Life at the Frozen Limit: Microbial Carbon Metabolism Across a Late Pleistocene Permafrost Chronosequence.

Permafrost is an extreme habitat yet it hosts microbial populations that remain active over millennia. Using permafrost collected from a Pleistocene chronosequence (19 to 33 ka), we hypothesized that the functional genetic potential of microbial communities in permafrost would reflect microbial strategies to metabolize permafrost soluble organic matter (OM) in situ over geologic time. We also hypothesized that changes in the metagenome across the chronosequence would correlate with shifts in carbon chemistry, permafrost age, and paleoclimate at the time of permafrost formation. We combined high-resolution characterization of water-soluble OM by Fourier-transform ion-cyclotron-resonance mass spectrometry (FT-ICR MS), quantification of organic anions in permafrost water extracts, and metagenomic sequencing to better understand the relationships between the molecular-level composition of potentially bioavailable OM, the microbial community, and permafrost age. Both age and paleoclimate had marked effects on both the molecular composition of dissolved OM and the microbial community. The relative abundance of genes associated with hydrogenotrophic methanogenesis, carbohydrate active enzyme families, nominal oxidation state of carbon (NOSC), and number of identifiable molecular formulae significantly decreased with increasing age. In contrast, genes associated with fermentation of short chain fatty acids (SCFAs), the concentration of SCFAs and ammonium all significantly increased with age. We present a conceptual model of microbial metabolism in permafrost based on fermentation of OM and the buildup of organic acids that helps to explain the unique chemistry of ancient permafrost soils. These findings imply long-term in situ microbial turnover of ancient permafrost OM and that this pooled biolabile OM could prime ancient permafrost soils for a larger and more rapid microbial response to thaw compared to younger permafrost soils.

Microbial survival strategies in ancient permafrost: insights from metagenomics.

In permafrost (perennially frozen ground) microbes survive oligotrophic conditions, sub-zero temperatures, low water availability and high salinity over millennia. Viable life exists in permafrost tens of thousands of years old but we know little about the metabolic and physiological adaptations to the challenges presented by life in frozen ground over geologic time. In this study we asked whether increasing age and the associated stressors drive adaptive changes in community composition and function. We conducted deep metagenomic and 16 S rRNA gene sequencing across a Pleistocene permafrost chronosequence from 19 000 to 33 000 years before present (kyr). We found that age markedly affected community composition and reduced diversity. Reconstruction of paleovegetation from metagenomic sequence suggests vegetation differences in the paleo record are not responsible for shifts in community composition and function. Rather, we observed shifts consistent with long-term survival strategies in extreme cryogenic environments. These include increased reliance on scavenging detrital biomass, horizontal gene transfer, chemotaxis, dormancy, environmental sensing and stress response. Our results identify traits that may enable survival in ancient cryoenvironments with no influx of energy or new materials.

Hydrologic Controls on Nitrogen Cycling Processes and Functional Gene Abundance in Sediments of a Groundwater Flow-Through Lake.

The fate and transport of inorganic nitrogen (N) is a critically important issue for human and aquatic ecosystem health because discharging N-contaminated groundwater can foul drinking water and cause algal blooms. Factors controlling N-processing were examined in sediments at three sites with contrasting hydrologic regimes at a lake on Cape Cod, MA. These factors included water chemistry, seepage rates and direction of groundwater flow, and the abundance and potential rates of activity of N-cycling microbial communities. Genes coding for denitrification, anaerobic ammonium oxidation (anammox), and nitrification were identified at all sites regardless of flow direction or groundwater dissolved oxygen concentrations. Flow direction was, however, a controlling factor in the potential for N-attenuation via denitrification in the sediments. Potential rates of denitrification varied from 6 to 4500 pmol N/g/h from the inflow to the outflow side of the lake, owing to fundamental differences in the supply of labile organic matter. The results of laboratory incubations suggested that when anoxia and limiting labile organic matter prevailed, the potential existed for concomitant anammox and denitrification. Where oxic lake water was downwelling, potential rates of nitrification at shallow depths were substantial (1640 pmol N/g/h). Rates of anammox, denitrification, and nitrification may be linked to rates of organic N-mineralization, serving to increase N-mobility and transport downgradient.

Carbon isotope analysis of dissolved organic carbon in fresh and saline (NaCl) water via continuous flow cavity ring-down spectroscopy following wet chemical oxidation.

