The regulation of oxygen to low concentrations in marine oxygen-minimum zones

The Bay of Bengal hosts persistent, measurable, but sub-micromolar, concentrations of oxygen in its oxygen-minimum zone (OMZ). Such low-oxygen conditions are not necessarily rare in the global ocean and seem also to characterize the OMZ of the Pescadero Basin in the Gulf of California, as well as the outer edges of otherwise anoxic OMZs, such as can be found, for example, in the Eastern Tropical North Pacific. We show here that biological controls on oxygen consumption are required to allow the semistable persistence of low-oxygen conditions in OMZ settings; otherwise, only small changes in physical mixing or rates of primary production would drive the OMZ between anoxic and oxic states with potentially large swings in oxygen concentration. We propose that two controls are active: an oxygen-dependent control on oxygen respiration and an oxygen inhibition of denitrification. These controls, working alone and together, can generate low-oxygen concentrations over a wide variability in ocean mixing parameters. More broadly, we discuss the oxygen regulation of organic matter cycling and N2 production in OMZ settings. Modern biogeochemical models of nitrogen and oxygen cycling in OMZ settings do contain some of the parameterizations that we explore here. However, these models have not been applied to understanding the persistence of low, but measurable, concentrations of oxygen in settings like the Bay of Bengal, nor have they been applied to understanding what biological/physical processes control the transition from a weakly oxygenated state to a “functionally” anoxic state with implications for nitrogen cycling. Therefore, we believe that the approach here illuminates the relationship between oxygen and the biogeochemical cycling of carbon and nitrogen in settings like the Bay of Bengal. Furthermore, we believe that our results could further inform large-scale ocean models seeking to explore how global warming might influence the spread of low-oxygen waters, influencing the cycles of oxygen, carbon, and nitrogen in OMZ settings

Oxygen at Nanomolar Levels Reversibly Suppresses Process Rates and Gene Expression in Anammox and Denitrification in the Oxygen Minimum Zone off Northern Chile

A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O[subscript 2] and the sensitivity of the anaerobic N[subscript 2]-producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O[subscript 2] at nanomolar levels affects anammox and denitrification rates and the transcription of nitrogen cycle genes in the anoxic OMZ off Chile. Rates of anammox and denitrification were reversibly suppressed, most likely at the enzyme level. Fifty percent inhibition of N[subscript 2] and N[subscript 2]O production by denitrification was achieved at 205 and 297 nM O[subscript 2], respectively, whereas anammox was 50% inhibited at 886 nM O2. Coupled metatranscriptomic analysis revealed that transcripts encoding nitrous oxide reductase (nosZ), nitrite reductase (nirS), and nitric oxide reductase (norB) decreased in relative abundance above 200 nM O[subscript 2]. This O[subscript 2] concentration did not suppress the transcription of other dissimilatory nitrogen cycle genes, including nitrate reductase (narG), hydrazine oxidoreductase (hzo), and nitrite reductase (nirK). However, taxonomic characterization of transcripts suggested inhibition of narG transcription in gammaproteobacteria, whereas the transcription of anammox narG, whose gene product is likely used to oxidatively replenish electrons for carbon fixation, was not inhibited. The taxonomic composition of transcripts differed among denitrification enzymes, suggesting that distinct groups of microorganisms mediate different steps of denitrification. Sulfide addition (1 µM) did not affect anammox or O[subscript 2] inhibition kinetics but strongly stimulated N[subscript 2]O production by denitrification. These results identify new O[subscript 2] thresholds for delimiting marine nitrogen loss and highlight the utility of integrating biogeochemical and metatranscriptomic analyses.Gordon and Betty Moore FoundationAgouron InstituteDanish National Research Foundation (Grant DNRF53

Experimental Incubations Elicit Profound Changes in Community Transcription in OMZ Bacterioplankton

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for “challenging” microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4–13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations

Sustained increases in atmospheric oxygen and marine productivity in the Neoproterozoic and Palaeozoic eras

