Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic

Agogué, Hélène; Brink, Marilyn R. Buchholtz ten; Dinasquet, Julie; Herndl, Gerhard J.

doi:10.1038/nature07535

Cited by 243 publications

(276 citation statements)

References 30 publications

(9 reference statements)

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“…Normalization of read numbers by gene length resulted in a roughly equivalent copy number of amoA and 16S genes (amoA:16S ratio of B1.4), indicating that the majority of GB MGI cells have amoA and are thus capable of ammonia oxidation. These findings are consistent with those of Konstantinidis et al (2009) from 4000 m depth at station ALOHA and distinct from those of Agogué et al (2008), which found smaller amoA:16S ratios in deep Atlantic waters.…”

Section: Resultssupporting

confidence: 82%

“…Conflicting results leave open the question of whether individual MGI are capable of both heterotrophy and autotrophy or there are sub-groups that specialize in each. Whereas studies of cultures and surface waters indicate autotrophy, observations of a lower ratio of MGI amoA to 16S rRNA gene copies (Agogué et al, 2008) and decreasing MGI carbon fixation with depth (Varela et al, 2011) in the Atlantic suggest that deep-sea MGI are predominantly organoheterotrophic. Recent studies also show that the presence (and expression) of amoA genes does not necessarily indicate CO 2 fixation (Mubmann et al, 2011;Tourna et al, 2011).…”

Section: Species-resolved Transcriptomics Of Ammonia Oxidation Genesmentioning

confidence: 99%

“…Despite their abundance and biogeochemical importance, fundamental questions remain regarding the physiology and metabolism of MGI. Several studies of MGI have provided evidence for both autotrophic ammonia oxidation (Konneke et al, 2005;Ingalls et al, 2006) and heterotrophy (Ouverney and Fuhrman, 2000;Agogué et al, 2008;Mubmann et al, 2011;Tourna et al, 2011). Autotrophic ammonia oxidation has now been confirmed in a few cultured representatives (De La Torre et al, 2008;Tourna et al, 2011), including Nitrosopumilus maritimus (Konneke et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

“…A recent PCR-based study found that deep waters (41000 m depth) of the North Atlantic have lower ratios of MGI amoA to 16S rRNA gene copies than subsurface waters, suggesting that most deep-sea MGI are heterotrophic (Agogué et al, 2008). However, metagenomic sequencing of North Pacific waters at 4000 m depth revealed an equal ratio of MGI amoA to 16S rRNA genes (Konstantidis et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

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Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

2012

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Ammonia-oxidizing Archaea (AOA) are among the most abundant microorganisms in the oceans and have crucial roles in biogeochemical cycling of nitrogen and carbon. To better understand AOA inhabiting the deep sea, we obtained community genomic and transcriptomic data from ammonium-rich hydrothermal plumes in the Guaymas Basin (GB) and from surrounding deep waters of the Gulf of California. Among the most abundant and active lineages in the sequence data were marine group I (MGI) Archaea related to the cultured autotrophic ammonia-oxidizer, Nitrosopumilus maritimus. Assembly of MGI genomic fragments yielded 2.9 Mb of sequence containing seven 16S rRNA genes (95.4–98.4% similar to N. maritimus), including two near-complete genomes and several lower-abundance variants. Equal copy numbers of MGI 16S rRNA genes and ammonia monooxygenase genes and transcription of ammonia oxidation genes indicates that all of these genotypes actively oxidize ammonia. De novo genomic assembly revealed the functional potential of MGI populations and enhanced interpretation of metatranscriptomic data. Physiological distinction from N. maritimus is evident in the transcription of novel genes, including genes for urea utilization, suggesting an alternative source of ammonia. We were also able to determine which genotypes are most active in the plume. Transcripts involved in nitrification were more prominent in the plume and were among the most abundant transcripts in the community. These unique data sets reveal populations of deep-sea AOA thriving in the ammonium-rich GB that are related to surface types, but with key genomic and physiological differences.