This work examines the performance and limitations of a wet chemical oxidation carbon analyser interfaced with a cavity ring-down spectrometer (WCO-CRDS) in a continuous flow (CF) configuration for measuring δ(13)C of dissolved organic carbon (δ(13)C-DOC) in natural water samples. Low-chloride matrix (<5 g Cl/L) DOC solutions were analysed with as little as 2.5 mg C/L in a 9 mL aliquot with a precision of 0.5 ‰. In high-chloride matrix (10-100 g Cl/L) DOC solutions, bias towards lighter δ(13)C-DOC was observed because of incomplete oxidation despite using high-concentration oxidant, extended reaction time, or post-wet chemical oxidation gas-phase combustion. However, through a combination of dilution, chloride removal, and increasing the oxidant:sample ratio, high-salinity samples with sufficient DOC (>22.5 µg C/aliquot) may be analysed. The WCO-CRDS approach requires more total carbon (µg C/aliquot) than conventional CF-isotope ratio mass spectrometer, but is nonetheless applicable to a wide range of DOC concentration and water types, including brackish water, produced water, and basinal brines.

Short-term variability of 7Be atmospheric deposition and watershed response in a Pacific coastal stream, Monterey Bay, California, USA.

Beryllium-7 is a powerful and commonly used tracer for environmental processes such as watershed sediment provenance, soil erosion, fluvial and nearshore sediment cycling, and atmospheric fallout. However, few studies have quantified temporal or spatial variability of (7)Be accumulation from atmospheric fallout, and parameters that would better define the uses and limitations of this geochemical tracer. We investigated the abundance and variability of (7)Be in atmospheric deposition in both rain events and dry periods, and in stream surface-water samples collected over a ten-month interval at sites near northern Monterey Bay (37°N, 122°W) on the central California coast, a region characterized by a rainy winters, dry summers, and small mountainous streams with flashy hydrology. The range of (7)Be activity in rainwater samples from the main sampling site was 1.3-4.4 Bq L(-1), with a mean (±standard deviation) of 2.2 ± 0.9 Bq L(-1), and a volume-weighted average of 2.0 Bq L(-1). The range of wet atmospheric deposition was 18-188 Bq m(-2) per rain event, with a mean of 72 ± 53 Bq m(-2). Dry deposition fluxes of (7)Be ranged from less than 0.01 up to 0.45 Bq m(-2) d(-1), with an estimated dry season deposition of 7 Bq m(-2) month(-1). Annualized (7)Be atmospheric deposition was approximately 1900 Bq m(-2) yr(-1), with most deposition via rainwater (>95%) and little via dry deposition. Overall, these activities and deposition fluxes are similar to values found in other coastal locations with comparable latitude and Mediterranean-type climate. Particulate (7)Be values in the surface water of the San Lorenzo River in Santa Cruz, California, ranged from <0.01 Bq g(-1) to 0.6 Bq g(-1), with a median activity of 0.26 Bq g(-1). A large storm event in January 2010 characterized by prolonged flooding resulted in the entrainment of (7)Be-depleted sediment, presumably from substantial erosion in the watershed. There were too few particulate (7)Be data over the storm to accurately model a (7)Be load, but the results suggest enhanced watershed export of (7)Be from small, mountainous river systems compared to other watershed types.

Asian industrial lead inputs to the North Pacific evidenced by lead concentrations and isotopic compositions in surface waters and aerosols.

Recent trends of atmospheric lead deposition to the North Pacific were investigated with analyses of lead in aerosols and surface waters collected on the fourth Intergovernmental Oceanographic Commission Contaminant Baseline Survey from May to June, 2002. Lead concentrations of the aerosols varied by 2 orders of magnitude (0.1-26.4 pmol/m(3)) due in part to variations in dust deposition during the cruise. The ranges in lead aerosol enrichment factors relative to iron (1-119) and aluminum (3-168) were similar, evidencing the transport of Asian industrial lead aerosols across the North Pacific. The oceanic deposition of some of those aerosols was substantiated by the gradient of lead concentrations of North Pacific waters, which varied 3-fold (32.7-103.5 pmol/kg), were highest along with the Asian margin of the basin, and decreased eastward. The hypothesized predominance of Asian industrial lead inputs to the North Pacific was further corroborated by the lead isotopic composition of ocean surface waters ((206)Pb/(207)Pb = 1.157-1.169; (208)Pb/(206)Pb = 2.093-2.118), which fell within the range of isotopic ratios reported in Asian aerosols that are primarily attributed to Chinese industrial lead emissions.

Stability of dimethyl mercury in seawater and its conversion to monomethyl mercury.

Dimethyl mercury (DMHg) is commonly detected in the world's oceans, but little is known about the mechanisms responsible for DMHg degradation in natural waters or the products of this degradation. Similarly, the potential for the conversion of DMHg to monomethyl mercury (MMHg) under the acidic conditions commonly used to preserve samples for MMHg analysis has not been fully addressed. We provide evidence suggesting that DMHg in natural seawater is not readily photodegraded by sunlight as previously thought. Other experiments demonstrated that DMHg in seawater is, however, readily decomposed under acidic conditions, with MMHg as the predominant product. This facile conversion of DMHg to MMHg at low pH both necessitates an alternative preservation method to acidification for samples to be analyzed for MMHg when DMHg is present, and requires that data from previous studies of MMHg in seawater employing sample acidification be revisited in instances where appreciable DMHg concentrations were possible.

