Description: Around 50% of humankind relies on groundwater aquifers as a source of drinking water. We investigated the age, geochemistry, and microbiology of 138 groundwaters from 87 monitoring wells (〈250m depth) located in 14 aquifers in the Canadian Prairie. This data collection contains geological, physical, geochemical, gas, isotope and other contextual data, as well as microbial cell counts, 16S rRNA gene sequences, community diversity metrics and micrographs. Geochemistry and microbial ecology showed consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially of organic carbon-rich strata, contained on average more cells (up to 1.4'107/mL) than younger groundwaters, challenging current estimates of global groundwater population sizes. Substantial concentrations of dissolved oxygen (0.52±0.12mg/L [mean±SE]; n=57) in older groundwaters could support aerobic lifestyles in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicated that “dark oxygen” was produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.

Description: Groundwater ecosystems are globally widespread yet still poorly understood. We investigated the microbiology of 〉100 groundwater samples from 90 monitoring wells (〈250m depth) located in 14 aquifers in the Canadian Prairie. This file contains microscopic images of 45 groundwater samples from aquifers in the Canadian Prairie, collected between 2015 and 2020. The study area comprised 14 major aquifers and a geographic area of ~210.000 km2. The goal of the study was to understand the links between the biogeochemistry and microbial ecology of groundwater ecosystems in diverse geological settings on a broad spatial scale. Details concerning cell staining and microscopy can be found in the associated publication by Ruff et al. 2023.

Description: The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.

Description: The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.

Description: Benthic nitrogen cycling in the Mauritanian upwelling region (NW Africa) was studied in June 2014 from the shelf to the upper slope where minimum bottom water O 2 concentrations of 25 µM were recorded. Benthic incubation chambers were deployed at 9 stations to measure fluxes of O 2 , dissolved inorganic carbon (DIC) and nutrients (NO 3 - , NO 2 - , NH 4 + , PO 4 3- , H 4 SiO 4 ) along with the N and O isotopic composition of nitrate (δ 15 N-NO 3 - and δ 18 O-NO 3 - ) and ammonium (δ 15 N-NH 4 + ). O 2 and DIC fluxes were similar to those measured during a previous campaign in 2011 whereas NH 4 + and PO 4 3- fluxes on the shelf were 2 – 3 times higher and possibly linked to a long-term decline in bottom water O 2 concentrations. The mean isotopic fractionation of NO 3 - uptake on the margin, inferred from the loss of NO 3 - inside the chambers, was 1.5 ± 0.4 ‰ for 15/14 N ( 15 ϵ app ) and 2.0 ± 0.5 ‰ for 18/16 O ( 18 ϵ app ). The mean 18 ϵ app : 15 ϵ app ratio on the shelf (〈 100 m) was 2.1 ± 0.3, and higher than the value of 1 expected for microbial NO 3 - reduction. The 15 ϵ app are similar to previously reported isotope effects for NO 3 - respiration in marine sediments but lower than determined in 2011 at a same site on the shelf. The sediments were also a source of 15 N-enriched NH 4 + (9.0 ± 0.7 ‰). A numerical model tuned to the benthic flux data and that specifically accounts for the efflux of 15 N-enriched NH 4 + from the seafloor, predicted a net benthic isotope effect of N loss ( 15 ϵ sed ) of 3.6 ‰; far above the more widely considered value of ~0‰. This result is further evidence that the assumption of a universally low or negligible benthic N isotope effect is not applicable to oxygen-deficient settings. The model further suggests that 18 ϵ app : 15 ϵ app trajectories > 1 in the benthic chambers are most likely due to aerobic ammonium oxidation and nitrite oxidation in surface sediments rather than anammox, in agreement with published observations in the water column of oxygen deficient regions.

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 12 (2015): 7483-7502, doi:10.5194/bg-12-7483-2015.

