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Reports of biogenic methane (CH₄) synthesis associated with a range of organisms have steadily accumulated in the literature. This has not happened without controversy and in most cases the process is poorly understood at the gene and enzyme levels. In marine and freshwater environments, CH₄ supersaturation of oxic surface waters has been termed the “methane paradox” because biological CH₄ synthesis is viewed to be a strictly anaerobic process carried out by O₂-sensitive methanogens. Interest in this phenomenon has surged within the past decade because of the importance of understanding sources and sinks of this potent greenhouse gas. In our work on Yellowstone Lake in Yellowstone National Park, we demonstrate microbiological conversion of methylamine to CH₄ and isolate and characterize an Acidovorax sp. capable of this activity. Furthermore, we identify and clone a gene critical to this process (encodes pyridoxylamine phosphate-dependent aspartate aminotransferase) and demonstrate that this property can be transferred to Escherichia coli with this gene and will occur as a purified enzyme. This previously unrecognized process sheds light on environmental cycling of CH₄, suggesting that O₂-insensitive, ecologically relevant aerobic CH₄ synthesis is likely of widespread distribution in the environment and should be considered in CH₄ modeling efforts.

The atmospheric and deep sea reservoirs of carbon dioxide are linked via physical, chemical, and biological processes. The last of these include photosynthesis, particle settling, and organic matter remineralization, and are collectively termed the \"biological carbon pump.\" Herein, we present results from a 13-y (1992-2004) sediment trap experiment conducted in the permanently oligotrophic North Pacific Subtropical Gyre that document a large, rapid, and predictable summertime (July 15-August 15) pulse in particulate matter export to the deep sea (4,000 m). Peak daily fluxes of particulate matter during the summer export pulse (SEP) average 408, 283, 24.1, 1.1, and 67.5 μmol.m⁻².d⁻¹ for total carbon, organic carbon, nitrogen, phosphorus (PP), and biogenic silica, respectively. The SEP is approximately threefold greater than mean wintertime particle fluxes and fuels more efficient carbon sequestration because of low remineralization during downward transit that leads to elevated total carbon/PP and organic carbon/PP particle stoichiometry (371:1 and 250:1, respectively). Our long-term observations suggest that seasonal changes in the microbial assemblage, namely, summertime increases in the biomass and productivity of symbiotic nitrogen-fixing cyanobacteria in association with diatoms, are the main cause of the prominent SEP. The recurrent SEP is enigmatic because it is focused in time despite the absence of any obvious predictable stimulus or habitat condition. We hypothesize that changes in day length (photoperiodism) may be an important environmental cue to initiate aggregation and subsequent export of organic matter to the deep sea.

Trace elements sustain biological productivity, yet the significance of trace element mobilization and export in subglacial runoff from ice sheets is poorly constrained at present. Here, we present size-fractionated (0.02, 0.22, and 0.45 μm) concentrations of trace elements in subglacial waters from the Greenland Ice Sheet (GrIS) and the Antarctic Ice Sheet (AIS). Concentrations of immobile trace elements (e.g., Al, Fe, Ti) far exceed global riverine and open ocean mean values and highlight the importance of subglacial aluminosilicate mineral weathering and lack of retention of these species in sediments. Concentrations are higher from the AIS than the GrIS, highlighting the geochemical consequences of prolonged water residence times and hydrological isolation that characterize the former. The enrichment of trace elements (e.g., Co, Fe, Mn, and Zn) in subglacial meltwaters compared with seawater and typical riverine systems, together with the likely sensitivity to future ice sheet melting, suggests that their export in glacial runoff is likely to be important for biological productivity. For example, our dissolved Fe concentration (20,900 nM) and associated flux values (1.4 Gmol y−1) from AIS to the Fe-deplete Southern Ocean exceed most previous estimates by an order of magnitude. The ultimate fate of these micronutrients will depend on the reactivity of the dominant colloidal size fraction (likely controlled by nanoparticulate Al and Fe oxyhydroxide minerals) and estuarine processing. We contend that ice sheets create highly geochemically reactive particulates in subglacial environments, which play a key role in trace elemental cycles, with potentially important consequences for global carbon cycling.

