Deeper Anoxic Layers Research Articles

Hydrocarbon-degrading microbial populations in permanently cold deep-sea sediments in the NW Atlantic

Permanently cold deep-sea sediments (2500–3500 m water depth) with and without indications of thermogenic hydrocarbon seepage were exposed to naphtha to examine the presence and potential of cold-adapted aerobic hydrocarbon-degrading microbial populations. Monitoring these microcosms for volatile hydrocarbons by GC–MS revealed sediments without in situ hydrocarbons responded more rapidly to naphtha amendment than hydrocarbon seep sediments overall, but seep sediments removed aromatic hydrocarbons benzene, toluene, ethylbenzene and xylene (BTEX) more readily. Naphtha-driven aerobic respiration was more evident in surface sediment (0–20 cmbsf) than deeper anoxic layers (>130 cmbsf) that responded less rapidly. In all cases, enrichment of Gammaproteobacteria included lineages of Oleispira, Pseudomonas, and Alteromonas known to be associated with marine oil spills. On the other hand, taxa known to be prevalent in situ and diagnostic for thermogenic hydrocarbon seepage in deep sea sediment, did not respond to naphtha amendment. This suggests a limited role for these prevalent seep-associated populations in the context of aerobic hydrocarbon biodegradation.

Stable oxic-anoxic transitional interface is beneficial to retard soil carbon loss in drained peatland

Peatlands are vital carbon sink globally and have been drained severely. An oxic-anoxic transitional (OAO) interface was created in drained peatlands profile during long-term water table fluctuation. Here, we aimed to investigate how the CO2 release at the OAO interface respond to climate warming and exogenous carbons addition. We found that the carbon at OAO interface was complex, with higher proportion of aromatics, aliphatics and Fe-bound organic carbons. The microbial activity and diversity at OAO interlayer were lowest. Through a lab incubation, we found that the cumulative CO2 emission at OAO interface was 12.36 ± 1.57 mg CO2 g−1C, 117.6% and 36.6% lower than the upper oxic soil (26.89 ± 1.05 μg CO2 g−1C) and deep anoxic (16.88 ± 1.56 μg CO2 g−1C) layer, respectively. Moreover, the CO2 emission at the OAO interface was least warming-responsive under anoxic dominated conditions. These results reveal that the OAO interface could work as a buffer to retard drained peatland carbon lose under warming climate. However, the CO2 emission at the OAO interface was extremely sensitive to exogenous carbons, which increased by 53.9%–72.1% after exogenous carbon addition, implying that the buffer capacity of OAO interface will collapse if being exposed to available carbons from plant or soil macromolecular carbons. Our results demonstrated that maintain a stable OAO interface was beneficial to reduce drained peatlands carbon loss, and the priority is to ease the priming effect caused by exogenous carbons.

Effects of fiddler crab bioturbation on the geochemical migration and bioavailability of heavy metals in coastal wetlands

Fiddler crabs, found in coastal wetlands worldwide, function as ecosystem engineers. Their burrowing activity can significantly alter biogeochemistry at the local scale, however, the mobility of heavy metals (HMs) in burrow sediments remains unclear. Here, we used diffusive gradients in thin-film probes to obtain bioavailable Fe and HMs (Cu, Zn, Ni, Cd, Pb, Co, and Mo) in crab burrows from coastal wetlands (mudflats, salt marshes, and mangroves). The depth-profile results showed that most HMs were enriched at shallow and deep depths but deficient at middle depths. We highlighted that bioturbation improved oxic conditions, enhanced HM concentrations, and favored dissolved HM retention in burrow sediments, which served as a sink for overlying water HMs via burrow flushing but a potential source of particle HMs via enhanced resuspension. In deep anoxic layers, Fe(III) reduction drove the remobilization of HMs, except Cu and Mo, leading to the co-release of HMs with Fe. This Fe-HM coupling/decoupling was verified using enhanced two-dimensional high-resolution imaging, which revealed highly spatial heterogeneity of multiple HMs. Moreover, the hydrological conditions regulating bioturbation effects on HM behavior varied across different coastal wetlands. With coastal environmental changes, the key role of ubiquitous bioturbation in HM migration and bioavailability should be reconsidered.

