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.     

Rapid Redox Signal Transmission by “Cable Bacteria” beneath a Photosynthetic Biofilm

Recently, long filamentous bacteria, belonging to the family Desulfobulbaceae, were shown to induce electrical currents over long distances in the surface layer of marine sediments. These “cable bacteria” are capable of harvesting electrons from free sulfide in deeper sediment horizons and transferring these electrons along their longitudinal axes to oxygen present near the sediment-water interface. In the present work, we investigated the relationship between cable bacteria and a photosynthetic algal biofilm. In a first experiment, we investigated sediment that hosted both cable bacteria and a photosynthetic biofilm and tested the effect of an imposed diel light-dark cycle by continuously monitoring sulfide at depth. Changes in photosynthesis at the sediment surface had an immediate and repeatable effect on sulfide concentrations at depth, indicating that cable bacteria can rapidly transmit a geochemical effect to centimeters of depth in response to changing conditions at the sediment surface. We also observed a secondary response of the free sulfide at depth manifest on the time scale of hours, suggesting that cable bacteria adjust to a moving oxygen front with a regulatory or a behavioral response, such as motility. Finally, we show that on the time scale of days, the presence of an oxygenic biofilm results in a deeper and more acidic suboxic zone, indicating that a greater oxygen supply can enable cable bacteria to harvest a greater quantity of electrons from marine sediments. Rapid acclimation strategies and highly efficient electron harvesting are likely key advantages of cable bacteria, enabling their success in high sulfide generating coastal sediments.     

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.     

Oxygen consumption and ammonia accumulation in the hypolimnion of Walker Lake, Nevada

Walker Lake (area = 140 km², Z _mean = 19.3 m) is a large, terminal lake in western Nevada. As a result of anthropogenic desiccation, the lake has decreased in volume by 75% since the 1880s. The hypolimnion of the lake, now too small to meet the oxygen demand exerted by decaying matter, rapidly goes anoxic after thermal stratification. Field and laboratory studies were conducted to examine the feasibility of using oxygenation to avoid hypolimnetic anoxia and subsequent accumulation of ammonia in the hypolimnion, and to estimate the required DO capacity of an oxygenation system for the lake. The accumulation of inorganic nitrogen in water overlaying sediment was measured in laboratory chambers under various DO levels. Rates of ammonia accumulation ranged from 16.8 to 23.5 mg-N m^–2 d^–1 in chambers with 0, 2.5 and 4.8 mg L^–1 DO, and ammonia release was not significantly different between treatments. Beggiatoa sp. on the sediment surface of the moderately aerated chambers (2.5 and 4.8 mg L^–1 DO) indicated that oxygen penetration into sediment was minimal. In contrast, ammonia accumulation was reversed in chambers with 10 mg L^–1 DO, where oxygen penetration into sediment stimulated nitrification and denitrification. Ammonia accumulation in anoxic chambers (18.1 and 20.6 mg-N m^–2 d^–1) was similar to ammonia accumulation in the hypolimnion from July through September of 1998 (16.5 mg-N m^–2 d^–1). Areal hypolimnetic oxygen demand averaged 1.2 g O₂ m^–2 d^–1 for 1994–1996 and 1998. Sediment oxygen demand (SOD) determined in experimental chambers averaged approximately 0.14 g O₂ m^–2 d^–1. Continuous water currents at the sediment-water interface of 5–6 cm s^–1 resulted in a substantial increase in SOD (0.38 g O₂ m^–2 d^–1). The recommended oxygen delivery capacity of an oxygenation system, taking into account increased SOD due to mixing in the hypolimnion after system start-up, is 215 Mg d^–1. Experimental results suggest that the system should maintain high levels of DO at the sediment-water interface (10 mg L^–1) to insure adequate oxygen penetration into the sediments, and a subsequent inhibition of ammonia accumulation in the hypolimnion of the lake.     

