Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean.

Ammonia-oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%-40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen-containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%-1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.

Towards Integrating Evolution, Metabolism, and Climate Change Studies of Marine Ecosystems.

Global environmental changes are challenging the structure and functioning of ecosystems. However, a mechanistic understanding of how global environmental changes will affect ecosystems is still lacking. The complex and interacting biological and physical processes spanning vast temporal and spatial scales that constitute an ecosystem make this a formidable problem. A unifying framework based on ecological theory, that considers fundamental and realized niches, combined with metabolic, evolutionary, and climate change studies, is needed to provide the mechanistic understanding required to evaluate and forecast the future of marine communities, ecosystems, and their services.

A double-tracer radioisotope approach to assess simultaneous bioaccumulation of caesium in the olive flounder Paralichthys olivaceus.

To better understand bioaccumulation of radiocaesium in the commercially important Japanese flatfish, Paralichthys olivaceus, the uptake and depuration kinetics of caesium via both seawater and food were assessed simultaneously using controlled aquaria. The pre-conditioned fish were exposed to radionuclides via the two different pathways (aqueous versus dietary) concurrently using two isotopes of caesium, 137Cs and 134Cs, respectively. Dissolved caesium uptake was linear and did not reach a steady state over the course of the 8-day exposure period. Consumption of 134Cs-labelled food led to higher bioaccumulation rates of radioactive Cs than via seawater exposure of 137Cs during uptake and following depuration, though the model-derived long-lived biological half-lives of both pathways was approximately 66 d. Further development of this method for assessing multiple radiocaesium bioaccumulation pathways simultaneously could lead to a promising new approach for studying Cs contamination in marine organisms.

Response to Comment on "Dilution limits dissolved organic carbon utilization in the deep ocean".

Our recent finding that dilution limits dissolved organic carbon (DOC) utilization in the deep ocean has been criticized based on the common misconception that lability equates to rapid and complete utilization. Even when considering the redefinition of recalcitrant DOC recently proposed by Jiao et al., the dilution hypothesis best explains our experimental observations.

Ocean chemistry. Dilution limits dissolved organic carbon utilization in the deep ocean.

Oceanic dissolved organic carbon (DOC) is the second largest reservoir of organic carbon in the biosphere. About 72% of the global DOC inventory is stored in deep oceanic layers for years to centuries, supporting the current view that it consists of materials resistant to microbial degradation. An alternative hypothesis is that deep-water DOC consists of many different, intrinsically labile compounds at concentrations too low to compensate for the metabolic costs associated to their utilization. Here, we present experimental evidence showing that low concentrations rather than recalcitrance preclude consumption of a substantial fraction of DOC, leading to slow microbial growth in the deep ocean. These findings demonstrate an alternative mechanism for the long-term storage of labile DOC in the deep ocean, which has been hitherto largely ignored.

Conservation of dissolved organic matter molecular composition during mixing of the deep water masses of the northeast Atlantic Ocean.

Characterizing the composition of marine dissolved organic matter (DOM) is important for gaining insight into its role in oceanic biogeochemical cycles. Using Fourier transform ion cyclotron resonance mass spectrometry, we analyzed the molecular composition of solid phase extracted (SPE) DOM from the northeast Atlantic to investigate the specificity of the DOM pool of the individual major water masses of the North Atlantic. All 272 measured samples from depths ranging from 87 to 5609 m and latitudes from 24°N to 68°N shared 96% similarity (on a Bray-Curtis scale) in their DOM composition. Small variations between subsurface and deep samples and among latitudinal groupings were identified, but overall, water mass specific SPE-DOM composition was not apparent. A strong correlation between a calculated degradation index and water mass age indicates variability in portions of the DOM pool, and ocean-scale differences were observed between the North Atlantic and deep North Pacific. However, within the deep northeast Atlantic, conservative mixing primarily drives the molecular composition of SPE-DOM.

Export of submicron particulate organic matter to mesopelagic depth in an oligotrophic gyre.

