Abundance and phylogenetic identity of archaeoplankton in the permanent oxygen minimum zone of the eastern tropical South Pacific

Belmar, Lucy; Molina, Verónica; Ulloa, Osvaldo

doi:10.1111/j.1574-6941.2011.01159.x

Cited by 55 publications

(67 citation statements)

References 76 publications

(130 reference statements)

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“…3). These patterns are consistent with the general vertical distribution of archaeal groups in the ETSP AMZ (31) and with the segregation of aerobic ammonia-oxidizing archaea and anaerobic anammox bacteria in the Arabian Sea (32).…”

Section: How Does Aerobic Metabolism Vary With Time and Space In Amzs?supporting

confidence: 72%

Microbial oceanography of anoxic oxygen minimum zones

Ulloa

Canfield

DeLong

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N 2 ) and nitrous oxide (N 2 O) gases. Anaerobic microbial processes, including the two pathways of N 2 production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitriterich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two "end points" represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.

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Section: How Does Aerobic Metabolism Vary With Time and Space In Amzs?supporting

confidence: 72%

Microbial oceanography of anoxic oxygen minimum zones

Ulloa

Canfield

DeLong

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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386

403

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“…The most abundant thaumarchaeal phylotype observed was affiliated with the Nitrosopumilus cluster, a group that contains cultivated, ammonium-oxidizing representatives (39) and has been observed in a wide array of marine environments (41,42). The Thaumarchaeota observed here displayed close relationships to those observed in permanent and seasonally anoxic OMZs and anoxic basins, such as the eastern tropical South Pacific and Saanich Inlet, respectively (43,44) (Fig. S1).…”

Section: Resultsmentioning

confidence: 66%

Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters

Bristow

Dalsgaard

Tiano

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O 2 ) sensitivity of these processes down to the O 2 concentrations present in the OMZ core (<10 nmol·L −1 ) is therefore essential for understanding and modeling nitrogen loss in OMZs. We determined rates of ammonium and nitrite oxidation in the seasonal OMZ off Concepcion, Chile at manipulated O 2 levels between 5 nmol·L −1 and 20 μmol·L −1 . Rates of both processes were detectable in the low nanomolar range (5-33 nmol·L −1 O 2 ), but demonstrated a strong dependence on O 2 concentrations with apparent half-saturation constants (K m s) of 333 ± 130 nmol·L −1 O 2 for ammonium oxidation and 778 ± 168 nmol·L −1 O 2 for nitrite oxidation assuming one-component Michaelis-Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis-Menten model, indicating a high-affinity component with a K m of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O 2 affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O 2 is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.is a key factor regulating biogeochemical cycling in the marine environment (1). Although the vast majority of the ocean remains well oxygenated, subsurface regions of extreme oxygen depletion can persist along eastern boundaries of the world's ocean basins. These regions are known as oxygen minimum zones (OMZs) and are located within the eastern tropical North and South Pacific, the Arabian Sea, and off the coast of Namibia, where oxygen depletion results from poor ventilation and a high export of organic matter from productive surface waters, generating high rates of subsurface oxygen consumption (2, 3).Oceanic waters characterized by oxygen-deficient conditions (<4.5 μmol·L −1 O 2 ) account for <0.1% of total ocean volume but for >30% of fixed nitrogen (N) loss (3-6) due to the onset of anaerobic processes, including denitrification and anammox (7-10). Both field and modeling observations point to the expansion of low oxygen regions as a result of global warming (11). Thus, to evaluate the biogeochemical impact of these regions, it is imperative to understand fully how oxygen controls the cycling of substrates involved in nitrogen loss pathways.Recent studies have quantified the oxygen sensitivity of anaerobic OMZ nitrogen transformations, finding that denitrification has relatively low oxygen tolerance with a half-inhibition concentration (IC 50 ) of 0.3 μmol·L −1 , compared with higher values for...

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“…They have been classified into two major groups, MGIIA and MGIIB, by their 16S ribosomal RNA (rRNA) (Massana et al, 2000;Martin-Cuadrado et al, 2008;Galand et al, 2009;Belmar et al, 2011). Two other groups, MGIIC and D, related to hydrothermal and deep samples have also been proposed (Belmar et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

“…Marine Euryarchaeota group II (MGII) are widely distributed in the global ocean (Massana et al, 2000) and are the dominant archaeal community within the euphotic zone of temperate waters (DeLong, 1992;Massana et al, 1997Massana et al, , 2000Karner et al, 2001;Herndl et al, 2005;DeLong et al, 2006;Belmar et al, 2011). They have been classified into two major groups, MGIIA and MGIIB, by their 16S ribosomal RNA (rRNA) (Massana et al, 2000;Martin-Cuadrado et al, 2008;Galand et al, 2009;Belmar et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

et al. 2014

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We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4 Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50 m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.

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Abundance and phylogenetic identity of archaeoplankton in the permanent oxygen minimum zone of the eastern tropical South Pacific

Cited by 55 publications

References 76 publications

Microbial oceanography of anoxic oxygen minimum zones

Microbial oceanography of anoxic oxygen minimum zones

Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters

A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

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