A geologically rapid Neoproterozoic oxygenation event is commonly linked to the appearance of marine animal groups in the fossil record. However, there is still debate about what evidence from the sedimentary geochemical record—if any—provides strong support for a persistent shift in surface oxygen immediately preceding the rise of animals. We present statistical learning analyses of a large dataset of geochemical data and associated geological context from the Neoproterozoic and Palaeozoic sedimentary record and then use Earth system modelling to link trends in redox-sensitive trace metal and organic carbon concentrations to the oxygenation of Earth’s oceans and atmosphere. We do not find evidence for the wholesale oxygenation of Earth’s oceans in the late Neoproterozoic era. We do, however, reconstruct a moderate long-term increase in atmospheric oxygen and marine productivity. These changes to the Earth system would have increased dissolved oxygen and food supply in shallow-water habitats during the broad interval of geologic time in which the major animal groups first radiated. This approach provides some of the most direct evidence for potential physiological drivers of the Cambrian radiation, while highlighting the importance of later Palaeozoic oxygenation in the evolution of the modern Earth system

Fluctuations in late Neoproterozoic atmospheric oxidation — Cr isotope chemostratigraphy and iron speciation of the late Ediacaran lower Arroyo del Soldado Group (Uruguay)

Oxygenation of the Earth's atmosphere occurred in two major steps, near the beginning and near the end of the Proterozoic Eon (2500 to 542 Ma ago), but the details of this history are unclear. Chromium isotopes in iron-rich chemical sediments offer a potential to highlight fine-scale fluctuations in the oxygenation of the oceans and atmosphere and to add a further dimension in the use of redox-sensitive tracers to solve the question regarding fluctuations of atmospheric oxygen levels and their consequences for Earth's climate. We observe strong positive fractionations in Cr isotopes (δ^(53)Cr up to + 5.0‰) in iron-rich cherts and banded iron formation horizons within the Arroyo del Soldado Group (Ediacaran; Uruguay) that can be explained by rapid, effective oxidation of Fe(II)-rich surface waters. These fluctuations are correlated with variations in ratios of highly reactive iron (Fe_(HR)) to total iron (Fe_(tot)) which indicate a predominance of anoxic water columns (Fe_(HR)/Fe_(tot) > 0.38) during the onset of oxidation pulses. We favor the scenario by which isotopically heavy Cr(VI) entered the basin after pulses of oxidative weathering on land and in which Fe(II) accumulated in the water column. Neodymium isotopes reveal that these oxygenation pulses were followed by increased influxes to the basin of continental crust-derived detrital components of Paleoproterozoic (Nd T_(DM) model ages = 2.1–2.2 Ga) provenance typical of the Rio de la Plata Craton. The association of positive δ^(53)Cr–ferruginous (Fe_(HR)/Fe_(tot) > 0.38) stratigraphic intervals with low-diversity acritarch assemblages dominated by Bavlinella faveolata strongly support models postulating a stratified, eutrophic Neoproterozoic ocean. Thus, even within a few million years of the Precambrian–Cambrian boundary, paleoceanographic conditions resembled more those of Paleoproterozoic oceans than Phanerozoic and present oceans. This highlights the sheer magnitude of ecological changes at the Precambrian–Cambrian transition, changes which ultimately led to the demise of the Precambrian world and the birth of the metazoan-dominated Phanerozoic

Sulfur and oxygen isotope study of sulfate reduction in experiments with natural populations from Fællestrand, Denmark

This study investigates the sulfur and oxygen isotope fractionations of dissimilatory sulfate reduction and works to reconcile the relationships between the oxygen and sulfur isotopic and elemental systems. We report results of experiments with natural populations of sulfate-reducing bacteria using sediment and seawater from a marine lagoon at Fællestrand on the northern shore of the island of Fyn, Denmark. The experiments yielded relatively large magnitude sulfur isotope fractionations for dissimilatory sulfate reduction (up to approximately 45‰ for 34S/32S) with higher δ18O accompanying higher δ34S, similar to that observed in previous studies. The seawater used in the experiments was spiked by addition of 17O-labeled water and the 17O content of residual sulfate was found to depend on the fraction of sulfate reduced in the experiments. The 17O data provides evidence for recycling of sulfur from metabolic intermediates and for an 18O/16O fractionation of ∼25-30‰ for dissimilatory sulfate reduction. The close correlation between the 17O data and the sulfur isotope data suggests that isotopic exchange between cell water and external water (reactor water) was rapid under experimental conditions. The molar ratio of oxygen exchange to sulfate reduction was found to be about 2.5. This value is slightly lower than observed in studies of natural ecosystems [e.g., Wortmann U. G., Chernyavsky B., Bernasconi S. M., Brunner B., Böttcher M. E. and Swart P. K. (2007) Oxygen isotope biogeochemistry of pore water sulfate in the deep biosphere: dominance of isotope exchange reactions with ambient water during microbial sulfate reduction (ODP Site 1130). Geochim. Cosmochim. Acta 71, 4221-4232]. Using recent models of sulfur isotope fractionations we find that our combined sulfur and oxygen isotopic data places constraints on the proportion of sulfate recycled to the medium (78-96%), the proportion of sulfur intermediate sulfite that was recycled by way of APS to sulfate and released back to the external sulfate pool (∼70%), and also that a fraction of the sulfur intermediates between sulfite and sulfide were recycled to sulfate. These parameters can be constrained because of the independent information provided by δ18O, δ34S, δ17O labels, and Δ33S. © 2008 Elsevier Ltd. All rights reserved