Partitioning methane flux by the eddy covariance method in a cool temperate bog based on a Bayesian framework

The responses of CH4 fluxes to environmental drivers are known to be complex in wetlands and are not easily interpreted due to their nonlinear nature. To better understand the observed CH4 flux, we developed a method to partition this flux into CH4 production, oxidation, and three transport pathways. Based on a Bayesian method with six-year eddy covariance measurements from a cool temperate bog in northern Japan, we estimated the parameters of a simple two-layer model, which considered the processes in surface oxic and deep anoxic layers. The constrained model explained 87% of the variation in the observed CH4 flux at the daily to seasonal timescales. The model estimated that 64% of CH4 was transported by ebullition compared with 36% by plant-mediated transport during snow-free periods. The model predicted that CH4 was mostly emitted from the deep anoxic layer rather than from the surface layer. The model explained 56% of the interannual variations in the annual CH4 flux, which was mostly controlled by CH4 production. Posterior distributions of the parameters depended on the data coverage that constrained the model, strongly indicating that long-term data are indispensable for constraining process models. Even when using the six-year data, all parameters were not well constrained probably because the data did not contain enough information to constrain the processes. Thus, the method must be tested in various wetlands with additional long-term data to evaluate its applicability and limitations.

Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake.

Cueva de la Mora (CM) is an acidic, meromictic pit lake in the Iberian Pyrite Belt characterized by extremely high metal(loid) concentrations and strong gradients in oxygen, metal, and nutrient concentrations. We hypothesized that geochemical variations with depth would result in differences in community composition and in metal resistance strategies among active microbial populations. We also hypothesized that metal resistance gene (MRG) expression would correlate with toxicity levels for dissolved metal species in the lake. Water samples were collected in the upper oxic layer, chemocline, and deep anoxic layer of the lake for shotgun metagenomic and metatranscriptomic sequencing. Metagenomic analyses revealed dramatic differences in the composition of the microbial communities with depth, consistent with changing geochemistry. Based on relative abundance of taxa identified in each metagenome, Eukaryotes (predominantly Coccomyxa) dominated the upper layer, while Archaea (predominantly Thermoplasmatales) dominated the deep layer, and a combination of Bacteria and Eukaryotes were abundant at the chemocline. We compared metal resistance across communities using a curated list of protein-coding MRGs with KEGG Orthology identifiers (KOs) and found that there were broad differences in the metal resistance strategies (e.g., intracellular metal accumulation) expressed by Eukaryotes, Bacteria, and Archaea. Although normalized abundances of MRG and MRG expression were generally higher in the deep layer, expression of metal-specific genes was not strongly related to variations in specific metal concentrations, especially for Cu and As. We also compared MRG potential and expression in metagenome assembled genomes (MAGs) from the deep layer, where metal concentrations are highest. Consistent with previous work showing differences in metal resistance mechanisms even at the strain level, MRG expression patterns varied strongly among MAG populations from the same depth. Some MAG populations expressed very few MRG known to date, suggesting that novel metal resistance strategies remain to be discovered in uncultivated acidophiles.

