Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eastern Mediterranean Sea

Corte, Daniele De; Yokokawa, Taichi; Varela, Marta M.; Agogué, Hélène; Herndl, Gerhard J.

doi:10.1038/ismej.2008.94

Cited by 125 publications

(94 citation statements)

References 32 publications

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“…The number of archaeal OTUs obtained in this study was lower than in previous studies on the deep tropical East Atlantic (Winter et al, 2008) and in the deep Eastern Mediterranean Sea (Moeseneder et al, 2001a b;De Corte et al, 2009).…”

Section: Viral and Heterotrophic Prokaryotic Productioncontrasting

confidence: 50%

Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

et al. 2010

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Viral and prokaryotic abundance, production and diversity were determined throughout the water column of the subtropical Atlantic Ocean to assess potential variations in the relation between viruses and prokaryotes. Prokaryotic abundance and heterotrophic activity decreased by one and three orders of magnitude, respectively, from the epi-to the abyssopelagic layer. Although the lytic viral production (VP) decreased with depth, lysogenic VP was variable throughout the water column and did not show any trend with depth. The bacterial, archaeal and viral community composition were depth-stratified as determined by the automated ribosomal intergenic spacer analysis, terminalrestriction fragment length polymorphism and randomly amplified polymorphic DNA-PCR, respectively. Generally, the number of operational taxonomic units (OTUs) did not reveal consistent trends throughout the water column. Viral and prokaryotic abundance were strongly related to heterotrophic prokaryotic production, suggesting similar linkage strength between the viral and prokaryotic communities from the lower epi-to the abyssopelagic layer in the Atlantic Ocean. Strikingly, the prokaryotic and viral parameters exhibited a similar variability throughout the water column down to the abyssopelagic layers, suggesting that the dark ocean is as dynamic a system as is the lower epipelagic layer. It also indicates that viruses are apparently having a similar role for prokaryotic mortality in the dark oceanic realm as in surface waters. The more than twofold increase in bacterial OTUs from 2750 m depth to 45000 m depth and the concurrent decrease in viral OTUs, however, suggests that viruses might exhibit a wider host range in deep waters than in surface waters.

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Section: Viral and Heterotrophic Prokaryotic Productioncontrasting

confidence: 50%

Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

et al. 2010

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“…Also, the ratio of MG1C amoA genes to MG1C 16S rRNA genes in these samples was 0.51 ( Figure 1b). Although lower than values reported for ammonia-oxidizing enrichments (Wuchter et al, 2006) or cultures (Konneke et al, 2005) (1:1 to 2.8:1) or the gene dosage in MG1C genomes (1:1) (Hallam et al, 2006a;Walker et al, 2010), this ratio is much higher than ratios used to infer heterotrophy in other populations de Corte et al, 2008;Kalanetra et al, 2009).…”

Section: Ammonia Uptake and Oxidationmentioning

confidence: 53%

“…Studies of the distributions of planktonic ammonia oxidizing organisms have shown that ammonia-oxidizing Crenarchaeota (ammoniaoxidizing archaea, AOA) tend to be numerically dominant in the open ocean (Wuchter et al, 2006;Mincer et al, 2007;Agogue et al, 2008;Beman et al, 2008;de Corte et al, 2008;Kalanetra et al, 2009;Santoro et al, 2010) and fjords Zaikova et al, 2010). Most studies of AOA populations in estuaries (Francis et al, 2005;Beman and Francis, 2006;Caffrey et al, 2007;Mosier and Francis, 2008;Santoro et al, 2008;Magalhaes et al, 2009;Bernhard et al, 2010) have focused on sediments.…”

Section: Introductionmentioning

confidence: 99%

Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage

et al. 2010

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Quantitative PCR (qPCR) analysis revealed elevated relative abundance (1.8% of prokaryotes) of marine group 1 Crenarchaeota (MG1C) in two samples of southeastern US coastal bacterioplankton, collected in August 2008, compared with samples collected from the same site at different times (mean 0.026%). We analyzed the MG1C sequences in metatranscriptomes from these samples to gain an insight into the metabolism of MG1C population growing in the environment, and for comparison with ammonia-oxidizing bacteria (AOB) in the same samples. Assemblies revealed low diversity within sequences assigned to most individual MG1C open reading frames (ORFs) and high homology with 'Candidatus Nitrosopumilus maritimus' strain SCM1 genome sequences. Reads assigned to ORFs for ammonia uptake and oxidation accounted for 37% of all MG1C transcripts. We did not recover any reads for Nmar_1354-Nmar_1357, proposed to encode components of an alternative, nitroxyl-based ammonia oxidation pathway; however, reads from Nmar_1259 and Nmar_1667, annotated as encoding a multicopper oxidase with homology to nirK, were abundant. Reads assigned to two homologous ORFs (Nmar_1201 and Nmar_1547), annotated as hypothetical proteins were also abundant, suggesting that their unknown function is important to MG1C. Superoxide dismutase and peroxiredoxin-like transcripts were more abundant in the MG1C transcript pool than in the complete metatranscriptome, suggesting an enhanced response to oxidative stress by the MG1C population. qPCR indicated low AOB abundance (0.0010% of prokaryotes), and we found no transcripts related to ammonia oxidation and only one RuBisCO transcript among the transcripts assigned to AOB, suggesting they were not responding to the same environmental cues as the MG1C population.

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“…Intriguingly, abundances of the 16S rRNA and the amoA genes differ markedly. Studies in marine environments reported an archaeal amoA to 16 S ratio of 0.5:1 and lower (De Corte et al, 2009). In Lake Redon ratios of 5:1-8:1 were observed, suggesting that either not all 16S genes of amoA gene containing organisms were detected with the qPCR assay or that the archaea present in the lake have a higher copy number of amoA genes per genome.…”

Section: Discussionmentioning

confidence: 99%

Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

et al. 2012

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Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter–spring (that is, the 0 oC slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer—autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC−1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC−1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC−1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments.

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Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eastern Mediterranean Sea

Cited by 125 publications

References 32 publications

Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean

Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage

Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

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