Daniel B. Albert

Field and laboratory studies of methane oxidation in an anoxic marine sediment: Evidence for a methanogen‐sulfate reducer consortium

Field and laboratory studies of anoxic sediments from Cape Lookout Bight, North Carolina, suggest that anaerobic methane oxidation is mediated by a consortium of methanogenic and sulfate-reducing bacteria. A seasonal survey of methane oxidation and CO2 reduction rates indicates that methane production was confined to sulfate-depleted sediments at all times of year, while methane oxidation occurred in two modes. In the summer, methane oxidation was confined to sulfate-depleted sediments and occurred at rates lower than those of CO2 reduction. In the winter, net methane oxidation occurred in an interval at the base of the sulfate-containing zone. Sediment incubation experiments suggest both methanogens and sulfate reducers were responsible for the observed methane oxidation. In one incubation experiment both modes of oxidation were partially inhibited by 2-bromoethanesulfonic acid (a specific inhibitor of methanogens). This evidence, along with the apparent confinement of methane oxidation to sulfate-depleted sediments in the summer, indicates that methanogenic bacteria are involved in methane oxidation. In a second incubation experiment, net methane oxidation was induced by adding sulfate to homogenized methanogenic sediments, suggesting that sulfate reducers also play a role in the process. We hypothesize that methanogens oxidize methane and produce hydrogen via a reversal of CO2 reduction. The hydrogen is efficiently removed and maintained at low concentrations by sulfate reducers. Pore water H2 concentrations in the sediment incubation experiments (while net methane oxidation was occurring) were low enough that methanogenic bacteria could derive sufficient energy for growth from the oxidation of methane. The methanogen-sulfate reducer consortium is consistent not only with the results of this study, but may also be a feasible mechanism for previously documented anaerobic methane oxidation in both freshwater and marine environments.

Thermodynamic control on hydrogen concentrations in anoxic sediments

Abstract Molecular hydrogen plays a central role in bacterially mediated anoxic sediment chemistry, as both an important electron transfer agent and a key thermodynamic control. We studied the response of hydrogen concentrations to changes in temperature, specific electron acceptor, sulfate concentration, and pH in a series of laboratory experiments using sediments from Cape Lookout Bight, North Carolina. Hydrogen concentrations were found to depend significantly on each of these factors in a fashion that suggests thermodynamic control. In general, the change in hydrogen concentrations was apparently driven by a necessity to maintain a constant ΔG for the predominant terminal electron-accepting process. We hypothesize this situation derives from highly competetive conditions that force terminal metabolic bacteria to operate right at their thermodynamic limits. The response of hydrogen to individual controls in the laboratory experiments was reflected in relatively quantitiative fashion in down-core, seasonal, and inter-environmental variations observed in sediment cores from Cape Lookout Bight and the White Oak River, NC.

Apparent minimum free energy requirements for methanogenic Archaea and sulfate‐reducing bacteria in an anoxic marine sediment

Among the most fundamental constraints governing the distribution of microorganisms in the environment is the availability of chemical energy at biologically useful levels. To assess the minimum free energy yield that can support microbial metabolism in situ, we examined the thermodynamics of H2-consuming processes in anoxic sediments from Cape Lookout Bight, NC, USA. Depth distributions of H2 partial pressure, along with a suite of relevant concentration data, were determined in sediment cores collected in November (at 14.5°C) and August (at 27°C) and used to calculate free energy yields for methanogenesis and sulfate reduction. At both times of year, and for both processes, free energy yields gradually decreased (became less negative) with depth before reaching an apparent asymptote. Sulfate-reducing bacteria exhibited an asymptote of −19.1±1.7 kJ (mol SO2−4)−1, while methanogenic Archaea were apparently supported by energy yields as small as −10.6±0.7 kJ (mol CH4)−1.

Methanogen Diversity Evidenced by Molecular Characterization of Methyl Coenzyme M Reductase A (mcrA) Genes in Hydrothermal Sediments of the Guaymas Basin

ABSTRACT The methanogenic community in hydrothermally active sediments of Guaymas Basin (Gulf of California, Mexico) was analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Members of the Methanomicrobiales and Methanosarcinales dominated the mcrA and 16S rRNA clone libraries from the upper 15 cm of the sediments. Within the H2/CO2- and formate-utilizing family Methanomicrobiales, two mcrA and 16S rRNA lineages were closely affiliated with cultured species of the genera Methanoculleus and Methanocorpusculum. The most frequently recovered mcrA PCR amplicons within the Methanomicrobiales did not branch with any cultured genera. Within the nutritionally versatile family Methanosarcinales, one 16S rRNA amplicon and most of the mcrA PCR amplicons were affiliated with the obligately acetate utilizing species Methanosaeta concilii. The mcrA clone libraries also included phylotypes related to the methyl-disproportionating genus Methanococcoides. However, two mcrA and two 16S rRNA lineages within the Methanosarcinales were unrelated to any cultured genus. Overall, the clone libraries indicate a diversified methanogen community that uses H2/CO2, formate, acetate, and methylated substrates. Phylogenetic affiliations of mcrA and 16S rRNA clones with thermophilic and nonthermophilic cultured isolates indicate a mixed mesophilic and thermophilic methanogen community in the surficial Guaymas sediments.