Hydrochemical properties and chemocline of the Sansha Yongle Blue Hole in the South China Sea

Blue holes can provide valuable information regarding paleoclimate, climate change, karst processes, marine ecology, and carbonate geochemistry. The Sansha Yongle Blue Hole, located on Yongle Atoll in the Paracel Islands in the South China Sea, is the deepest blue hole in the world. A comprehensive investigation of the blue hole was conducted to determine the hydrochemical properties and associated redox processes active in the water column. Results indicate the presence of two thermoclines, one at 13–20 m and a second at 70–150 m, dividing the water column into five stratified water layers. Based on redox state, the water column can be divided into three layers: an oxic layer in the top 70 m, a chemocline at 70–100 m, which acts as a redox boundary, and an anoxic deep layer. In the oxic layer, photosynthesis in the oxic layer above the seasonal thermocline, results in nutrient uptake, transformation of inorganic carbon to organic carbon in the top mixed layer above the seasonal thermocline; Below the seasonal thermocline, organic matter degradation and nitrification, which are the main biological process at depths around 30 m and 50–70 m, lead to the accumulation of nitrate and a decrease in dissolved oxygen and pH; whereas photosynthesis is dominant at depths of 30–50 m, leading to increase in dissolved oxygen and pH. Within the chemocline, organic matter decays via a variety of reactions (e.g. aerobic mineralization, denitrification and anammox), leading to sharp decreases in the oxidizing chemical species (e.g., dissolved oxygen and nitrate) and corresponding increases in the reduced species (e.g., ammonium and sulfide). Within this layer, about 60% of the nitrogen is lost and chemoautotrophic/photoautotrophic production may contribute significantly to particulate organic carbon. Within the deep anoxic layer, sulfate reduction and degradation of organic matter result in accumulations of sulfide, dissolved inorganic carbon, and nutrients.

Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota.

Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen fixation, nitrite reduction, and arsenic detoxification. Interestingly, these Thorarchaeotal genomes are inferred to contain the tetrahydromethanopterin and tetrahydrofolate Wood-Ljungdahl (WL) pathways for CO2 reduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisphosphate carboxylase-like proteins (normally without RuBisCO activity) and a near-complete Calvin-Benson-Bassham cycle. The existence of eukaryotic selenocysteine insertion sequences and many genes for proteins previously considered eukaryote-specific in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryotic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their roles in ecosystems.

The impact of electrogenic sulfide oxidation on elemental cycling and solute fluxes in coastal sediment

Filamentous sulfide oxidizing cable bacteria are capable of linking the oxidation of free sulfide in deep anoxic layers of marine sediments to the reduction of oxygen or nitrate in surface sediments by conducting electrons over centimeter-scale distances. Previous studies have shown that this newly discovered microbial process, referred to as electrogenic sulfide oxidation (e-SOx), may alter elemental cycling in sediments, but the nature and rates of the resulting biogeochemical transformations and their influence on benthic-pelagic coupling remain largely unknown. Here we quantify changes in sediment geochemistry and solute fluxes at the sediment–water interface as e-SOx develops and declines over time in laboratory incubations of organic-rich sediments from a seasonally hypoxic coastal basin (Marine Lake Grevelingen, The Netherlands).Our results show that e-SOx enhanced sediment O2 consumption and acidified subsurface sediment, resulting in the dissolution of calcium carbonate and iron sulfide minerals in deeper sediment horizons and the associated accumulation of dissolved iron, manganese, and calcium in porewater. Remobilized Fe diffusing upward was reoxidized at the sediment–water interface, producing an amorphous Fe oxide crust, while dissolved Fe diffusing downward was reprecipitated in the form of FeS as it encountered the free sulfide horizon. The development of e-SOx enhanced the diffusive release of dissolved Mn at the sediment–water interface, capped the phosphate efflux, generated a buildup of organic matter in surface sediments, and strongly stimulated the release of alkalinity from the sediment. About 75% of this alkalinity production was associated with net CaCO3 dissolution, while the remaining 25% was attributed to a pumping mechanism that transfers alkalinity from anodic H2S oxidation (an alkalinity sink) in deeper sediments to cathodic O2 reduction (an alkalinity source) near the sediment–water interface. The resulting sediment alkalinity efflux buffers the release of dissolved inorganic carbon at the sediment–water interface, and may therefore counteract the influence of benthic respiration on coastal ocean pH. Overall, our results demonstrate that e-SOx development strongly affects the biogeochemical cycles of C, P, Ca, Fe, Mn, and S in coastal sediments.