Description: Nitrogen (N) is a key component of fundamental biomolecules. Hence, its cycling and availability are central factors governing the extent of ecosystems across the Earth. In the organic-lean sediment porewaters underlying the oligotrophic ocean, where low levels of microbial activity persist despite limited organic matter delivery from overlying water, the extent and modes of nitrogen transformations have not been widely investigated. Here we use the N and oxygen (O) isotopic composition of porewater nitrate (NO3−) from a site in the oligotrophic North Atlantic (Integrated Ocean Drilling Program – IODP) to determine the extent and magnitude of microbial nitrate production (via nitrification) and consumption (via denitrification). We find that NO3- accumulates far above bottom seawater concentrations (~ 21 μM) throughout the sediment column (up to ~ 50 μM) down to the oceanic basement as deep as 90 m b.s.f. (below sea floor), reflecting the predominance of aerobic nitrification/remineralization within the deep marine sediments. Large changes in the δ15N and δ18O of nitrate, however, reveal variable influence of nitrate respiration across the three sites. We use an inverse porewater diffusion–reaction model, constrained by the N and O isotope systematics of nitrification and denitrification and the porewater NO3- isotopic composition, to estimate rates of nitrification and denitrification throughout the sediment column. Results indicate variability of reaction rates across and within the three boreholes that are generally consistent with the differential distribution of dissolved oxygen at this site, though not necessarily with the canonical view of how redox thresholds separate nitrate regeneration from dissimilative consumption spatially. That is, we provide stable isotopic evidence for expanded zones of co-occurring nitrification and denitrification. The isotope biogeochemical modeling also yielded estimates for the δ15N and δ18O of newly produced nitrate (δ15NNTR (NTR, referring to nitrification) and δ18ONTR), as well as the isotope effect for denitrification (15ϵDNF) (DNF, referring to denitrification), parameters with high relevance to global ocean models of N cycling. Estimated values of δ15NNTR were generally lower than previously reported δ15N values for sinking particulate organic nitrogen in this region. We suggest that these values may be, in part, related to sedimentary N2 fixation and remineralization of the newly fixed organic N. Values of δ18ONTR generally ranged between −2.8 and 0.0 ‰, consistent with recent estimates based on lab cultures of nitrifying bacteria. Notably, some δ18ONTR values were elevated, suggesting incorporation of 18O-enriched dissolved oxygen during nitrification, and possibly indicating a tight coupling of NH4+ and NO2− oxidation in this metabolically sluggish environment. Our findings indicate that the production of organic matter by in situ autotrophy (e.g., nitrification, nitrogen fixation) supplies a large fraction of the biomass and organic substrate for heterotrophy in these sediments, supplementing the small organic-matter pool derived from the overlying euphotic zone. This work sheds new light on an active nitrogen cycle operating, despite exceedingly low carbon inputs, in the deep sedimentary biosphere.

Description: Funding for this work was provided in part by the International Ocean Drilling Program, Woods Hole Oceanographic Institution and a grant from the Center for Dark Energy Biosphere Investigations (C-DEBI) to SW and WZ and a postdoc fellowship to CB from C-DEBI. WZ was supported in part by NSF grant OCE-1131671.

Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 15595, doi:10.1038/ncomms15595.

Description: Although increasing atmospheric nitrous oxide (N2O) has been linked to nitrogen loading, predicting emissions remains difficult, in part due to challenges in disentangling diverse N2O production pathways. As coastal ecosystems are especially impacted by elevated nitrogen, we investigated controls on N2O production mechanisms in intertidal sediments using novel isotopic approaches and microsensors in flow-through incubations. Here we show that during incubations with elevated nitrate, increased N2O fluxes are not mediated by direct bacterial activity, but instead are largely catalysed by fungal denitrification and/or abiotic reactions (e.g., chemodenitrification). Results of these incubations shed new light on nitrogen cycling complexity and possible factors underlying variability of N2O fluxes, driven in part by fungal respiration and/or iron redox cycling. As both processes exhibit N2O yields typically far greater than direct bacterial production, these results emphasize their possibly substantial, yet widely overlooked, role in N2O fluxes, especially in redox-dynamic sediments of coastal ecosystems.

Description: D.D.B. acknowledges support from the Max Planck Institute for Marine Microbiology. This work was supported by the National Science Foundation grants to W.Z. and S.D.W. (OCE-1260373) and to S.D.W. (EAR-1252161).

Description: Author Posting. © The Oceanography Society, 2018. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 31, no. 1, supplement (2018): 39-41.

Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Visser, A., Wankel, S. D., Niklaus, P. A., Byrne, J. M., Kappler, A. A., & Lehmann, M. F. Impact of reactive surfaces on the abiotic reaction between nitrite and ferrous iron and associated nitrogen and oxygen isotope dynamics. Biogeosciences, 17(16), (2020): 4355-4374, doi:10.5194/bg-17-4355-2020.

