Bonnie X. Chang

Denitrification as the dominant nitrogen loss process in the Arabian Sea

Primary production in over half of the world’s oceans is limited by fixed nitrogen availability. The main loss term from the fixed nitrogen inventory is the production of dinitrogen gas (N2) by heterotrophic denitrification or the more recently discovered autotrophic process, anaerobic ammonia oxidation (anammox). Oceanic oxygen minimum zones (OMZ) are responsible for about 35% of oceanic N2 production and up to half of that occurs in the Arabian Sea. Although denitrification was long thought to be the only loss term, it has recently been argued that anammox alone is responsible for fixed nitrogen loss in the OMZs. Here we measure denitrification and anammox rates and quantify the abundance of denitrifying and anammox bacteria in the OMZ regions of the Eastern Tropical South Pacific and the Arabian Sea. We find that denitrification rather than anammox dominates the N2 loss term in the Arabian Sea, the largest and most intense OMZ in the world ocean. In seven of eight experiments in the Arabian Sea denitrification is responsible for 87–99% of the total N2 production. The dominance of denitrification is reproducible using two independent isotope incubation methods. In contrast, anammox is dominant in the Eastern Tropical South Pacific OMZ, as detected using one of the isotope incubation methods, as previously reported. The abundance of denitrifying bacteria always exceeded that of anammox bacteria by up to 7- and 19-fold in the Eastern Tropical South Pacific and Arabian Sea, respectively. Geographic and temporal variability in carbon supply may be responsible for the different contributions of denitrification and anammox in these two OMZs. The large contribution of denitrification to N2 loss in the Arabian Sea indicates the global significance of denitrification to the oceanic nitrogen budget.

Nitrogen losses in anoxic marine sediments driven by Thioploca-anammox bacterial consortia

Ninety per cent of marine organic matter burial occurs in continental margin sediments, where a substantial fraction of organic carbon escapes oxidation and enters long-term geologic storage within sedimentary rocks. In such environments, microbial metabolism is limited by the diffusive supply of electron acceptors. One strategy to optimize energy yields in a resource-limited habitat is symbiotic metabolite exchange among microbial associations. Thermodynamic and geochemical considerations indicate that microbial co-metabolisms are likely to play a critical part in sedimentary organic carbon cycling. Yet only one association, between methanotrophic archaea and sulphate-reducing bacteria, has been demonstrated in marine sediments in situ, and little is known of the role of microbial symbiotic interactions in other sedimentary biogeochemical cycles. Here we report in situ molecular and incubation-based evidence for a novel symbiotic consortium between two chemolithotrophic bacteria—anaerobic ammonium-oxidizing (anammox) bacteria and the nitrate-sequestering sulphur-oxidizing Thioploca species—in anoxic sediments of the Soledad basin at the Mexican Pacific margin. A mass balance of benthic solute fluxes and the corresponding nitrogen isotope composition of nitrate and ammonium fluxes indicate that anammox bacteria rely on Thioploca species for the supply of metabolic substrates and account for about 57 ± 21 per cent of the total benthic N2 production. We show that Thioploca–anammox symbiosis intensifies benthic fixed nitrogen losses in anoxic sediments, bypassing diffusion-imposed limitations by efficiently coupling the carbon, nitrogen and sulphur cycles.

Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium

Marine oxygen minimum zones (OMZs) are expanding regions of intense nitrogen cycling. Up to half of the nitrogen available for marine organisms is removed from the ocean in these regions. Metagenomic studies have identified an abundant group of sulfur-oxidizing bacteria (SUP05) with the genetic potential for nitrogen cycling and loss in OMZs. However, SUP05 have defied cultivation and their physiology remains untested. We cultured, sequenced and tested the physiology of an isolate from the SUP05 clade. We describe a facultatively anaerobic sulfur-oxidizing chemolithoautotroph that produces nitrite and consumes ammonium under anaerobic conditions. Genetic evidence that closely related strains are abundant at nitrite maxima in OMZs suggests that sulfur-oxidizing chemoautotrophs from the SUP05 clade are a potential source of nitrite, fueling competing nitrogen removal processes in the ocean.

Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean

Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day−1) occurred in coastal surface waters and lowest detectable rates (~0.2 nM day−1) were found in the anoxic region of offshore stations. BNF was not detectable in most samples from oxygen-depleted waters. The composition of the N2-fixing assemblage was investigated by sequencing of nifH genes. The diazotrophic assemblage in surface waters contained mainly Proteobacterial sequences (Cluster I nifH), while both Proteobacterial sequences and sequences with high identities to those of anaerobic microbes characterized as Clusters III and IV type nifH sequences were found in the anoxic waters. Our results indicate modest input of N through BNF in oxygen-depleted zones mainly due to the activity of proteobacterial diazotrophs.