Cable Bacteria in Freshwater Sediments.

In marine sediments cathodic oxygen reduction at the sediment surface can be coupled to anodic sulfide oxidation in deeper anoxic layers through electrical currents mediated by filamentous, multicellular bacteria of the Desulfobulbaceae family, the so-called cable bacteria. Until now, cable bacteria have only been reported from marine environments. In this study, we demonstrate that cable bacteria also occur in freshwater sediments. In a first step, homogenized sediment collected from the freshwater stream Giber Å, Denmark, was incubated in the laboratory. After 2 weeks, pH signatures and electric fields indicated electron transfer between vertically separated anodic and cathodic half-reactions. Fluorescence in situ hybridization revealed the presence of Desulfobulbaceae filaments. In addition, in situ measurements of oxygen, pH, and electric potential distributions in the waterlogged banks of Giber Å demonstrated the presence of distant electric redox coupling in naturally occurring freshwater sediment. At the same site, filamentous Desulfobulbaceae with cable bacterium morphology were found to be present. Their 16S rRNA gene sequence placed them as a distinct sister group to the known marine cable bacteria, with the genus Desulfobulbus as the closest cultured lineage. The results of the present study indicate that electric currents mediated by cable bacteria could be important for the biogeochemistry in many more environments than anticipated thus far and suggest a common evolutionary origin of the cable phenotype within Desulfobulbaceae with subsequent diversification into a freshwater and a marine lineage.

Mapping electron sources and sinks in a marine biogeobattery

Filamentous, multicellular bacteria of the Desulfobulbaceae family form a biogeobattery in marine sediments by mediating an electric coupling between sulfide oxidation in deeper anoxic layers and oxygen reduction at the sediment surface. The electric fields generated in such biogeobatteries were determined with microelectrodes and correlated well with geochemical indicators of microbial electrogenic activity in the top 2 cm of the sediment. The electric fields collapsed within less than a minute when oxygen was removed and reestablished when oxygen was reintroduced, demonstrating a direct coupling between aerobic microbial activity and presence of electric fields. Modeling of the electric potential distribution was used to quantify and localize electron sources and sinks. Most anodic oxidation was confined to the lower part of the anoxic zone with nondetectable free sulfide, suggesting that iron sulfide was the main sulfide source and had already been depleted in the upper part of the anoxic zone. The flow of electrons from anoxic sediment layers fuelled up to 80% of the aerobic activity of the sediment. Responses of the electric field to the presence and absence of nitrate, nitrite, or nitrous oxide in the overlying water readily demonstrated potentials for cathodic reduction of nitrite or nitric oxide and possibly nitrate but not nitrous oxide.

Natural occurrence of microbial sulphur oxidation by long-range electron transport in the seafloor

Recently, a novel mode of sulphur oxidation was described in marine sediments, in which sulphide oxidation in deeper anoxic layers was electrically coupled to oxygen reduction at the sediment surface. Subsequent experimental evidence identified that long filamentous bacteria belonging to the family Desulfobulbaceae likely mediated the electron transport across the centimetre-scale distances. Such long-range electron transfer challenges some long-held views in microbial ecology and could have profound implications for sulphur cycling in marine sediments. But, so far, this process of electrogenic sulphur oxidation has been documented only in laboratory experiments and so its imprint on the seafloor remains unknown. Here we show that the geochemical signature of electrogenic sulphur oxidation occurs in a variety of coastal sediment environments, including a salt marsh, a seasonally hypoxic basin, and a subtidal coastal mud plain. In all cases, electrogenic sulphur oxidation was detected together with an abundance of Desulfobulbaceae filaments. Complementary laboratory experiments in intertidal sands demonstrated that mechanical disturbance by bioturbating fauna destroys the electrogenic sulphur oxidation signal. A survey of published geochemical data and 16S rRNA gene sequences identified that electrogenic sulphide oxidation is likely present in a variety of marine sediments with high sulphide generation and restricted bioturbation, such as mangrove swamps, aquaculture areas, seasonally hypoxic basins, cold sulphide seeps and possibly hydrothermal vent environments. This study shows for the first time that electrogenic sulphur oxidation occurs in a wide range of marine sediments and that bioturbation may exert a dominant control on its natural distribution.