Description: Anaerobic nitrate-dependent Fe(II) oxidation (NDFeO) is widespread in various aquatic environments and plays a major role in iron and nitrogen redox dynamics. However, evidence for truly enzymatic, autotrophic NDFeO remains limited, with alternative explanations involving the coupling of heterotrophic denitrification with the abiotic oxidation of structurally bound or aqueous Fe(II) by reactive intermediate nitrogen (N) species (chemodenitrification). The extent to which chemodenitrification is caused (or enhanced) by ex vivo surface catalytic effects has not been directly tested to date. To determine whether the presence of either an Fe(II)-bearing mineral or dead biomass (DB) catalyses chemodenitrification, two different sets of anoxic batch experiments were conducted: 2 mM Fe(II) was added to a low-phosphate medium, resulting in the precipitation of vivianite (Fe3(PO4)2), to which 2 mM nitrite (NO−2) was later added, with or without an autoclaved cell suspension (∼1.96×108 cells mL−1) of Shewanella oneidensis MR-1. Concentrations of nitrite (NO−2), nitrous oxide (N2O), and iron (Fe2+, Fetot) were monitored over time in both set-ups to assess the impact of Fe(II) minerals and/or DB as catalysts of chemodenitrification. In addition, the natural-abundance isotope ratios of NO−2 and N2O (δ15N and δ18O) were analysed to constrain the associated isotope effects. Up to 90 % of the Fe(II) was oxidized in the presence of DB, whereas only ∼65 % of the Fe(II) was oxidized under mineral-only conditions, suggesting an overall lower reactivity of the mineral-only set-up. Similarly, the average NO−2 reduction rate in the mineral-only experiments (0.004±0.003 mmol L−1 d−1) was much lower than in the experiments with both mineral and DB (0.053±0.013 mmol L−1 d−1), as was N2O production (204.02±60.29 nmol L−1 d−1). The N2O yield per mole NO−2 reduced was higher in the mineral-only set-ups (4 %) than in the experiments with DB (1 %), suggesting the catalysis-dependent differential formation of NO. N-NO−2 isotope ratio measurements indicated a clear difference between both experimental conditions: in contrast to the marked 15N isotope enrichment during active NO−2 reduction (15εNO2=+10.3 ‰) observed in the presence of DB, NO−2 loss in the mineral-only experiments exhibited only a small N isotope effect (〈+1 ‰). The NO−2-O isotope effect was very low in both set-ups (18εNO2 〈1 ‰), which was most likely due to substantial O isotope exchange with ambient water. Moreover, under low-turnover conditions (i.e. in the mineral-only experiments as well as initially in experiments with DB), the observed NO−2 isotope systematics suggest, transiently, a small inverse isotope effect (i.e. decreasing NO−2 δ15N and δ18O with decreasing concentrations), which was possibly related to transitory surface complexation mechanisms. Site preference (SP) of the 15N isotopes in the linear N2O molecule for both set-ups ranged between 0 ‰ and 14 ‰, which was notably lower than the values previously reported for chemodenitrification. Our results imply that chemodenitrification is dependent on the available reactive surfaces and that the NO−2 (rather than the N2O) isotope signatures may be useful for distinguishing between chemodenitrification catalysed by minerals, chemodenitrification catalysed by dead microbial biomass, and possibly true enzymatic NDFeO.

Description: This research has been supported by the Deutsche Forschungsgemeinschaft (DFG; grant no. GRK 1708, “Molecular principles of bacterial survival strategies”) and the University of Basel, Switzerland.

Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Long, M. H., Sutherland, K., Wankel, S. D., Burdige, D. J., & Zimmerman, R. C. Ebullition of oxygen from seagrasses under supersaturated conditions. Limnology and Oceanography, (2019), doi:10.1002/lno.11299.

Description: Gas ebullition from aquatic systems to the atmosphere represents a potentially important fraction of primary production that goes unquantified by measurements of dissolved gas concentrations. Although gas ebullition from photosynthetic surfaces has often been observed, it is rarely quantified. The resulting underestimation of photosynthetic activity may significantly bias the determination of ecosystem trophic status and estimated rates of biogeochemical cycling from in situ measures of dissolved oxygen. Here, we quantified gas ebullition rates in Zostera marina meadows in Virginia, U.S.A. using simple funnel traps and analyzed the oxygen concentration and isotopic composition of the captured gas. Maximum hourly rates of oxygen ebullition (3.0 mmol oxygen m−2 h−1) were observed during the coincidence of high irradiance and low tides, particularly in the afternoon when oxygen and temperature maxima occurred. The daily ebullition fluxes (up to 11 mmol oxygen m−2 d−1) were roughly equivalent to net primary production rates determined from dissolved oxygen measurements indicating that bubble ebullition can represent a major component of primary production that is not commonly included in ecosystem‐scale estimates. Oxygen content comprised 20–40% of the captured bubble gas volume and correlated negatively with its δ18O values, consistent with a predominance of mixing between the higher δ18O of atmospheric oxygen in equilibrium with seawater and the lower δ18O of oxygen derived from photosynthesis. Thus, future studies interested in the metabolism of highly productive, shallow water ecosystems, and particularly those measuring in situ oxygen flux, should not ignore the bubble formation and ebullition processes described here.

Description: Two anonymous reviewers provided thoughtful contributions that improved this manuscript. We thank Miraflor Santos, Victoria Hill, David Ruble, Jeremy Bleakney, and Brian Collister for assistance in the field and the staff of the Anheuser‐Busch Coastal Research Center for logistical support. This work was supported by NSF OCE grants 1633951 (to MHL) and 1635403 (to RCZ and DJB), NASA Fellowship NESSF NNX15AR62H (to KS), and a fellowship from the Hansewissenschaftskolleg (Institute for Advanced Studies; to SDW).