Succession of cable bacteria and electric currents in marine sediment

Filamentous Desulfobulbaceae have been reported to conduct electrons over centimetre-long distances, thereby coupling oxygen reduction at the surface of marine sediment to sulphide oxidation in sub-surface layers. To understand how these ‘cable bacteria'' establish and sustain electric conductivity, we followed a population for 53 days after exposing sulphidic sediment with initially no detectable filaments to oxygen. After 10 days, cable bacteria and electric currents were established throughout the top 15 mm of the sediment, and after 21 days the filament density peaked with a total length of 2 km cm⁻². Cells elongated and divided at all depths with doubling times over the first 10 days of <20 h. Active, oriented movement must have occurred to explain the separation of O₂ and H₂S by 15 mm. Filament diameters varied from 0.4–1.7 μm, with a general increase over time and depth, and yet they shared 16S rRNA sequence identity of >98%. Comparison of the increase in biovolume and electric current density suggested high cellular growth efficiency. While the vertical expansion of filaments continued over time and reached 30 mm, the electric current density and biomass declined after 13 and 21 days, respectively. This might reflect a breakdown of short filaments as their solid sulphide sources became depleted in the top layers of the anoxic zone. In conclusion, cable bacteria combine rapid and efficient growth with oriented movement to establish and exploit the spatially separated half-reactions of sulphide oxidation and oxygen consumption.     

Influence of Low Oxygen Tensions and Sorption to Sediment Black Carbon on Biodegradation of Pyrene