Atmospheric carbon dioxide (CO₂) is increasing at an accelerating rate, primarily due to fossil fuel combustion and land use change. A substantial fraction of anthropogenic CO₂ emissions is absorbed by the oceans, resulting in a reduction of seawater pH. Continued acidification may over time have profound effects on marine biota and biogeochemical cycles. Although the physical and chemical basis for ocean acidification is well understood, there exist few field data of sufficient duration, resolution, and accuracy to document the acidification rate and to elucidate the factors governing its variability. Here we report the results of nearly 20 years of time-series measurements of seawater pH and associated parameters at Station ALOHA in the central North Pacific Ocean near Hawaii. We document a significant long-term decreasing trend of -0.0019 ± 0.0002 y⁻¹ in surface pH, which is indistinguishable from the rate of acidification expected from equilibration with the atmosphere. Superimposed upon this trend is a strong seasonal pH cycle driven by temperature, mixing, and net photosynthetic CO₂ assimilation. We also observe substantial interannual variability in surface pH, influenced by climate-induced fluctuations in upper ocean stability. Below the mixed layer, we find that the change in acidification is enhanced within distinct subsurface strata. These zones are influenced by remote water mass formation and intrusion, biological carbon remineralization, or both. We suggest that physical and biogeochemical processes alter the acidification rate with depth and time and must therefore be given due consideration when designing and interpreting ocean pH monitoring efforts and predictive models.

We present nearly 9 yrs (June 2005–December 2013) of measurements of upper-ocean (0 m to 125 m) dinitrogen (N₂) fixation rates, coupled with particulate nitrogen (PN) export at 150 m, from Station ALOHA (22° 45′N, 158°W) in the North Pacific Subtropical Gyre. Between June 2005 and June 2012, N₂ fixation rates were measured based on adding the 15N₂ tracer as a gas bubble. Beginning in August 2012, 15N₂ was first dissolved into filtered seawater and the 15N₂-enriched water was subsequently added to N₂ fixation incubations. Direct comparisons between methodologies revealed a robust relationship, with the addition of 15N₂-enriched seawater resulting in twofold greater depth-integrated rates than those derived from adding a 15N₂ gas bubble. Based on this relationship, we corrected the initial period of measurements, and the resulting rates of N₂ fixation averaged 230 ± 136 μmol N m−2 d−1 for the full time series (n = 71). Analysis of the 15N isotopic composition of sinking PN, together with an isotope mass balance model, revealed that N₂ fixation supported 26–47% of PN export during calendar years 2006–2013. The N export derived from these fractional contributions and measured N₂ fixation rates ranged between 502 and 919 μmol N m−2 d−1, which are equivalent to rates of net community production (NCP) of 1.5 to 2.7 mol C m−2 yr−1, consistent with previous independent estimates of NCP at this site.

Life in environments devoid of photosynthesis, such as on early Earth or in contemporary dark subsurface ecosystems, is supported by chemical energy. How, when, and where chemical nutrients released from the geosphere fuel chemosynthetic biospheres is fundamental to understanding the distribution and diversity of life, both today and in the geologic past. Hydrogen (H₂) is a potent reductant that can be generated when water interacts with reactive components of mineral surfaces such as silicate radicals and ferrous iron. Such reactive mineral surfaces are continually generated by physical comminution of bedrock by glaciers. Here, we show that dissolved H₂ concentrations in meltwaters from an iron and silicate mineral-rich basaltic glacial catchment were an order of magnitude higher than those from a carbonate-dominated catchment. Consistent with higher H₂ abundance, sediment microbial communities from the basaltic catchment exhibited significantly shorter lag times and faster rates of net H₂ oxidation and dark carbon dioxide (CO₂) fixation than those from the carbonate catchment, indicating adaptation to use H₂ as a reductant in basaltic catchments. An enrichment culture of basaltic sediments provided with H₂, CO₂, and ferric iron produced a chemolithoautotrophic population related to Rhodoferax ferrireducens with a metabolism previously thought to be restricted to (hyper) thermophiles and acidophiles. These findings point to the importance of physical and chemical weathering processes in generating nutrients that support chemosynthetic primary production. Furthermore, they show that differences in bedrock mineral composition can influence the supplies of nutrients like H₂ and, in turn, the diversity, abundance, and activity of microbial inhabitants.

Aquatic habitats beneath ice masses contain active microbial ecosystems capable of cycling important greenhouse gases, such as methane (CH 4 ). A large methane reservoir is thought to exist beneath the West Antarctic Ice Sheet, but its quantity, source and ultimate fate are poorly understood. For instance, O 2 supplied by basal melting should result in conditions favourable for aerobic methane oxidation. Here we use measurements of methane concentrations and stable isotope compositions along with genomic analyses to assess the sources and cycling of methane in Subglacial Lake Whillans (SLW) in West Antarctica. We show that sub-ice-sheet methane is produced through the biological reduction of CO 2 using H 2 . This methane pool is subsequently consumed by aerobic, bacterial methane oxidation at the SLW sediment–water interface. Bacterial oxidation consumes >99% of the methane and represents a significant methane sink, and source of biomass carbon and metabolic energy to the surficial SLW sediments. We conclude that aerobic methanotrophy may mitigate the release of methane to the atmosphere upon subglacial water drainage to ice sheet margins and during periods of deglaciation. Subglacial lakes contain active microbial ecosystems capable of cycling methane. In a subglacial lake in West Antarctica, methane that is produced is subsequently consumed, limiting the potential for methane emissions during lake drainage.