Electric coupling between distant nitrate reduction and sulfide oxidation in marine sediment

Filamentous bacteria of the Desulfobulbaceae family can conduct electrons over centimeter-long distances thereby coupling oxygen reduction at the surface of marine sediment to sulfide oxidation in deeper anoxic layers. The ability of these cable bacteria to use alternative electron acceptors is currently unknown. Here we show that these organisms can use also nitrate or nitrite as an electron acceptor thereby coupling the reduction of nitrate to distant oxidation of sulfide. Sulfidic marine sediment was incubated with overlying nitrate-amended anoxic seawater. Within 2 months, electric coupling of spatially segregated nitrate reduction and sulfide oxidation was evident from: (1) the formation of a 4–6-mm-deep zone separating sulfide oxidation from the associated nitrate reduction, and (2) the presence of pH signatures consistent with proton consumption by cathodic nitrate reduction, and proton production by anodic sulfide oxidation. Filamentous Desulfobulbaceae with the longitudinal structures characteristic of cable bacteria were detected in anoxic, nitrate-amended incubations but not in anoxic, nitrate-free controls. Nitrate reduction by cable bacteria using long-distance electron transport to get privileged access to distant electron donors is a hitherto unknown mechanism in nitrogen and sulfur transformations, and the quantitative importance for elements cycling remains to be addressed.

The Importance of Vertical and Horizontal Dimensions of the Sediment Matrix in Structuring Nematodes Across Spatial Scales

Intensive surveys have been conducted to unravel spatial patterns of benthic infauna communities. Although it has been recognized that benthic organisms are spatially structured along the horizontal and vertical dimensions of the sediment, little is known on how these two dimensions interact with each other. In this study we investigated the interdependence between the vertical and horizontal dimensions in structuring marine nematodes assemblages. We tested whether the similarity in nematode species composition along the horizontal dimension was dependent on the vertical layer of the sediment. To test this hypothesis, three-cm interval sediment samples (15 cm depth) were taken independently from two bedforms in three estuaries. Results indicated that assemblages living in the top layers are more abundant, species rich and less variable, in terms of species presence/absence and relative abundances, than assemblages living in the deeper layers. Results showed that redox potential explained the greatest amount (12%) of variability in species composition, more than depth or particle size. The fauna inhabiting the more oxygenated layers were more homogeneous across the horizontal scales than those from the reduced layers. In contrast to previous studies, which suggested that reduced layers are characterized by a specific set of tolerant species, the present study showed that species assemblages in the deeper layers are more causal (characterized mainly by vagrant species). The proposed mechanism is that at the superficial oxygenated layers, species have higher chances of being resuspended and displaced over longer distances by passive transport, while at the deeper anoxic layers they are restricted to active dispersal from the above and nearby sediments. Such restriction in the dispersal potential together with the unfavorable environmental conditions leads to randomness in the presence of species resulting in the high variability between assemblages along the horizontal dimension.