Sixty percent of the world ocean by area is contained in oligotrophic gyres [Longhurst A (1995) Prog Oceanog 36:77-16], the biomass of which is dominated by picophytoplankton, including cyanobacteria and picoeukaryotic algae, as well as picoheterotrophs. Despite their recognized importance in carbon cycling in the surface ocean, the role of small cells and their detrital remains in the transfer of particulate organic matter (POM) to the deep ocean remains disputed. Because oligotrophic marine conditions are projected to expand under current climate trends, a better understanding of the role of small particles in the global carbon cycle is a timely goal. Here we use the lipid profiles, radiocarbon, and stable carbon isotopic signatures of lipids from the North Pacific Subtropical Gyre to show that in the surface ocean, lipids from submicron POM (here called extra-small POM) are distinct from larger classes of suspended POM. Remarkably, this distinct extra-small POM signature dominates the total lipids collected at mesopelagic depth, suggesting that the lipid component of mesopelagic POM primarily contains the exported remains of small particles. Transfer of submicron material to mesopelagic depths in this location is consistent with model results that claim the biological origin of exported carbon should be proportional to the distribution of cell types in the surface community, irrespective of cell size [Richardson TL, Jackson GA (2007) Science 315:838-840]. Our data suggest that the submicron component of exported POM is an important contributor to the global biological pump, especially in oligotrophic waters.

The radiocarbon signature of microorganisms in the mesopelagic ocean.

Several lines of evidence indicate that microorganisms in the meso- and bathypelagic ocean are metabolically active and respiring carbon. In addition, growing evidence suggests that archaea are fixing inorganic carbon in this environment. However, direct quantification of the contribution from deep ocean carbon sources to community production in the dark ocean remains a challenge. In this study, carbon flow through the microbial community at 2 depths in the mesopelagic zone of the North Pacific Subtropical Gyre was examined by exploiting the unique radiocarbon signatures (Delta(14)C) of the 3 major carbon sources in this environment. The radiocarbon content of nucleic acids, a biomarker for viable cells, isolated from size-fractionated particles (0.2-0.5 microm and >0.5 microm) showed the direct incorporation of carbon delivered by rapidly sinking particles. Most significantly, at the 2 mesopelagic depths examined (670 m and 915 m), carbon derived from in situ autotrophic fixation supported a significant fraction of the free-living microbial community (0.2-0.5 microm size fraction), but the contribution of chemoautotrophy varied markedly between the 2 depths. Results further showed that utilization of the ocean's largest reduced carbon reservoir, (14)C-depleted, dissolved organic carbon, was negligible in this environment. This isotopic portrait of carbon assimilation by the in situ, free-living microbial community, integrated over >50,000 L of seawater, implies that recent, photosynthetic carbon is not always the major carbon source supporting microbial community production in the mesopelagic realm.

Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon.

An ammonia-oxidizing, carbon-fixing archaeon, Candidatus "Nitrosopumilus maritimus," recently was isolated from a salt-water aquarium, definitively confirming that chemoautotrophy exists among the marine archaea. However, in other incubation studies, pelagic archaea also were capable of using organic carbon. It has remained unknown what fraction of the total marine archaeal community is autotrophic in situ. If archaea live primarily as autotrophs in the natural environment, a large ammonia-oxidizing population would play a significant role in marine nitrification. Here we use the natural distribution of radiocarbon in archaeal membrane lipids to quantify the bulk carbon metabolism of archaea at two depths in the subtropical North Pacific gyre. Our compound-specific radiocarbon data show that the archaea in surface waters incorporate modern carbon into their membrane lipids, and archaea at 670 m incorporate carbon that is slightly more isotopically enriched than inorganic carbon at the same depth. An isotopic mass balance model shows that the dominant metabolism at depth indeed is autotrophy (83%), whereas heterotrophic consumption of modern organic carbon accounts for the remainder of archaeal biomass. These results reflect the in situ production of the total community that produces tetraether lipids and are not subject to biases associated with incubation and/or culture experiments. The data suggest either that the marine archaeal community includes both autotrophs and heterotrophs or is a single population with a uniformly mixotrophic metabolism. The metabolic and phylogenetic diversity of the marine archaea warrants further exploration; these organisms may play a major role in the marine cycles of nitrogen and carbon.