Relationships between methane (CH4) fluxes and environmental conditions have been extensively explored in saturated soils, while research has been less prevalent in aerated soils because of the relatively small magnitudes of CH4 fluxes that occur in dry soils. Our study builds on previous carbon cycle research at Tenderfoot Creek Experimental Forest, Montana, to identify how environmental conditions reflected by topographic metrics can be leveraged to estimate watershed scale CH4 fluxes from point scale measurements. Here, we measured soil CH4 concentrations and fluxes across a range of landscape positions (7 riparian, 25 upland), utilizing topographic and seasonal (29 May–12 September) gradients to examine the relationships between environmental variables, hydrologic dynamics, and CH4 emission and uptake. Riparian areas emitted small fluxes of CH4 throughout the study (median: 0.186 µg CH4–C m−2 h−1) and uplands increased in sink strength with dry-down of the watershed (median: −22.9 µg CH4–C m−2 h−1). Locations with volumetric water content (VWC) below 38 % were methane sinks, and uptake increased with decreasing VWC. Above 43 % VWC, net CH4 efflux occurred, and at intermediate VWC net fluxes were near zero. Riparian sites had near-neutral cumulative seasonal flux, and cumulative uptake of CH4 in the uplands was significantly related to topographic indices. These relationships were used to model the net seasonal CH4 flux of the upper Stringer Creek watershed (−1.75 kg CH4–C ha−1). This spatially distributed estimate was 111 % larger than that obtained by simply extrapolating the mean CH4 flux to the entire watershed area. Our results highlight the importance of quantifying the space–time variability of net CH4 fluxes as predicted by the frequency distribution of landscape positions when assessing watershed scale greenhouse gas balances.

The Subglacial Antarctic Lakes Scientific Access (SALSA) Project accessed Mercer Subglacial Lake using environmentally clean hot-water drilling to examine interactions among ice, water, sediment, rock, microbes and carbon reservoirs within the lake water column and underlying sediments. A ~0.4 m diameter borehole was melted through 1087 m of ice and maintained over ~10 days, allowing observation of ice properties and collection of water and sediment with various tools. Over this period, SALSA collected: 60 L of lake water and 10 L of deep borehole water; microbes >0.2 μm in diameter from in situ filtration of ~100 L of lake water; 10 multicores 0.32–0.49 m long; 1.0 and 1.76 m long gravity cores; three conductivity–temperature–depth profiles of borehole and lake water; five discrete depth current meter measurements in the lake and images of ice, the lake water–ice interface and lake sediments. Temperature and conductivity data showed the hydrodynamic character of water mixing between the borehole and lake after entry. Models simulating melting of the ~6 m thick basal accreted ice layer imply that debris fall-out through the ~15 m water column to the lake sediments from borehole melting had little effect on the stratigraphy of surficial sediment cores.

Ice streams that flow into Ross Ice Shelf are underlain by water-saturated sediments, a dynamic hydrological system, and subglacial lakes that intermittently discharge water downstream across grounding zones of West Antarctic Ice Sheet (WAIS). A 2.06 m composite sediment profile was recently recovered from Mercer Subglacial Lake, a 15 m deep water cavity beneath a 1087 m thick portion of the Mercer Ice Stream. We examined microbial abundances, used 16S rRNA gene amplicon sequencing to assess community structures, and characterized extracellular polymeric substances (EPS) associated with distinct lithologic units in the sediments. Bacterial and archaeal communities in the surficial sediments are more abundant and diverse, with significantly different compositions from those found deeper in the sediment column. The most abundant taxa are related to chemolithoautotrophs capable of oxidizing reduced nitrogen, sulfur, and iron compounds with oxygen, nitrate, or iron. Concentrations of dissolved methane and total organic carbon together with water content in the sediments are the strongest predictors of taxon and community composition. δ¹³C values for EPS (−25 to −30‰) are consistent with the primary source of carbon for biosynthesis originating from legacy marine organic matter. Comparison of communities to those in lake sediments under an adjacent ice stream (Whillans Subglacial Lake) and near its grounding zone provide seminal evidence for a subglacial metacommunity that is biogeochemically and evolutionarily linked through ice sheet dynamics and the transport of microbes, water, and sediments beneath WAIS.