Sorption to sediment black carbon (BC) may limit the aerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) in resuspension events and intact sediment beds. We examined this hypothesis experimentally under conditions that were realistic in terms of oxygen concentrations and BC content. A new method, based on synchronous fluorescence observations of ¹⁴C-pyrene, was developed for continuously measuring the uptake of dissolved pyrene by Mycobacterium gilvum VM552, a representative degrader of PAHs. The effect of oxygen and pyrene concentrations on pyrene uptake followed Michaelis-Menten kinetics, resulting in a dissolved oxygen half-saturation constant (K_om) of 14.1 μM and a dissolved pyrene half-saturation constant (K_pm) of 6 nM. The fluorescence of ¹⁴C-pyrene in air-saturated suspensions of sediments and induced cells followed time courses that reflected simultaneous desorption and biodegradation of pyrene, ultimately causing a quasi-steady-state concentration of dissolved pyrene balancing desorptive inputs and biodegradation removals. The increasing concentrations of ¹⁴CO₂ in these suspensions, as determined with liquid scintillation, evidenced the strong impact of sorption to BC-rich sediments on the biodegradation rate. Using the best-fit parameter values, we integrated oxygen and sorption effects and showed that oxygen tensions far below saturation levels in water are sufficient to enable significant decreases in the steady-state concentrations of aqueous-phase pyrene. These findings may be relevant for bioaccumulation scenarios that consider the effect of sediment resuspension events on exposure to water column and sediment pore water, as well as the direct uptake of PAHs from sediments.The aerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) constitutes one of the main processes for dissipation of these toxic compounds from polluted soils and sediments. The oxygen dependence of this process has long sustained the belief that the anaerobic conditions usually found in environments such as sediments in estuaries and ports are the main cause of a long persistence of PAH pollution. However, recent findings have demonstrated that microorganisms can also use other electron acceptors, such as nitrate and sulfate, to oxidize PAHs in sediments (30, 33). Less attention has been given to aerobic biodegradation operating at low oxygen tensions. This process may also be important at the interface between anoxic sediments and the overlying waters. Resuspension of PAH-polluted anoxic sediments can result in the exposure of sediment particles to low concentrations of oxygen in the immediately overlying water column, thereby promoting the aerobic biodegradation of PAHs (22) under conditions in which they can be desorbed and taken up by competent microorganisms. The resulting decreases in the aqueous-phase concentration (and in the associated chemical activity) caused by oxygen-limited aerobic biodegradation may be relevant for bioaccumulation scenarios that consider exposure to the water column and sediment pore water, in addition to the direct uptake from sediments (23). Despite its significance, the capacity for prediction of aerobic biodegradation rates of PAHs at low oxygen tensions is still very limited. Whereas the oxygen dependence of fast biodegradation of PAHs in soils and sediments is a well-known phenomenon (5, 17), studies reporting precise measurements of the dissolved oxygen half-saturation constant (K_om) for biodegradation of PAHs—a key modeling parameter—are very scarce (7, 21). The only available estimation for a K_om value of a high-molecular-weight (HMW) PAH (5.9 μM) was provided for pyrene on the basis of growth rates on pyrene of a Mycobacterium strain in a fermenter (7). However, the pyrene concentration chosen (500 mg/liter)—well above the level of its aqueous solubility (0.13 mg/liter) known to support bacterial growth (34)—was not representative of those concentrations present in the environment.Besides the oxygen concentration, another factor that may control the biodegradation of sedimentary PAHs is their bioavailability. Due to their partitioning into sorbents, such chemicals exhibit only weak chemical activity gradients that promote their uptake and transformation by active microbial cells. Hence, the biodegradation rates are likely far below those corresponding to maximum rates, and they may reflect nonlinear biochemical dependencies. Also, these low rates may be due to the lower chemical activity of PAHs causing the microbial acquisition of the aqueous-phase chemicals to become a bottleneck for the biodegradation process (31). Examples of conflicts of bioavailability with biodegradation can be found when PAHs are predominantly sorbed onto solid aggregates (12) and dissolved in non-aqueous-phase liquids (28). Sorption is especially important in sediments. During recent years, the traditional, one-phase organic carbon (OC) partitioning model has been expanded for PAHs and other hydrophobic pollutants to include uptake both into OC and onto the ubiquitous, solid-phase products of incomplete combustion, collectively called black carbon (BC). Therefore, adsorption to BC and absorption to OC would occur in parallel during the sorption process (1, 2, 15). The new model has been useful in understanding field observations of the PAH solid-water distribution coefficient (K_d), which have evidenced a higher sorption capacity than would have been expected on the basis of OC content only (25, 26). Several studies have shown that strong sorption of PAHs to BC may also significantly limit biodegradation. For example, Ghosh et al. showed that 16 U.S. Environmental Protection Agency (USEPA) PAHs associated with carbonaceous coal-derived material present in harbor sediments exhibited negligible biodegradation rates in aerobic sediment slurries, whereas similar conditions led to significant losses (up to 75% after 2 months) of PAHs present in semisolid coal tar pitch (10). Little or no biodegradation was also observed for 3- to 6-ringed PAHs associated with BC-rich street dust added to soils to simulate diffuse pollution (18) and with naphthalene sorbed to granular activated carbon, a material similar to BC in its physicochemical characteristics, in suspensions of two different bacterial species with dissimilar modes of acquisition of the sorbed compound (14). Finally, Rhodes et al. examined the effect of BC on bioavailability of phenanthrene in soils (32). They found that the addition of BC to soils caused a significant decrease both in the total extent of mineralization and in extractability by the use of cyclodextrin solutions (32). Despite these advances in the field, it is still uncertain whether sorption to BC causes the sequestration of PAHs or whether their microbial assimilation is still possible, although at a very low rate. This gap in knowledge is a major limitation in predicting the fate of these chemicals in many contaminated sediments, making it difficult to achieve a proper perception of the risks posed by resuspensions in overlying waters and bioturbated sediment beds.We considered that sorption to sediment BC may limit the aerobic biodegradation of aqueous-phase PAHs such as pyrene and examined this hypothesis experimentally under conditions that were realistic in terms of concentrations of oxygen and suspended-solids typical for sediment resuspension events. For this aim, we developed a new method, based on synchronous fluorescence observations of ¹⁴C-pyrene, for both measuring the rates of uptake of dissolved pyrene at low oxygen concentrations by a representative PAH-degrading bacterial strain and simultaneously assessing the appearance of ¹⁴CO₂. The method also allowed us to characterize the evolution of aqueous-phase pyrene during biodegradation in initially equilibrated suspensions of sediment with a known content in black carbon. The information obtained experimentally was integrated in model calculations of the evolution of aqueous pyrene concentrations in sediment suspensions. To our knowledge, this is the first report connecting these two major factors—oxygen limitation and sorption to BC—in the biodegradation of HMW PAHs.     

Chemoautotrophic Carbon Fixation Rates and Active Bacterial Communities in Intertidal Marine Sediments

Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of ¹³C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, the Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m⁻² d⁻¹. Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O₂)⁻¹, which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.     