Transient simulations of the carbon and nitrogen dynamics in northern peatlands: from the Last Glacial Maximum to the 21st century

Abstract. The development of northern high-latitude peatlands played an important role in the carbon (C) balance of the land biosphere since the Last Glacial Maximum (LGM). At present, carbon storage in northern peatlands is substantial and estimated to be 500 ± 100 Pg C (1 Pg C = 1015 g C). Here, we develop and apply a peatland module embedded in a dynamic global vegetation and land surface process model (LPX-Bern 1.0). The peatland module features a dynamic nitrogen cycle, a dynamic C transfer between peatland acrotelm (upper oxic layer) and catotelm (deep anoxic layer), hydrology- and temperature-dependent respiration rates, and peatland specific plant functional types. Nitrogen limitation down-regulates average modern net primary productivity over peatlands by about half. Decadal acrotelm-to-catotelm C fluxes vary between −20 and +50 g C m−2 yr−1 over the Holocene. Key model parameters are calibrated with reconstructed peat accumulation rates from peat-core data. The model reproduces the major features of the peat core data and of the observation-based modern circumpolar soil carbon distribution. Results from a set of simulations for possible evolutions of northern peat development and areal extent show that soil C stocks in modern peatlands increased by 365–550 Pg C since the LGM, of which 175–272 Pg C accumulated between 11 and 5 kyr BP. Furthermore, our simulations suggest a persistent C sequestration rate of 35–50 Pg C per 1000 yr in present-day peatlands under current climate conditions, and that this C sink could either sustain or turn towards a source by 2100 AD depending on climate trajectories as projected for different representative greenhouse gas concentration pathways.

Spectrophotometric methods for the determination of photosynthetic pigments in stratified lakes: a critical analysis based on comparisons with HPLC determinations in a model lake

Spectrophotometric methods for the determination of photosynthetic pigments in stratified lakes: a critical analysis based on comparisons with HPLC determinations in a model lake High-performance liquid chromatography (HPLC) is an accurate method for photosynthetic pigment analysis; however, spectrophotometric equations are also frequently used for pigment quantification in aquatic systems. Here, we present a critical analysis of the most-used spectrophotometric equations by comparing the results obtained using these equations with unambiguous HPLC determinations. The study was performed in Lake La Cruz (central Spain). In this meromictic lake with strong thermal stratification, photosynthetic populations occur in different, vertically stratified layers. Eukaryotic algae and picocyanobacteria are mostly located in oxic layers, whereas purple sulphur bacteria grow at the oxic-anoxic interface and below, and green sulphur bacteria occur primarily in deeper anoxic layers. This broad diversity of photosynthetic microorganisms involves a complex mixture of photosynthetic pigments that often exhibit overlapping absorption spectra. We tested spectrophotometric equations using samples that represented the entire range of spatial and temporal variability of the lake. For chlorophyll-a, the best correlations with all tested equations were observed for oxic layers. Regardless of where the sample was obtained, the best fit for chlorophyll-a was produced by the equation of Overmann & Tilzer, which is specifically designed to handle mixtures of chlorophyll-a and bacteriochlorophyll-d from green sulphur bacteria. Trichromatic equations for determining chlorophyll-b and -c exhibited strong interferences in anoxic waters, whereas in the upper layers of the lake, concentrations of these pigments were usually below the detection limit, restricting the use of these equations. The equations of Takahashi & Ichimura for bacterial pigments slightly overestimated both bacteriochlorophyll-a and -d by approximately 10 % and underestimated bacteriochlorophyll-c by nearly 23 %, although for bacteriochlorophyll-d ,t he correlation was better than those obtained using the dichromatic equations of Parkin & Brock and Overmann & Tilzer, respectively. Total carotenoid abundance can be assessed with the equation designed for this purpose by Strickland & Parsons (1972); however, the accuracy of the results differs with depth and is strongly biased by the presence of the bacterial carotenoid okenone. On the other hand, dual-wavelength carotenoid-to-chlorophyll-a ratios (430/665 and 480/665) only produced acceptable results in the epilimnion, with the occurrence of the bacterial carotenoid okenone in the microaerobic and anoxic layers again producing significant interference. Additionally, the wide variation with depth of the carotenoid composition undermined the validity of these dual-wavelength ratios. In conclusion, our findings indicate that a complete and unambiguous study of photosynthetic pigments in highly stratified lakes with overlapping populations of phototrophic microorganisms requires the use of HPLC techniques. Anyway, our results demonstrate that chlorophyll-a and bacteriochlorophyll-a and -d can be directly measured in oxic and anoxic layers, respectively, using spectrophotometric methods with an error lower than 10 %. However, according to our results, chlorophyll-b and -c and bacteriochlorophyll-c cannot be accurately estimated by spectrophotometric methods in stratified lakes.

