fungal communities differed between habitats suggesting a lower dispersal capability than bacteria. Yeasts putatively adapted to cold habitats characteristic of snow and supraglacial sediments were similar, despite the fact that these habitats were not spatially connected. These findings suggest that environmental filtering selects particular fungi in cold habitats. Atmospheric deposition provided important sources of dissolved organic C, nitrate and ammonium. Overall, microbial colonizers triggering soil development in alpine environments mainly originate from endogenous glacier habitats, whereas atmospheric deposition contributes to the establishment of microbial communities by providing sources of C and N.

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Section: Origin Of Microbial Pioneers In Deglaciated Soilsmentioning

confidence: 81%

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier

2016

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“…PCoA was also conducted to evaluate similarities of different AS samples using three different approaches, that is, RDP Classifier taxa, OTUs and UniFrac. For the first two approaches, taxa or OTUs are regarded as equally related, whereas UniFrac incorporates the degree of divergence in the phylogenetic tree of OTUs into PCoA (Hamady et al, 2010;Qian et al, 2010). The PCoA analysis results are shown in Figure 3 (UniFrac at 3% cutoff) and Supplementary Figure S5a (order) and Supplementary Figure S5b (OTUs at 3% cutoff).…”

Section: Similarity Analysis Of the 15 Sludge Samplesmentioning

confidence: 99%

“…Although bacteria-specific primers were applied, very small portions of unexpected archaeal sequences might be obtained (Qian et al, 2010). To remove these Pyrosequencing reveals bacterial diversity of AS T Zhang et al cross-talking sequences, the effective sequences of each AS sample were submitted to the RDP Classifier (Wang et al, 2007) to identify the archaeal and bacterial sequences, and filter out the archaeal sequences using a self-written Python script.…”

Section: Post-run Analysismentioning

confidence: 99%

“…The number of OTUs in each AS sample was counted from this matrix and summarized in Supplementary Table S1. Then, the CA was conducted using the unweighted-pair group mean averages, based on the Bray-Curtis distance calculated from the matrix using PAST software (McLellan et al, 2010;Qian et al, 2010). Similarly, CA was also conducted using a matrix of the RDP taxa (at each level from genus to class) and their abundances in each sample.…”

Section: Post-run Analysismentioning

confidence: 99%

“…High-throughput sequencing is a promising method, as it provides enough sequencing depth to cover the complex microbial communities (Shendure and Ji, 2008). So far, it has been applied to analyze microbial communities in marine water (Qian et al, 2010), soil (Roesch et al, 2007;Lauber et al, 2009), human hand surface (Fierer et al, 2008), human distal intestine (Claesson et al, 2009), etc. But few studies have been conducted using this method to investigate AS, though this approach has been used to study the microbial community in the raw sewage (McLellan et al, 2010) and the residual biosolids after digestion of AS (Bibby et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

2011

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Activated sludge (AS) contains highly complex microbial communities. In this study, PCR-based 454 pyrosequencing was applied to investigate the bacterial communities of AS samples from 14 sewage treatment plants of Asia (mainland China, Hong Kong, and Singapore), and North America (Canada and the United States). A total of 259 K effective sequences of 16S rRNA gene V4 region were obtained from these AS samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in AS, that is, 1183-3567 OTUs in a sludge sample, at 3% cutoff level and sequencing depth of 16 489 sequences. Clear geographical differences among the AS samples from Asia and North America were revealed by (1) cluster analyses based on abundances of OTUs or the genus/family/order assigned by Ribosomal Database Project (RDP) and (2) the principal coordinate analyses based on OTUs abundances, RDP taxa abundances and UniFrac of OTUs and their distances. In addition to certain unique bacterial populations in each AS sample, some genera were dominant, and core populations shared by multiple samples, including two commonly reported genera of Zoogloea and Dechloromonas, three genera not frequently reported (i.e., Prosthecobacter, Caldilinea and Tricoccus) and three genera not well described so far (i.e., Gp4 and Gp6 in Acidobacteria and Subdivision3 genera incertae sedis of Verrucomicrobia). Pyrosequencing analyses of multiple AS samples in this study also revealed the minority populations that are hard to be explored by traditional molecular methods and showed that a large proportion of sequences could not be assigned to taxonomic affiliations even at the phylum/class levels.

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Descent toward the Icehouse: Eocene sea surface cooling inferred from GDGT distributions

et al. 2015

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The TEX 86 proxy, based on the distribution of marine isoprenoidal glycerol dialkyl glycerol tetraether lipids (GDGTs), is increasingly used to reconstruct sea surface temperature (SST) during the Eocene epoch (56.0-33.9 Ma). Here we compile published TEX 86 records, critically reevaluate them in light of new understandings in TEX 86 palaeothermometry, and supplement them with new data in order to evaluate long-term temperature trends in the Eocene. We investigate the effect of archaea other than marine Thaumarchaeota upon TEX 86 values using the branched-to-isoprenoid tetraether index (BIT), the abundance of GDGT-0 relative to crenarchaeol (%GDGT-0), and the Methane Index (MI). We also introduce a new ratio, % GDGT RS , which may help identify Red Sea-type GDGT distributions in the geological record. Using the offset between TEX 86 H and TEX 86 L (ΔH-L) and the ratio between GDGT-2 and GDGT-3 ([2]/[3]), we evaluate different TEX 86 calibrations and present the first integrated SST compilation for the Eocene (55 to 34 Ma). Although the available data are still sparse some geographic trends can now be resolved. In the high latitudes (>55°), there was substantial cooling during the Eocene (~6°C). Our compiled record also indicates tropical cooling of~2.5°C during the same interval. Using an ensemble of climate model simulations that span the Eocene, our results indicate that only a small percentage (~10%) of the reconstructed temperature change can be ascribed to ocean gateway reorganization or paleogeographic change. Collectively, this indicates that atmospheric carbon dioxide (pCO 2 ) was the likely driver of surface water cooling during the descent toward the icehouse.

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Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

Cited by 162 publications

References 50 publications

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier

454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

Descent toward the Icehouse: Eocene sea surface cooling inferred from GDGT distributions

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