Dissolved Oxygen Saturation Controls PAH Biodegradation in Freshwater Estuary Sediments

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in terrestrial and aquatic environments and can represent a significant constituent of the carbon pool in coastal sediments. We report here the results of an 18-month seasonal study of PAH biodegradation and heterotrophic bacterial production and their controlling biogeochemical factors from 186 sediment samples taken in a tidally influenced freshwater estuary. For each sampling event, measurements were averaged from 25–45 stations covering ∼250 km². There was a clear relationship between bacterial production and ambient temperature, but none between production and bottom water dissolved oxygen (DO) % saturation or PAH concentrations. In contrast with other studies, we found no effect of temperature on the biodegradation of naphthalene, phenanthrene, or fluoranthene. PAH mineralization correlated with bottom water DO saturation above 70% (r² > 0.99). These results suggest that the proportional utilization of PAH carbon to natural organic carbon is as much as three orders of magnitude higher during cooler months, when water temperatures are lower and DO % saturation is higher. Infusion of cooler, well-oxygenated water to the water column overlying contaminated sediments during the summer months may stimulate PAH metabolism preferentially over non-PAH organic matter.     

Polycyclic Aromatic Hydrocarbon-Induced Structural Shift of Bacterial Communities in Mangrove Sediment

Mangrove sediment is well known for its susceptibility to anthropogenic pollution, including polycyclic aromatic hydrocarbons (PAHs), but knowledge of the sediment microbial community structure with regards to exposure to PAHs is limited. The study aims to assess the effects of PAHs on the bacterial community of mangrove sediment using both 16s rDNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and traditional enrichment methods. Both the exposure time and the PAH concentration reduced the microbial diversity, as determined by the DGGE bands. Although PAHs could act as carbon sources for microorganisms, PAHs, at a concentration as low as 20 mg l⁻¹, posed a toxic effect to the microbial community. Sequencing of DGGE bands showed that marine bacteria from the genera of Vibrio, Roseobacter, and Ferrimonas were most abundant after PAH exposure, which suggests that both marine and terrestrial bacteria coexisted in the mangrove sediment, but that the marine microbes were more difficult to isolate using the traditional culture method. DGGE determination further demonstrated that the consistency among triplicates of the enriched consortia was significantly less than that of the sediment slurries. The present study reveals that the mangrove sediment microbial structure is susceptible to PAH contamination, and complex microbial community interactions occur in mangrove sediment.     

Seasonal changes in the microbial population of the water column and sediments of the Ongagawa River,northern Kyushu,Japan

The total viable count, population density of Escherichia coli and coliform bacteria, and nitrogen in the microbiomass (microbiomass-N) in sediments were monitored monthly at 12 points in the Ongagawa River basin from June 2002 to May 2006. The measurement of the sediment microbiomass-N was used for evaluation of the sediment’s microbial population in the river ecosystem. An extraordinarily high population of E. coli was observed during the season when there was stagnant water in the basin, with a high population and an insufficient drain diffusion system, and, thus hydrological water control is indispensable to prevent rapid E. coli growth. Microbiomass-N in sediments showed a negative correlation or independent fluctuation in relation to the bacterial population in the water column of the river. Seasonal changes in extracted nitrogen (N) in river sediments did not show correspondence with microbiomass-N in sediments. The microbiomass-N in sediments changed independently of the bacterial population in the river water, indicating that the high population of bacteria in the water does not lead to a high microbial population in river sediments. Ordination of the microbial parameters by canonical correspondence analysis (CCA) showed that microbiomass-N in sediments was quite different from other parameters. Relatively higher H⁺ (lower pH), PO₄ ³⁻ concentration and dissolved oxygen (DO) were the determinant parameters of higher microbiomass-N in sediments. A relative microbial abundance between the water column and sediments as well as each of the microbial populations in the water column and sediments could be a quantitative parameter for evaluating the biochemical processes of stream water.     

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

Nitrate is an important nutrient and electron acceptor for microorganisms, having a key role in nitrogen (N) cycling and electron transfer in anoxic sediments. High-nitrate inputs into sediments could have a significant effect on N cycling and its associated microbial processes. However, few studies have been focused on the effect of nitrate addition on the functional diversity, composition, structure and dynamics of sediment microbial communities in contaminated aquatic ecosystems with persistent organic pollutants (POPs). Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants including polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs), before and after nitrate injection using a comprehensive functional gene array (GeoChip 4.0). Our results showed that the sediment microbial community functional composition and structure were markedly altered, and that functional genes involved in N-, carbon (C)-, sulfur (S)-and phosphorus (P)- cycling processes were highly enriched after nitrate injection, especially those microorganisms with diverse metabolic capabilities, leading to potential in situ bioremediation of the contaminated sediment, such as PBDE and PAH reduction/degradation. This study provides new insights into our understanding of sediment microbial community responses to nitrate addition, suggesting that indigenous microorganisms could be successfully stimulated for in situ bioremediation of POPs in contaminated sediments with nitrate addition.     

