Metabolic flexibility of aerobic methanotrophs under anoxic conditions in Arctic lake sediments.

Methane (CH4) emissions from Arctic lakes are a large and growing source of greenhouse gas to the atmosphere with critical implications for global climate. Because Arctic lakes are ice covered for much of the year, understanding the metabolic flexibility of methanotrophs under anoxic conditions would aid in characterizing the mechanisms responsible for limiting CH4 emissions from high-latitude regions. Using sediments from an active CH4 seep in Lake Qalluuraq, Alaska, we conducted DNA-based stable isotope probing (SIP) in anoxic mesocosms and found that aerobic Gammaproteobacterial methanotrophs dominated in assimilating CH4. Aerobic methanotrophs were also detected down to 70 cm deep in sediments at the seep site, where anoxic conditions persist. Metagenomic analyses of the heavy DNA from 13CH4-SIP incubations showed that these aerobic methanotrophs had the capacity to generate intermediates such as methanol, formaldehyde, and formate from CH4 oxidation and to oxidize formaldehyde in the tetrahydromethanopterin (H4MPT)-dependent pathway under anoxic conditions. The high levels of Fe present in sediments, combined with Fe and CH4 profiles in the persistent CH4 seep site, suggested that oxidation of CH4, or, more specifically, its intermediates such as methanol and formaldehyde might be coupled to iron reduction. Aerobic methanotrophs also possessed genes associated with nitrogen and hydrogen metabolism, which might provide potentially alternative energy conservation options under anoxic conditions. These results expand the known metabolic spectrum of aerobic methanotrophs under anoxic conditions and necessitate the re-assessment of the mechanisms underlying CH4 oxidation in the Arctic, especially under lakes that experience extended O2 limitations during ice cover.

Discrete Sample Introduction Module for Quantitative and Isotopic Analysis of Methane and Other Gases by Cavity Ring-Down Spectroscopy.

Carbon dioxide (CO2) and methane (CH4) are natural and anthropogenic products that play a central role in the global carbon cycle and regulating Earth's climate. Applications utilizing laser absorption spectroscopy, which continuously measure concentrations and stable isotope ratios of these greenhouse gases, are routinely employed to measure the source and magnitude of atmospheric inputs. We developed a discrete sample introduction module (DSIM) to enable measurements of methane and CO2 concentrations and δ13C values from limited volume (5-100 mL) gas samples when interfaced with a commercially available cavity ring-down spectroscopy (CRDS) analyzer. The analysis has a dynamic range that spans six orders of magnitude from 100% analyte to the lower limit of instrument detection (2 ppm). We demonstrate system performance for methane by comparing concentrations and δ13C results from the DSIM-CRDS system and traditional methods for a variety of sample types, including low concentration (nanomolar CH4) seawater and high concentration (>90% CH4) natural gas. The expansive concentration range of the field-portable DSIM-CRDS system can measure enhances analytical performance for investigating methane and CO2 dynamics and, potentially, other gases measured by laser absorption spectroscopy.

Water salinity and inundation control soil carbon decomposition during salt marsh restoration: An incubation experiment.

Coastal wetlands are a significant carbon (C) sink since they store carbon in anoxic soils. This ecosystem service is impacted by hydrologic alteration and management of these coastal habitats. Efforts to restore tidal flow to former salt marshes have increased in recent decades and are generally associated with alteration of water inundation levels and salinity. This study examined the effect of water level and salinity changes on soil organic matter decomposition during a 60-day incubation period. Intact soil cores from impounded fresh water marsh and salt marsh were incubated after addition of either sea water or fresh water under flooded and drained water levels. Elevating fresh water marsh salinity to 6 to 9 ppt enhanced CO2 emission by 50%-80% and most typically decreased CH4 emissions, whereas, decreasing the salinity from 26 ppt to 19 ppt in salt marsh soils had no effect on CO2 or CH4 fluxes. The effect from altering water levels was more pronounced with drained soil cores emitting ~10-fold more CO2 than the flooded treatment in both marsh sediments. Draining soil cores also increased dissolved organic carbon (DOC) concentrations. Stable carbon isotope analysis of CO2 generated during the incubations of fresh water marsh cores in drained soils demonstrates that relict peat OC that accumulated when the marsh was saline was preferentially oxidized when sea water was introduced. This study suggests that restoration of tidal flow that raises the water level from drained conditions would decrease aerobic decomposition and enhance C sequestration. It is also possible that the restoration would increase soil C decomposition of deeper deposits by anaerobic oxidation, however this impact would be minimal compared to lower emissions expected due to the return of flooding conditions.

