Uncultured archaea in deep marine subsurface sediments: have we caught them all?

Teske, Andreas; Sørensen, Ketil Bernt

doi:10.1038/ismej.2007.90

Cited by 412 publications

(385 citation statements)

References 74 publications

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“…PCR amplification of the V3 region of the 16S rRNA gene The total DNA in replicate samples was pooled together for PCR using the forward primer U341F (5 0 -CCTACGGGRSGCAGCAG-3 0 ) (Hansen et al, 1998) and reverse primer R685 (5 0 -ATCTACGC ATTTCACCGCTAC-3 0 ) for bacteria (Wang et al, 2004), and the forward primer A344F (5 0 -AYGGGGY GCASCAGGSG-3 0 ) and reverse primer A519R (5 0 -GG TDTTACCGCGGCKGCTG-3 0 ) for archaea (Teske and Sorensen, 2007) in separate reactions. A set of sixnucleotide (nt) barcodes was designed and added to the 5 0 end of U341F, R685, A344F and A519R for the multiplexing of samples in the pyrosequencing runs.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2010

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The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (2 and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2010

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“…DNA extracts of three samples (200, 700 and 1500 m) previously collected from the water column overlying Atlantis II Deep in central Red Sea (21120.76 0 N, 38104.68 0 E; October 2008; Ngugi and Stingl, 2012) were also included for phylogenetic community comparison with that of the BSI. Pyrotag sequencing was done using 16S rRNA gene primers for the V3-V6 (B343F/B1099rc; Liu et al, 2007) and V6-V9 (A934F/U1492R; Lane, 1991;Teske and Sorensen, 2008) regions for bacteria and archaea, respectively. Cell sorting and single-cell genomics were conducted at the Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences (East Boothbay, ME, USA) as described in Rinke et al (2014).…”

Section: Methodsmentioning

confidence: 99%

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

et al. 2014

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The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares B54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

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“…The archaeal 16S rRNA gene clone libraries for the cool, warm and hot AOM zones show significant differences ( Supplementary Figures S3-5). The cool and hot AOM zones are dominated by archaeal phylotypes of the uncultured Miscellaneous Crenarchaeotal Group archaea, one of the most frequently recovered archaeal lineages in marine subsurface sediments (Fry et al, 2008;Teske and Sørensen, 2008), by uncultured members of the Thermoproteales (Supplementary Figure S4), by ANME-1, and by relatives of thermophilic, mostly sulfate-and iron-reducing Archaeoglobales (Supplementary Figure S5). …”

Section: S Rrna Archaeal Diversitymentioning

confidence: 99%

Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments

et al. 2011

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Anaerobic oxidation of methane (AOM) was investigated in hydrothermal sediments of Guaymas Basin based on d 13 C signatures of CH 4 , dissolved inorganic carbon and porewater concentration profiles of CH 4 and sulfate. Cool, warm and hot in-situ temperature regimes (15-20 1C, 30-35 1C and 70-95 1C) were selected from hydrothermal locations in Guaymas Basin to compare AOM geochemistry and 16S ribosomal RNA (rRNA), mcrA and dsrAB genes of the microbial communities. 16S rRNA gene clone libraries from the cool and hot AOM cores yielded similar archaeal types such as Miscellaneous Crenarchaeotal Group, Thermoproteales and anaerobic methane-oxidizing archaea (ANME)-1; some of the ANME-1 archaea formed a separate 16S rRNA lineage that at present seems to be limited to Guaymas Basin. Congruent results were obtained by mcrA gene analysis. The warm AOM core, chemically distinct by lower porewater sulfide concentrations, hosted a different archaeal community dominated by the two deep subsurface archaeal lineages Marine Benthic Group D and Marine Benthic Group B, and by members of the Methanosarcinales including ANME-2 archaea. This distinct composition of the methane-cycling archaeal community in the warm AOM core was confirmed by mcrA gene analysis. Functional genes of sulfate-reducing bacteria and archaea, dsrAB, showed more overlap between all cores, regardless of the core temperature. 16S rRNA gene clone libraries with Euryarchaeota-specific primers detected members of the Archaeoglobus clade in the cool and hot cores. A V6-tag high-throughput sequencing survey generally supported the clone library results while providing high-resolution detail on archaeal and bacterial community structure. These results indicate that AOM and the responsible archaeal communities persist over a wide temperature range.

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Uncultured archaea in deep marine subsurface sediments: have we caught them all?

Cited by 412 publications

References 74 publications

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

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

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments

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