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Section: Resultssupporting

confidence: 82%

Section: Species-resolved Transcriptomics Of Ammonia Oxidation Genesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

2012

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“…They occur in the ocean (Karner et al, 2001), in soils (Leininger et al, 2006) and lakes (Schleper et al, 1997), and in marine and estuarine surface sediments (Francis et al, 2005;Beman and Francis, 2006;Park et al, 2008). In the present day ocean, these Archaea are found to be among the most abundant micro-organisms (Karner et al, 2001;Agogué et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum zone. Part II: Selective preservation and degradation in sediments and consequences for the TEX86

Lengger

Hopmans

Reichart

et al. 2012

Geochimica et Cosmochimica Acta

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The TEX 86 is a proxy based on a ratio of pelagic archaeal glycerol dibiphytanyl glycerol tetraether lipids (GDGTs), and used for estimating past sea water temperatures. Concerns exist that in situ production of GDGTs lipids by sedimentary Archaea may affect its validity. In this study, we investigated the influence of benthic GDGT production on the TEX 86 by analyzing the concentrations and distributions of GDGTs present as intact polar lipids (IPLs) and as core lipids (CLs) in three sediment cores deposited under contrasting redox conditions across a depth range from 900 to 3000 m below sea level in and below the Arabian Sea oxygen minimum zone (OMZ). Direct analysis of IPLs with crenarchaeol as CL via HPLC/ESI-MS 2 revealed that surface sediments in the OMZ were relatively depleted in the phospholipid hexose, phosphohexose (HPH)-crenarchaeol compared to suspended particulate matter from the water column, suggesting preferential and rapid degradation of this IPL. In sediment cores recovered from deeper, more oxic environments, concentrations of HPH-crenarchaeol peaked at the surface, probably due to in situ production by ammonia-oxidizing Archaea, followed by a rapid decrease with increasing depth. No surface maximum was observed in the sediment core from within the OMZ. In contrast, the glycolipids, monohexose-crenarchaeol and dihexose-crenarchaeol, did not change in concentration with depth in the sediment, indicating that they were relatively well preserved and likely mostly derived from fossil pelagic GDGTs. These results suggest that phospholipids are more sensitive to degradation, while glycolipids might be preserved over longer time scales, in line with previous incubation and modeling studies. Furthermore, in situ produced IPL-GDGTs did not accumulate as IPLs, and did not influence the CL-TEX 86 . This suggests that in-situ produced GDGT lipids were more susceptible to degradation than fossil CL and IPL and did not accumulate as CL. In agreement, no significant changes of TEX 86 with sediment depth in the core lipids were observed. However, consistent differences between IPL-derived TEX 86 and CL-TEX 86 were found. These could be explained by a different composition of CL-GDGT of the glyco-and phospholipids, in combination with dissimilar degradation rates of phospholipids vs. glycolipids. We also observed consistent differences in both IPL-derived and CL-TEX 86 between the different cores, equivalent to 3°C when converted to temperature, despite the proximity of the core locations. These differences may potentially be due to a larger addition of GDGTs produced in deeper, colder waters to the (sub)surface-derived GDGTs for the deeper core sites.

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Diversity of Archaea

Swan

Valentine

2009

Encyclopedia of Life Sciences

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The Archaea are a group of microbes that form one of three domains of life on Earth. Studies with isolated strains have revealed an archaeal metabolic diversity rivaling that found within the domain Bacteria, and molecular surveys have revealed that archaea occupy a broader range of environments than was suspected based on the physiology of isolates. Archaea are also the most abundant and active microbial component in some environments, typically where their adaptations to chronic energy stress provide selective advantage over bacteria. Ongoing studies of uncultured archaea are likely to reveal important impacts on Earth's elemental and energy cycles.

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Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic

Cited by 243 publications

References 30 publications

Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum zone. Part II: Selective preservation and degradation in sediments and consequences for the TEX86

Diversity of Archaea

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