Internal wave-induced redox shifts affect biogeochemistry and microbial activity in sediments: a simulation experiment

Internal waves (seiches) are well-studied physical processes in stratified lakes, but their effects on sediment porewater chemistry and microbiology are still largely unexplored. Due to pycnocline oscillations, sediments are exposed to recurrent changes between epilimnetic and hypolimnetic water. This results in strong differences of environmental conditions, which should be reflected in the responses of redox-sensitive biogeochemical processes at both, the sediment–water interface and deeper sediment layers. We tested in a series of mesocosm experiments the influence of seiche-induced redox changes on porewater chemistry and bacterial activity in the sediments under well controlled conditions. Thereby, we excluded effects of changes in current and temperature regimes. For a period of 10 days, intact sediment cores from oligotrophic Lake Stechlin were incubated under constant (either oxic or anoxic) or alternating redox conditions. Solute concentrations were measured as porewater profiles in the sediment, while microbial activity was determined in the upper 0.5 cm of sediment. Oxic and alternating redox conditions resulted in similar ammonium, phosphate, and methane porewater concentrations, while concentrations of each analyte were considerably higher in anoxic cores. Microbial activity was clearly lower in the anoxic cores than in the oxic and the alternating cores. In conclusion, cores with intermittent anoxic phases of up to 24 hours do not differ in biogeochemistry and microbial activities from static oxic sediments. However, due to various physical processes seiches cause oxygen to penetrate deeper into sediment layers, which affects sediment redox gradients and increase microbial activity in seiche-influenced sediments.     

Oxygenation of anoxic sediments triggers hatching of zooplankton eggs

Many coastal marine systems have extensive areas with anoxic sediments and it is not well known how these conditions affect the benthic–pelagic coupling. Zooplankton lay their eggs in the pelagic zone, and some sink and lie dormant in the sediment, before hatched zooplankton return to the water column. In this study, we investigated how oxygenation of long-term anoxic sediments affects the hatching frequency of dormant zooplankton eggs. Anoxic sediments from the brackish Baltic Sea were sampled and incubated for 26 days with constant aeration whereby, the sediment surface and the overlying water were turned oxic. Newly hatched rotifers and copepod nauplii (juveniles) were observed after 5 and 8 days, respectively. Approximately 1.5 × 10⁵ nauplii m⁻² emerged from sediment turned oxic compared with 0.02 × 10⁵ m⁻² from controls maintained anoxic. This study demonstrated that re-oxygenation of anoxic sediments activated a large pool of buried zooplankton eggs, strengthening the benthic–pelagic coupling of the system. Modelling of the studied anoxic zone suggested that a substantial part of the pelagic copepod population can derive from hatching of dormant eggs. We suggest that this process should be included in future studies to understand population dynamics and carbon flows in marine pelagic systems.     

Prokaryotic diversity in sediments beneath two polar glaciers with contrasting organic carbon substrates

Microbial ecosystems beneath glaciers and ice sheets are thought to play an active role in regional and global carbon cycling. Subglacial sediments are assumed to be largely anoxic, and thus various pathways of organic carbon metabolism may occur here. We examine the abundance and diversity of prokaryotes in sediment beneath two glaciers (Lower Wright Glacier in Antarctica and Russell Glacier in Greenland) with different glaciation histories and thus with different organic carbon substrates. The total microbial abundance in the Lower Wright Glacier sediment, originating from young lacustrine sediment, was an order of magnitude higher (~8 × 10⁶ cells per gram of wet sediment) than in Russell Glacier sediment (~9 × 10⁵ cells g⁻¹) that is of Holocene-aged soil origin. 4% of the microbes from the Russell Glacier sediment and 0.04–0.35% from Lower Wright Glacier were culturable at 10°C. The Lower Wright Glacier subglacial community was dominated by Proteobacteria, followed by Firmicutes. The Russell Glacier library was much less diverse and also dominated by Proteobacteria. Low numbers and diversity of both Euryarchaeota and Crenarchaeota were found in both sediments. The identified clones were related to bacteria with both aerobic and anaerobic metabolisms, indicating the presence of both oxic and anoxic conditions in the sediments.     

Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments

Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following ¹³C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas ¹³C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and needs further study.     

Effect of transient oxic conditions on the composition of the nitrate-reducing community from the rhizosphere of Typha angustifolia

Within a nitrate-reducing bacterial community, a niche differentiation between denitrifying and nitrate ammonifying bacteria may be determinated by a complex of environmental parameters, such as the availability of carbon, nitrate, and oxygen. Hence, oxygen- and carbon-releasing aerenchymatous plants may affect the composition of the nitrate-reducing community in waterlogged sediment. The composition of the nitrate-reducing community in the rhizosphere of the aerenchymatous plant species Typha angustifolia was compared with the community in nonrhizospheric sediment. All three functional groups (NO₂ ^– accumulators, N₂O producers, and presumed NH₄ ⁺ producers) were present at both sites with an ratio of 36:45:12 and 43:22:18 for nonrhizospheric and rhizospheric sediments, respectively. Most of the isolated were gram-negative, and approximately 50% of these strains demonstrated an obligatory oxidative metabolism.In the absence of nitrate, Enterobacteriaceae (belonging to the NO₂ ^– accumulating group) became dominant during enrichment of bacteria from the rhizosphere of T. angustifolia in a chemostat with glycerol (20 mM) as substrate, both under strictly anoxic and transient oxic conditions. Addition of nitrate to the chemostats led to the predominance of denitrifying pseudomonads, irrespective of the presence or absence of oxygen. However, in the presence of nitrate under anoxic conditions, enterobacteria persisted in the medium together with pseudomonads.It was concluded that oxidative bacteria such as pseudomonads are the better competitors for limiting amounts of glycerol, provided oxygen or nitrate is present. In the absence of these electron acceptors, fermentative bacteria become dominant.     

Measurements of Seasonal Rates and Annual Budgets of Organic Carbon Fluxes in an Antarctic Coastal Environment at Signy Island, South Orkney Islands, Suggest a Broad Balance between Production and Decomposition

We report here the first comprehensive seasonal study of benthic microbial activity in an Antarctic coastal environment. Measurements were made from December 1990 to February 1992 of oxygen uptake and sulfate reduction by inshore coastal sediments at Signy Island, South Orkney Islands, Antarctica. From these measurements the rate of benthic mineralization of organic matter was calculated. In addition, both the deposition rate of organic matter to the bottom sediment and the organic carbon content of the bottom sediment were measured during the same period. Organic matter input to the sediment was small under winter ice cover, and the benthic respiratory activity and the organic content of the surface sediment declined during this period as available organic matter was depleted. On an annual basis, about 32% of benthic organic matter mineralization was anoxic, but the proportion of anoxic compared with oxic mineralization increased during the winter as organic matter was increasingly buried by the amphipod infauna. Fresh organic input occurred as the sea ice melted and ice algae biomass sedimented onto the bottom, and input was sustained during the spring after ice breakup by continued primary production in the water column. The benthic respiratory rate and benthic organic matter content correspondingly increased towards the end of winter with the input of this fresh organic matter. The rates of oxygen uptake during the southern summer (80 to 90 mmol of O₂ m^-2 day^-1) were as high as those reported for other sediments at much higher environmental temperatures, and the annual mineralization of organic matter was equally high (12 mol of C m^-2 year^-1). Seasonal variations of benthic activity in this antarctic coastal sediment were regulated by the input and availability of organic matter and not by seasonal water temperature, which was relatively constant at between -1.8 and 0.5°C. We conclude that despite the low environmental temperature, organic matter degradation broadly balanced organic matter production, although there may be significant interrannual variations in the sources of the organic matter inputs.     