Sulfur, iron-, and calcium cycling associated with natural electric currents running through marine sediment

Natural electric currents running through marine sediments have recently been found to couple oxygen reduction at the surface to sulfide oxidation in deeper anoxic layers. Here we show that such spatial separation of oxidation and reduction processes causes non-conventional sulfur, iron, and calcium mobilization and reallocation. Reduced marine sediment was incubated with overlying oxic water and the vertical distribution of solutes and solids was analyzed after 45–150days. As much as 44% of sediment oxygen consumption was driven by electric currents, and electrogenic oxidation of sulfide to sulfate with concurrent proton generation resulted in significant dissolution of iron sulfides and calcium carbonates in the anoxic layers of the sediment. Most of the mobilized iron diffused to the oxic zone where it formed oxidized iron minerals. Calcium precipitated in the oxic zone as magnesium-calcite. The electric coupling of biogeochemical processes in distant regions thus generates unique chemical conditions in marine sediments whereby key elements are mobilized and relocated, probably along with trace elements and nutrients. We suggest that such electrically coupled biogeochemistry flourishes in marine sediments after transient oxygen depletion, leaving distinct signatures of such events in the geological record.

Pyrosequencing analysis of the protist communities in a High Arctic meromictic lake: DNA preservation and change

High Arctic meromictic lakes are extreme environments characterized by cold temperatures, low nutrient inputs from their polar desert catchments and prolonged periods of low irradiance and darkness. These lakes are permanently stratified with an oxygenated freshwater layer (mixolimnion) overlying a saline, anoxic water column (monimolimnion). The physical and chemical properties of the deepest known lake of this type in the circumpolar Arctic, Lake A, on the far northern coast of Ellesmere Island, Canada, have been studied over the last 15 years, but little is known about the lake’s biological communities. We applied high-throughput sequencing of the V4 region of the 18S ribosomal RNA gene to investigate the protist communities down the water column at three sampling times: under the ice at the end of winter in 2008, during an unusual period of warming and ice-out the same year, and again under the ice in mid-summer 2009. Sequences of many protist taxa occurred throughout the water column at all sampling times, including in the deep anoxic layer where growth is highly unlikely. Furthermore, there were sequences for taxonomic groups including diatoms and marine taxa, which have never been observed in Lake A by microscopic analysis. However, the sequences of other taxa such as ciliates, chrysophytes, Cercozoa, and Telonema varied with depth, between years and during the transition to ice-free conditions. These seasonally active taxa in the surface waters of the lake are thus sensitive to depth and change with time. DNA from these taxa is superimposed upon background DNA from multiple internal and external sources that is preserved in the deep, cold, largely anoxic water column.

Diagenetic trends in the phenolic constituents of Sphagnum-dominated peat and its corresponding humic acid fraction