Mercury concentrations and loads in a large river system tributary to San Francisco Bay, California, U.S.A.

In order to estimate total mercury (HgT) loads entering San Francisco Bay, U.S.A., via the Sacramento-San Joaquin River system, unfiltered water samples were collected between January 2002 and January 2006 during high flow events and analyzed for HgT. Unfiltered HgT concentrations ranged from 3.2 to 75 ng/L and showed a strong correlation (r2 = 0.8, p < 0.001, n=78) to suspended sediment concentrations (SSC). During infrequent large floods, HgT concentrations relative to SSC were approximately twice as high as observed during smaller floods. This difference indicates the transport of more Hg-contaminated particles during high discharge events. Daily HgT loads in the Sacramento-San Joaquin River at Mallard Island ranged from below the limit of detection to 35 kg. Annual HgT loads varied from 61 +/- 22 kg (n=5) in water year (WY) 2002 to 470 +/- 170 kg (n=25) in WY 2006. The data collected will assist in understanding the long-term recovery of San Francisco Bay from Hg contamination and in implementing the Hg total maximum daily load, the long-term cleanup plan for Hg in the Bay.

Dimethylmercury in coastal upwelling waters, Monterey Bay, California.

Depth profiles of dimethylmercury (DMHg) concentration were determined at nearshore to offshore sites in Monterey Bay, California. The onset of spring upwelling in the bay was accompanied by increases in DMHg concentrations. Profiles show DMHg increasing gradually with depth in fall and winter from <0.03 pM at the surface to 0.5 pM at 200 m. During the spring, DMHg concentrations increased between 30 and 100 m, first within Monterey Bay, then offshore. This change was accompanied by an increase in DMHg concentrations in the surface water DMHg between fall/winter (<0.03 pM) and spring (0.06-0.29 pM). Microbial activity associated with the remineralization of sinking organic matter produced by the high primary production in the bay may result in the relatively high DMHg in subsurface water in the bay, which when upwelled may facilitate the incorporation of organomercury into biota. As a result, productive coastal upwelling areas may represent an important source of methylated mercury to surface waters, and thus be an important source of mercury to marine ecosystems.

Mercury in the San Francisco Estuary.

This review presents some of the published and other important literature on mercury contamination in San Francisco Estuary. Studies on human consumption of contaminated sportfish and on detecting ecological impacts of this contamination in wetland areas validate concerns regarding mercury's toxicity in this system. Mining, industrial, and environmental uses of mercury have occurred for more than a century, resulting in its large historic and continuing transport to the estuary. Consequently, there is a widespread distribution in the estuary, but more work is needed to show its relative chemical and biological availability from these sources. The uptake of mercury in the estuary has been shown in phytoplankton, but studies on biomagnification in local food webs have yet to draw a clear path to impairment in sportfish and waterbirds. In light of these concerns of impairment and the need for further information, large restoration activities planned for the estuary will require new technical approaches to solve important management questions, such as the location of key areas of methylmercury production.

Decadal mercury trends in San Francisco Estuary sediments.

Monitoring sediment quality and total mercury concentrations over the period 1993-2001 at 26 stations in San Francisco Estuary has shown the seasonal cycling of mercury sediment concentrations, as well as a significant (P < 0.05) decrease in those concentrations at eight stations across the estuary. This decrease in sediment mercury concentrations is attributed to the transport of relatively cleaner sediment to the estuary from the Sacramento River and San Joaquin River watersheds. Despite the decreases observed in some parts of the estuary, no corresponding trend has been found in concurrent studies on sport fish and bivalves in the estuary.

A review of factors influencing measurements of decadal variations in metal contamination in San Francisco Bay, California.

This review summarizes some of the principal results of systematic measurements of trace metal concentrations throughout San Francisco Bay that began in 1989, and that have yielded insights on the factors controlling temporal and spatial variations of those concentrations on seasonal to decadal time scales. Pronounced seasonal variation in some metal concentrations is associated with gradients in the system's hydrology and the diagenetic remobilization of metals from benthic sediments. Additional temporal variation is associated with interannual differences in hydrologic flushing (e.g., ENSO cycles) and episodic storm events. While intra- and inter-annual variabilities complicate assessments of long-term variations in metal concentrations, recent analyses using stable lead isotopic composition distributions and time-series models have deconvoluted decadal changes in lead and silver concentrations in the estuary. Decadal variations in concentrations of other contaminant metals (e.g., mercury) are now being characterized, as well as projections of future concentrations of other metals of concern (e.g., copper). These historic assessments and projections of trace metal variations attest to the importance of long-term, systematic monitoring programs to quantify past and future impacts on water quality in San Francisco Bay and other complex estuarine systems.