Determination of low-molecular-weight organic acid concentrations in seawater and pore-water samples via HPLC

Abstract A method is described for the preparation of 2-nitrophenylhydrazide derivatives of low-molecular-weight organic acids in aqueous samples and their subsequent analysis via HPLC with absorbance detection. The method has been optimized for derivatization of marine sediment pore-water samples and is suitable for use with fresh or saline waters with variable carbonate alkalinity. The HPLC analysis utilizes a reversed-phase column and ion-pairing solvents. Baseline resolution of lactate, acetate, formate, propionate, n - and iso -butyrate, and n - and iso -valerate is demonstrated. The chemical behavior of the derivatives allows their preconcentration on a concentrator column in the sample loop. The concentration sensitivity of the method is thereby extended into the sub-micromolar range and is currently limited only by the blank. The derivatives are colored and the absorption of derivatized samples at 550 nm can be used as the basis of a colorimetric assay for total carboxylic acids. Examples of the use of this method for quantifying C 1 to C 5 organic acids and total carboxylic acids in marine sediment pore waters are given.

Seasonal variations in production and consumption rates of dissolved organic carbon in an organic-rich coastal sediment

Abstract Dissolved organic carbon (DOC) concentrations in anoxic marine sediments are controlled by at least three processes: 1. (1) production of nonvolatile dissolved compounds, such as peptides and amino acids, soluble saccharides and fatty acids, via hydrolysis of particulate organic carbon (POC). 2. (2) conversion of these compounds to volatile fatty acids and alcohols by fermentative bacteria. 3. (3) consumption of volatile fatty acids and alcohols by terminal bacteria, such as sulfate reducers and methanogens. We monitored seasonal changes in concentration profiles of total DOC, nonacid-volatile (NAV) DOC and acid-volatile (AV) DOC in anoxic sediment from Cape Lookout Bight, North Carolina, USA, in order to investigate the factors that control seasonal variations in rates of hydrolysis, fermentation, and terminal metabolism. During the winter months, DOC concentrations increased continuously from 0.2 mM in the bottomwater to ~4 mM at a depth of 36 cm in the sediment column. During the summer, a large DOC maximum developed between 5 and 20 cm, with peak concentrations approaching 10 mM. The mid-depth summertime maximum was driven by increases in both NAV- and AV-DOC concentrations. Net NAV-DOC reaction rates were estimated by a diagenetic model applied to NAV-DOC concentration profiles. Depth-integrated production rates of NAV-DOC increased from February through July, suggesting that net rates of POC hydrolysis during this period are controlled by temperature. Net consumption of NAV-DOC during the late summer and early fall suggests reduced gross NAV-DOC production rates, presumably due to a decline in the availability of labile POC. A distinct subsurface peak in AV-DOC concentration developed during the late spring, when the sulfate depletion depth shoaled from 25 to 10 cm. We hypothesize that the AV-DOC maximum results from a decline in consumption by sulfate-reducing bacteria (due to sulfate limitation) and a lag in the development of an active population of methanogenic bacteria. A diagenetic model that incorporates a lag period in the sulfate reducer-methanogen transition successfully simulates the timing, magnitude, depth and shape of the AV-DOC peak.

Sulfate reduction rates and low molecular weight fatty acid concentrations in the water column and surficial sediments of the Black Sea

Sulfate reduction rates and concentrations of low molecular weight organic acids were measured in the water column and surficial sediments at two sites in the central Black Sea. Water column sulfate reduction rates were much lower than previously reported. The highest rate measured was 3.5 nM day−1 and on a depth integrated basis values of 1.2 and 0.22 mmol m−2 day−1 were obtained for the two sites. Sediment sulfate reduction rates were within the ranges previously reported but were higher than some for comparable abyssal sites. Rates were about 21 μM day−1 in the flocculent layer at the sediment-water interface, decreasing to 2–3μM day−1 at 20 cm depth. On an areal, depth integrated basis, rates at the two sites were 1.45 and 1.29 mmol m−2 day−1. Thus, the water column and sediments have comparable areal rates, but on a volume basis the sediment rates are several thousand times higher than the water column rates. Organic acid concentrations in the anoxic Black Sea water column were surprisingly high, reaching several μM in some cases. One deep sample contained 60μM acetate. Lactate, acetate and formate were the only acids detected in the water column. Some propionate was seen in sediment porewaters. Apparent turnover times of the organic acids in the water column, calculated for utilization solely by sulfate reducing bacteria, are tens to hundred of years. This suggests that sulfate reduction rates in the water column were not limited by organic substrate supply. In the sediments, apparent acid turnover times calculated in this way are generally less than one day, suggesting that sulfate reduction may be limited to by the supply of these substrates through fermentation reactions.