Pelagic photoferrotrophy and iron cycling in a modern ferruginous basin

8 páginas, 3 figurasIron-rich (ferruginous) ocean chemistry prevailed throughout most of Earth’s early history. Before the evolution and proliferation of oxygenic photosynthesis, biological production in the ferruginous oceans was likely driven by photoferrotrophic bacteria that oxidize ferrous iron {Fe(II)} to harness energy from sunlight, and fix inorganic carbon into biomass. Photoferrotrophs may thus have fuelled Earth’s early biosphere providing energy to drive microbial growth and evolution over billions of years. Yet, photoferrotrophic activity has remained largely elusive on the modern Earth, leaving models for early biological production untested and imperative ecological context for the evolution of life missing. Here, we show that an active community of pelagic photoferrotrophs comprises up to 30% of the total microbial community in illuminated ferruginous waters of Kabuno Bay (KB), East Africa (DR Congo). These photoferrotrophs produce oxidized iron {Fe(III)} and biomass, and support a diverse pelagic microbial community including heterotrophic Fe(III)-reducers, sulfate reducers, fermenters and methanogens. At modest light levels, rates of photoferrotrophy in KB exceed those predicted for early Earth primary production, and are sufficient to generate Earth’s largest sedimentary iron ore deposits. Fe cycling, however, is efficient, and complex microbial community interactions likely regulate Fe(III) and organic matter export from the photic zone.This work was partially supported by Belgian (FNRS 2.4.515.11 and BELSPO SD/AR/02A contracts), Danish (grant no. DNRF53 to DEC), and European (grant no. ERC-StG 240002, for stable isotope measurements) funds. AVB is a senior research associate at the FRS-FNRS. SAC was supported by the Agouron institute.Peer reviewe

The impact of Helicobacter pylori infection on the gastric microbiota of the rhesus macaque.

Helicobacter pylori colonization is highly prevalent among humans and causes significant gastric disease in a subset of those infected. When present, this bacterium dominates the gastric microbiota of humans and induces antimicrobial responses in the host. Since the microbial context of H. pylori colonization influences the disease outcome in a mouse model, we sought to assess the impact of H. pylori challenge upon the pre-existing gastric microbial community members in the rhesus macaque model. Deep sequencing of the bacterial 16S rRNA gene identified a community profile of 221 phylotypes that was distinct from that of the rhesus macaque distal gut and mouth, although there were taxa in common. High proportions of both H. pylori and H. suis were observed in the post-challenge libraries, but at a given time, only one Helicobacter species was dominant. However, the relative abundance of non-Helicobacter taxa was not significantly different before and after challenge with H. pylori. These results suggest that while different gastric species may show competitive exclusion in the gastric niche, the rhesus gastric microbial community is largely stable despite immune and physiological changes due to H. pylori infection

The impact of Helicobacter pylori infection on the gastric microbiota of the rhesus macaque.

Helicobacter pylori colonization is highly prevalent among humans and causes significant gastric disease in a subset of those infected. When present, this bacterium dominates the gastric microbiota of humans and induces antimicrobial responses in the host. Since the microbial context of H. pylori colonization influences the disease outcome in a mouse model, we sought to assess the impact of H. pylori challenge upon the pre-existing gastric microbial community members in the rhesus macaque model. Deep sequencing of the bacterial 16S rRNA gene identified a community profile of 221 phylotypes that was distinct from that of the rhesus macaque distal gut and mouth, although there were taxa in common. High proportions of both H. pylori and H. suis were observed in the post-challenge libraries, but at a given time, only one Helicobacter species was dominant. However, the relative abundance of non-Helicobacter taxa was not significantly different before and after challenge with H. pylori. These results suggest that while different gastric species may show competitive exclusion in the gastric niche, the rhesus gastric microbial community is largely stable despite immune and physiological changes due to H. pylori infection