Models of peat accumulation assume that peat decomposition occurs mostly above the water table, with little or no decomposition once it enters the deeper, saturated, anoxic zone. Few studies have used molecular biomarkers for tracing post depositional, decomposition-related trends in peat deposits. We studied the major diagenetic changes in the phenolic constituents within a Sphagnum-dominated ombrotrophic bog deposit. The yield of lignin-derived phenols and degree of decomposition, measured using alkaline cupric oxide oxidation of bulk peat samples and their corresponding humic acids, revealed that most of the degradation takes place in the surface layers corresponding to the acrotelm. In fact, total phenolic constituents of peat samples decrease from 36.1 to 21.6 mg g −1 OC (organic carbon) over the first 36 cm, whereas in the deeper anoxic layers, phenolic constituents tend to accumulate, reaching a highest concentration of 71.0 mg g −1 OC. The diagenetic alteration of these phenolic constituents during peat accumulation involves significant demethoxylation and an increasing yield of vanillyl oxidation products despite the low redox potential. Syringyl phenols tend to be particularly resistant to diagenetic alteration and are significantly enriched within the humic acid fraction (∼twofold) with respect to the bulk peat. This, together with the higher degree of oxidation, suggests that this organic matter fraction is enriched in more resistant, but nonetheless diagenetically altered, phenolic constituents. This suggests that humic acids constitute a refractory pool of organic C with a relatively low turnover rate. Our results confirm that the major processes involved in the variation in phenolic constituents with depth are strongly related to the post depositional environment and that evaluation of diagenetic trends in phenolic constituents may provide molecular-level information on the changes that fresh biomass undergoes during early diagenesis in peatlands.

Pathways of organic carbon oxidation in a deep lacustrine sediment, Lake Michigan

Rates of microbial iron reduction and other pathways of organic carbon (Corg) oxidation were investigated in sediment from a 100‐m deep site in Lake Michigan. Total benthic mineralization rates of 6.8 and 8.0 mmol m−2 d −1, respectively, were determined from benthic flux measurements and by summation of dissolved inorganic carbon (ΣCO2) accumulation rates measured in anoxic incubations of sediment in discrete depth intervals to 18 cm depth. Carbon oxidation rates were highest near the sediment surface and decreased asymptotically toward zero. A Corg half‐life of 0.06 yr was estimated in the oxic zone, but the half‐life increased by more than two orders of magnitude in the deep anoxic layers. Mineralization in the oxic zone (0‐2.1 cm) accounted for 37% of the total SCO2 production, whereas microbial iron reduction was the most important pathway of carbon oxidation, accounting for 44%; sulfate reduction accounted for 19%, and methanogenesis was negligible. Denitrification accounted for <3% of Corg oxidation. Sulfate reduction was suppressed in the upper 5 cm, where oxygen, manganese, and iron reduction prevailed. Below this zone, sulfate reduction peaked but coexisted with microbial iron reduction. All Mn reduction was apparently coupled to iron and sulfide oxidation in the upper 6 cm. Below that level, a transient accumulation of iron monosulfide and pyrite implied that sulfate reduction increased during the 19th century because of anthropogenic atmospheric sulfur deposition. Sediment mixing through bioturbation was crucial for the cycling of Mn, Fe, and S, and estimates of biodiffusion coefficients were 0.02‐0.3 cm2 d−1.

Impact of mechanical clam harvesting on a benthic habitat: evaluation by means of sediment profile imaging

1. Manila clam (Tapes philippinarum) harvesting in the Venice Lagoon has increased considerably in the last decade, owing to recently developed collection methods. However, these techniques have negative effects on benthic communities and on the structural and functional characteristics of the sediments. 2. A field survey was carried out in 2000 in the central basin of the Venice Lagoon to evaluate the efficacy of sediment profile imaging (SPI) in investigating disturbances caused by fishing activities and to compare the modifications of bottom sediments induced by different fishing gear (the ‘rusca’, currently used by local fishermen, and a rotating drum). 3. An environmental index, the organism–sediment index, derived from SPI analysis was applied. The efficacy of the SPI camera method in evaluating the disturbance of soft bottoms caused by clam harvesting was confirmed, as was the high degree of disturbance of sediment and benthic communities by mechanical clam harvesting. 4. The experimental hauls strongly modified the sediment features by resuspending the top layer of sediment and bringing the deep anoxic layer near the bottom. These effects could have a severe impact on the biogeochemical cycles and on the possibility of recolonization by benthic organisms in the short term. However, there was less disturbance when the rotating drum fishing gear was used. Copyright © 2004 John Wiley & Sons, Ltd.