BENTHIC FLUXES AND POREWATER CONCENTRATION PROFILES OF DISSOLVED ORGANIC CARBON IN SEDIMENTS FROM THE NORTH CAROLINA CONTINENTAL SLOPE

Abstract Numerous studies of marine environments show that dissolved organic carbon (DOC) concentrations in sediments are typically tenfold higher than in the overlying water. Large concentration gradients near the sediment–water interface suggest that there may be a significant flux of organic carbon from sediments to the water column. Furthermore, accumulation of DOC in the porewater may influence the burial and preservation of organic matter by promoting geopolymerization and/or adsorption reactions. We measured DOC concentration profiles (for porewater collected by centrifugation and “sipping”) and benthic fluxes (with in situ and shipboard chambers) at two sites on the North Carolina continental slope to better understand the controls on porewater DOC concentrations and quantify sediment–water exchange rates. We also measured a suite of sediment properties (e.g., sediment accumulation and bioturbation rates, organic carbon content, and mineral surface area) that allow us to examine the relationship between porewater DOC concentrations and organic carbon preservation. Sediment depth-distributions of DOC from a downslope transect (300–1000 m water depth) follow a trend consistent with other porewater constituents (ΣCO2 and SO42−) and a tracer of modern, fine-grained sediment (fallout Pu), suggesting that DOC levels are regulated by organic matter remineralization. However, remineralization rates appear to be relatively uniform across the sediment transect. A simple diagenetic model illustrates that variations in DOC profiles at this site may be due to differences in the depth of the active remineralization zone, which in turn is largely controlled by the intensity of bioturbation. Comparison of porewater DOC concentrations, organic carbon burial efficiency, and organic matter sorption suggest that DOC levels are not a major factor in promoting organic matter preservation or loading on grain surfaces. The DOC benthic fluxes are difficult to detect, but suggest that only 2% of the dissolved organic carbon escapes remineralization in the sediments by transport across the sediment-water interface.

Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

Background Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. Methodology/Principal Findings We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat (∼400 cm and ∼10 cm from the mats edge) contrasted with sharply diminished activity at ∼50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12–20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. Conclusions/Significance The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In contrast, 12–20 cm deep in the sediments microbial communities performing methane-cycling and sulfate reduction persist at lower metabolic rates regardless of mat cover, and may increase activity rapidly when subsurface flow changes.

Biogeochemical processes controlling methane in gassy coastal sediments—Part 1. A model coupling organic matter flux to gas production, oxidation and transport

A new kinetic model has been developed for predicting biogeochemical processes occurring in gassy, anoxic sediments dominated by sulfate reduction (SR), methane production (MP), and methane oxidation (MO). The model is composed of mass conservation equations in which reaction rates are balanced by diffusive and advective transport. It directly couples bio-geochemical zones using error functions that serve as a toggle to simulate cessation of sulfate reduction, initiation of methane production and oxidation, and production of gaseous methane when in situ solubility is exceeded. Model-derived sulfate and methane concentration distributions combined with kinetic rate expressions are used to calculate rates of SR, MP and MO. Application of the model to gassy coastal and estuarine sediments reveals the extreme sensitivity of predicted methane distributions to the flux (FG) and degradation rate constant (kG) of reactive organic matter. Sulfate and methane concentrations from Eckernforde Bay in the Kiel Bight of the German Baltic Sea, and Cape Lookout Bight and the White Oak River Estuary of North Carolina, USA, can be predicted accurately from independently determined (FG) values. Comparison of model-predicted results with a complete set of measured summertime concentration and rate data from the Cape Lookout site shows that introduction of 10–40% variations in individual rate parameters produce readily observable discrepancies in model results. In general, increases in the magnitude of FG and decreases in kG at the same total sediment accumulation rate increase the relative importance of methanogenesis in total organic matter remineralization as a result of more rapid depletion of dissolved pore water sulfate closer to the sediment–water interface. The predictive capabilities of the model should prove useful when concentration, rate, or flux measurements are not available.