Differential metabolism of dimethylsulfoniopropionate and acrylate in saline and brackish intertidal sediments

In anoxic Spartina altemiflora—dominated sediments along a naturally occuring salinity gradient (the Cooper River estuary, South Carolina, U.S.A.), dimethylsulfoniopropionate (DMSP) was metabolized to dimethyl sulfide (DMS) and acrylate by sediment microbes. The rate of DMSP degradation and acrylate mineralization by sediment microbes was similar at all sites along this 25-km transect. However, sediments amended with acrylate (or DMSP) showed significantly higher rates of N₂ fixation (measured as acetylene reduction activity) (ARA) in the saline sediments downstream than brackish sediments. These results are consistent with the fact that acrylate stimulated the rates of both denitrification and CO₂ production in the saline sediments at the mouth of the river more than tenfold over rates in brackish sediments. Enrichment experiments indicate that microbes capable of using DMSP or acrylate were not present in upstream sediments despite the fact that microbial biomass, percent organic matter, and both glucose-stimulated ARA and denitrification were highest upstream. It appears that acrylate utilizing, N₂ fixing, and denitrifying populations are insignificant in the lower salinity sediments of the estuary. These results may reflect the availability of DMSP, which averaged 10.3 nmol g wet wt^–1 of saline sediments and levels less than our detection limit (1 m) in brackish sediments. Correspondence to: D.C. Yoch.     

Effects of Spilled Oil on Bacterial Communities of Mediterranean Coastal Anoxic Sediments Chronically Subjected to Oil Hydrocarbon Contamination

The effects of spilled oil on sedimentary bacterial communities were examined in situ at 20 m water depth in a Mediterranean coastal area. Sediment collected at an experimental site chronically subjected to hydrocarbon inputs was reworked into PVC cores with or without a massive addition of crude Arabian light oil (∼20 g kg⁻¹ dry weight). Cores were reinserted into the sediment and incubated in situ at the sampling site (20 m water depth) for 135 and 503 days. The massive oil contamination induced significant shifts in the structure of the indigenous bacterial communities as shown by ribosomal intergenic spacer analysis (RISA). The vertical heterogeneity of the bacterial communities within the sediment was more pronounced in the oiled sediments particularly after 503 days of incubation. Response to oil of the deeper depth communities (8–10 cm) was slower than that of superficial depth communities (0–1 and 2–4 cm). Analysis of the oil composition by gas chromatography revealed a typical microbial alteration of n-alkanes during the experiment. Predominant RISA bands in oiled sediments were affiliated to hydrocarbonoclastic bacteria sequences. In particular, a 395-bp RISA band, which was the dominant band in all the oiled sediments for both incubation times, was closely related to hydrocarbonoclastic sulfate-reducing bacteria (SRB). These bacteria may have contributed to the main fingerprint changes and to the observed biodegradation of n-alkanes. This study provides useful information on bacterial dynamics in anoxic contaminated infralittoral sediments and highlights the need to assess more precisely the contribution of SRB to bioremediation in oil anoxic contaminated areas.     

Whole-Cell versus Total RNA Extraction for Analysis of Microbial Community Structure with 16S rRNA-Targeted Oligonucleotide Probes in Salt Marsh Sediments

rRNA-targeted oligonucleotide probes have become powerful tools for describing microbial communities, but their use in sediments remains difficult. Here we describe a simple technique involving homogenization, detergents, and dispersants that allows the quantitative extraction of cells from formalin-preserved salt marsh sediments. Resulting cell extracts are amenable to membrane blotting and hybridization protocols. Using this procedure, the efficiency of cell extraction was high (95.7% ± 3.7% [mean ± standard deviation]) relative to direct DAPI (4′,6′-diamidino-2-phenylindole) epifluorescence cell counts for a variety of salt marsh sediments. To test the hypothesis that cells were extracted without phylogenetic bias, the relative abundance (depth distribution) of five major divisions of the gram-negative mesophilic sulfate-reducing delta proteobacteria were determined in sediments maintained in a tidal mesocosm system. A suite of six 16S rRNA-targeted oligonucleotide probes were utilized. The apparent structure of sulfate-reducing bacteria communities determined from whole-cell and RNA extracts were consistent with each other (r² = 0.60), indicating that the whole-cell extraction and RNA extraction hybridization approaches for describing sediment microbial communities are equally robust. However, the variability associated with both methods was high and appeared to be a result of the natural heterogeneity of sediment microbial communities and methodological artifacts. The relative distribution of sulfate-reducing bacteria was similar to that observed in natural marsh systems, providing preliminary evidence that the mesocosm systems accurately simulate native marsh systems.