Enhanced CO2 uptake at a shallow Arctic Ocean seep field overwhelms the positive warming potential of emitted methane.

Continued warming of the Arctic Ocean in coming decades is projected to trigger the release of teragrams (1 Tg = 106 tons) of methane from thawing subsea permafrost on shallow continental shelves and dissociation of methane hydrate on upper continental slopes. On the shallow shelves (<100 m water depth), methane released from the seafloor may reach the atmosphere and potentially amplify global warming. On the other hand, biological uptake of carbon dioxide (CO2) has the potential to offset the positive warming potential of emitted methane, a process that has not received detailed consideration for these settings. Continuous sea-air gas flux data collected over a shallow ebullitive methane seep field on the Svalbard margin reveal atmospheric CO2 uptake rates (-33,300 ± 7,900 µmol m-2⋅d-1) twice that of surrounding waters and ∼1,900 times greater than the diffusive sea-air methane efflux (17.3 ± 4.8 µmol m-2⋅d-1). The negative radiative forcing expected from this CO2 uptake is up to 231 times greater than the positive radiative forcing from the methane emissions. Surface water characteristics (e.g., high dissolved oxygen, high pH, and enrichment of 13C in CO2) indicate that upwelling of cold, nutrient-rich water from near the seafloor accompanies methane emissions and stimulates CO2 consumption by photosynthesizing phytoplankton. These findings challenge the widely held perception that areas characterized by shallow-water methane seeps and/or strongly elevated sea-air methane flux always increase the global atmospheric greenhouse gas burden.

Methane cycling. Nonequilibrium clumped isotope signals in microbial methane.

Methane is a key component in the global carbon cycle, with a wide range of anthropogenic and natural sources. Although isotopic compositions of methane have traditionally aided source identification, the abundance of its multiply substituted "clumped" isotopologues (for example, (13)CH3D) has recently emerged as a proxy for determining methane-formation temperatures. However, the effect of biological processes on methane's clumped isotopologue signature is poorly constrained. We show that methanogenesis proceeding at relatively high rates in cattle, surface environments, and laboratory cultures exerts kinetic control on (13)CH3D abundances and results in anomalously elevated formation-temperature estimates. We demonstrate quantitatively that H2 availability accounts for this effect. Clumped methane thermometry can therefore provide constraints on the generation of methane in diverse settings, including continental serpentinization sites and ancient, deep groundwaters.

Methane-derived carbon flow through microbial communities in arctic lake sediments.

Aerobic methane (CH4 ) oxidation mitigates CH4 release and is a significant pathway for carbon and energy flow into aquatic food webs. Arctic lakes are responsible for an increasing proportion of global CH4 emissions, but CH4 assimilation into the aquatic food web in arctic lakes is poorly understood. Using stable isotope probing (SIP) based on phospholipid fatty acids (PLFA-SIP) and DNA (DNA-SIP), we tracked carbon flow quantitatively from CH4 into sediment microorganisms from an arctic lake with an active CH4 seepage. When 0.025 mmol CH4 g(-1) wet sediment was oxidized, approximately 15.8-32.8% of the CH4 -derived carbon had been incorporated into microorganisms. This CH4 -derived carbon equated to up to 5.7% of total primary production estimates for Alaskan arctic lakes. Type I methanotrophs, including Methylomonas, Methylobacter and unclassified Methylococcaceae, were most active at CH4 oxidation in this arctic lake. With increasing distance from the active CH4 seepage, a greater diversity of bacteria incorporated CH4 -derived carbon. Actinomycetes were the most quantitatively important microorganisms involved in secondary feeding on CH4 -derived carbon. These results showed that CH4 flows through methanotrophs into the broader microbial community and that type I methanotrophs, methylotrophs and actinomycetes are important organisms involved in using CH4 -derived carbon in arctic freshwater ecosystems.

Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments.

Methane (CH(4)) emitted from high-latitude lakes accounts for 2-6% of the global atmospheric CH(4) budget. Methanotrophs in lake sediments and water columns mitigate the amount of CH(4) that enters the atmosphere, yet their identity and activity in arctic and subarctic lakes are poorly understood. We used stable isotope probing (SIP), quantitative PCR (Q-PCR), pyrosequencing and enrichment cultures to determine the identity and diversity of active aerobic methanotrophs in the water columns and sediments (0-25 cm) from an arctic tundra lake (Lake Qalluuraq) on the north slope of Alaska and a subarctic taiga lake (Lake Killarney) in Alaska's interior. The water column CH(4) oxidation potential for these shallow (∼2 m deep) lakes was greatest in hypoxic bottom water from the subarctic lake. The type II methanotroph, Methylocystis, was prevalent in enrichment cultures of planktonic methanotrophs from the water columns. In the sediments, type I methanotrophs (Methylobacter, Methylosoma and Methylomonas) at the sediment-water interface (0-1 cm) were most active in assimilating CH(4), whereas the type I methanotroph Methylobacter and/or type II methanotroph Methylocystis contributed substantially to carbon acquisition in the deeper (15-20 cm) sediments. In addition to methanotrophs, an unexpectedly high abundance of methylotrophs also actively utilized CH(4)-derived carbon. This study provides new insight into the identity and activity of methanotrophs in the sediments and water from high-latitude lakes.

Shifts in identity and activity of methanotrophs in arctic lake sediments in response to temperature changes.

Methane (CH(4)) flux to the atmosphere is mitigated via microbial CH(4) oxidation in sediments and water. As arctic temperatures increase, understanding the effects of temperature on the activity and identity of methanotrophs in arctic lake sediments is important to predicting future CH(4) emissions. We used DNA-based stable-isotope probing (SIP), quantitative PCR (Q-PCR), and pyrosequencing analyses to identify and characterize methanotrophic communities active at a range of temperatures (4°C, 10°C, and 21°C) in sediments (to a depth of 25 cm) sampled from Lake Qalluuraq on the North Slope of Alaska. CH(4) oxidation activity was measured in microcosm incubations containing sediments at all temperatures, with the highest CH(4) oxidation potential of 37.5 µmol g(-1) day(-1) in the uppermost (depth, 0 to 1 cm) sediment at 21°C after 2 to 5 days of incubation. Q-PCR of pmoA and of the 16S rRNA genes of type I and type II methanotrophs, and pyrosequencing of 16S rRNA genes in (13)C-labeled DNA obtained by SIP demonstrated that the type I methanotrophs Methylobacter, Methylomonas, and Methylosoma dominated carbon acquisition from CH(4) in the sediments. The identity and relative abundance of active methanotrophs differed with the incubation temperature. Methylotrophs were also abundant in the microbial community that derived carbon from CH(4), especially in the deeper sediments (depth, 15 to 20 cm) at low temperatures (4°C and 10°C), and showed a good linear relationship (R = 0.82) with the relative abundances of methanotrophs in pyrosequencing reads. This study describes for the first time how methanotrophic communities in arctic lake sediments respond to temperature variations.

Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing.

Arctic lakes are a significant source of the greenhouse gas methane (CH(4) ), but the role that methane oxidizing bacteria (methanotrophs) play in limiting the overall CH(4) flux is poorly understood. Here, we used stable isotope probing (SIP) techniques to identify the metabolically active aerobic methanotrophs in upper sediments (0-1 cm) from an arctic lake in northern Alaska sampled during ice-free summer conditions. The highest CH(4) oxidation potential was observed in the upper sediment (0-1 cm depth) with 1.59 µmol g wet weight(-1) day(-1) compared with the deeper sediment samples (1-3 cm, 3-5 cm and 5-10 cm), which exhibited CH(4) oxidation potentials below 0.4 µmol g wet weight(-1) day(-1) . Both type I and type II methanotrophs were directly detected in the upper sediment total communities using targeted primer sets based on 16S rRNA genes. Sequencing of 16S rRNA genes and functional genes (pmoA and mxaF) in the (13) C-DNA from the upper sediment indicated that type I methanotrophs, mainly Methylobacter, Methylosoma, Methylomonas and Methylovulum miyakonense, dominated the assimilation of CH(4) . Methylotrophs, including the genera Methylophilus and/or Methylotenera, were also abundant in the (13) C-DNA. Our results show that a diverse microbial consortium acquired carbon from CH(4) in the sediments of this arctic lake.

Diversity and biogeochemical structuring of bacterial communities across the Porangahau ridge accretionary prism, New Zealand.

Sediments from the Porangahau ridge, located off the northeastern coast of New Zealand, were studied to describe bacterial community structure in conjunction with differing biogeochemical regimes across the ridge. Low diversity was observed in sediments from an eroded basin seaward of the ridge and the community was dominated by uncultured members of the Burkholderiales. Chloroflexi/GNS and Deltaproteobacteria were abundant in sediments from a methane seep located landward of the ridge. Gas-charged and organic-rich sediments further landward had the highest overall diversity. Surface sediments, with the exception of those from the basin, were dominated by Rhodobacterales sequences associated with organic matter deposition. Taxa related to the Desulfosarcina/Desulfococcus and the JS1 candidates were highly abundant at the sulfate-methane transition zone (SMTZ) at three sites. To determine how community structure was influenced by terrestrial, pelagic and in situ substrates, sequence data were statistically analyzed against geochemical data (e.g. sulfate, chloride, nitrogen, phosphorous, methane, bulk inorganic and organic carbon pools) using the Biota-Environmental matching procedure. Landward of the ridge, sulfate was among the most significant structuring factors. Seaward of the ridge, silica and ammonium were important structuring factors. Regardless of the transect location, methane was the principal structuring factor on SMTZ communities.

Geomicrobial characterization of gas hydrate-bearing sediments along the mid-Chilean margin.

Bacterial diversity in eight sediment cores from the mid-Chilean margin was studied using length heterogeneity (LH)-PCR, and described in relation to in situ geochemical conditions. DNA from the sulfate-methane transition (SMT) of three cores [one containing methane gas; two proximal to a gas hydrate mound (GHM)] was cloned and sequenced. Clones related to uncultured relatives of Desulfosarcina variabilis were found in all clone libraries and dominated one. Desulfosarcina variabilis related clones were similar to phylotypes observed at the SMT in association with anaerobic methane oxidation in the Eel River basin, Cascadia margin and the Gulf of Mexico. The LH-PCR amplicon associated with D. variabilis clones matched the amplicon that dominated most SMT samples, indicating environmental selection for D. variabilis relatives. Clones related to the Verrucomicrobia dominated the library for the methane gas-containing core. Uncultured Treponema relatives dominated the library for the core obtained on the edge of a GHM. Statistical analysis using geochemical data to describe variance in LH-PCR data revealed that stable carbon isotope ratios of dissolved inorganic carbon are the principal structuring factor on SMT communities. These data suggest that D. variabilis relatives are involved in anaerobic oxidation of methane at the SMT in Chilean margin sediments.

Radiocarbon dating of a very large African baobab.

In late 2004, Grootboom, probably the largest known African baobab (Adansonia digitata L.), collapsed unexpectedly in northeastern Namibia. Ten wood samples collected from different areas of the trunk were processed and investigated by accelerator mass spectrometry radiocarbon dating. The radiocarbon dates of three samples were greater than 1000 years BP (radiocarbon years before present, i.e., before AD 1950). The corresponding calibrated calendar age of the oldest sample was 1275 +/- 50 years, making Grootboom the oldest known angiosperm tree with reliable dating results. Variations in radiocarbon dates among the wood samples indicated that, morphologically, Grootboom was a quintuple tree, whereas genetically, it was a single individual. Ages of extreme lateral samples revealed that, over the past 500-600 years, Grootbooom had almost ceased growing, providing information about climate changes in central southern Africa. The sudden demise of Grootboom coincided with the spread of the poorly studied baobab disease, which has become epidemic in Namibia.

Transport, deposition and biodegradation of particle bound polycyclic aromatic hydrocarbons in a tidal basin of an industrial watershed.

Polycylic aromatic hydrocarbons (PAHs) are common contaminants in industrial watersheds. Their origin, transport and fate are important to scientists, environmental managers and citizens. The Philadelphia Naval Reserve Basin (RB) is a small semi-enclosed embayment near the confluence of the Schuylkill and Delaware Rivers in Pennsylvania (USA). We conducted a study at this site to determine the tidal flux of particles and particle-bound contaminants associated with the RB. Particle traps were placed at the mouth and inside the RB and in the Schuylkill and Delaware Rivers. There was net particle deposition into the RB, which was determined for three seasons. Spring and fall depositions were highest (1740 and 1230 kg of particles, respectively) while winter deposition was insignificant. PAH concentrations on settling particles indicated a net deposition of 12.7 g PAH in fall and 2.1 g PAH in spring over one tidal cycle. There was no significant PAH deposition in the winter. Biodegradation rates, calculated from 14C-labeled PAH substrate mineralization, could attenuate only about 0.25% of the PAH deposited during a tidal cycle in fall. However, in the spring, biodegradation could be responsible for degrading 50% of the settling PAHs. The RB appears to be a sink for PAHs in this watershed.