Distribution of autotrophic nitrifying bacteria in a polluted river (the Passaic).

The abundance of nitrifying bacteria, determined by most-probable-number procedures, within habitats of the Passaic River was as follows: rooted aquatic plants greater than algae approximately equal to rocks greater than sediments greater than greater than water. On the average, NH4+ oxidizers were 540-fold more abundant in the topmost 1 cm of sediment than in the water, and NO2- oxidizers were 250-fold more abundant. The population densities in this surface sediment at two nearby stations, one with a predominantly mineral stream bed and the other an organic ooze, did not differ significantly. Large numbers of nitrifiers were present to a depth of about 5 cm in a mineral sediment core.     

Effects of abiotic factors on the phylogenetic diversity of bacterial communities in acidic thermal springs

Acidic thermal springs offer ideal environments for studying processes underlying extremophile microbial diversity. We used a carefully designed comparative analysis of acidic thermal springs in Yellowstone National Park to determine how abiotic factors (chemistry and temperature) shape acidophile microbial communities. Small-subunit rRNA gene sequences were PCR amplified, cloned, and sequenced, by using evolutionarily conserved bacterium-specific primers, directly from environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Energy-dispersive X-ray spectroscopy, X-ray diffraction, and colorimetric assays were used to analyze sediment chemistry, while an optical emission spectrometer was used to evaluate water chemistry and electronic probes were used to measure the pH, temperature, and E(h) of the spring waters. Phylogenetic-statistical analyses found exceptionally strong correlations between bacterial community composition and sediment mineral chemistry, followed by weaker but significant correlations with temperature gradients. For example, sulfur-rich sediment samples contained a high diversity of uncultured organisms related to Hydrogenobaculum spp., while iron-rich sediments were dominated by uncultured organisms related to a diverse array of gram-positive iron oxidizers. A detailed analysis of redox chemistry indicated that the available energy sources and electron acceptors were sufficient to support the metabolic potential of Hydrogenobaculum spp. and iron oxidizers, respectively. Principal-component analysis found that two factors explained 95% of the genetic diversity, with most of the variance attributable to mineral chemistry and a smaller fraction attributable to temperature.     

Effects of Abiotic Factors on the Phylogenetic Diversity of Bacterial Communities in Acidic Thermal Springs

Acidic thermal springs offer ideal environments for studying processes underlying extremophile microbial diversity. We used a carefully designed comparative analysis of acidic thermal springs in Yellowstone National Park to determine how abiotic factors (chemistry and temperature) shape acidophile microbial communities. Small-subunit rRNA gene sequences were PCR amplified, cloned, and sequenced, by using evolutionarily conserved bacterium-specific primers, directly from environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Energy-dispersive X-ray spectroscopy, X-ray diffraction, and colorimetric assays were used to analyze sediment chemistry, while an optical emission spectrometer was used to evaluate water chemistry and electronic probes were used to measure the pH, temperature, and E_h of the spring waters. Phylogenetic-statistical analyses found exceptionally strong correlations between bacterial community composition and sediment mineral chemistry, followed by weaker but significant correlations with temperature gradients. For example, sulfur-rich sediment samples contained a high diversity of uncultured organisms related to Hydrogenobaculum spp., while iron-rich sediments were dominated by uncultured organisms related to a diverse array of gram-positive iron oxidizers. A detailed analysis of redox chemistry indicated that the available energy sources and electron acceptors were sufficient to support the metabolic potential of Hydrogenobaculum spp. and iron oxidizers, respectively. Principal-component analysis found that two factors explained 95% of the genetic diversity, with most of the variance attributable to mineral chemistry and a smaller fraction attributable to temperature.     

Microbial methane oxidation in the River Saar

In the River Saar, the distribution of methane-oxidizing bacteria and their metabolic activity were determined in vertical and longitudinal profiles. At the sediment surface about two orders of magnitude more methane oxidizers were detected than in the overlying water. In the river as well as in laboratory experiments, the rate of methane oxidation was closely related to the concentration of methane. Most of the methane produced by methanogenic bacteria in the the sediment escaped into the atmosphere. On the average only 1.2% of the produced methane was oxidized in the water phase.     

High concentrations of viruses in the sediments of Lac Gilbert, Québec

Viruses were found to be very abundant in the top layer of the sediments of Lac Gilbert, Québec. Viruses were extracted from the sediments using pyrophosphate buffer, and viruses from the diluted extracts were pelleted onto grids and enumerated using transmission electron microscopy. Viral abundance in the sediments ranged from 6.5 × 10⁸ to 1.83 × 10¹⁰ ml^–1, which is 10- to 1,000-fold greater than the number observed in the water column. This increase corresponds well with the 100- to 1,000-fold increase in bacterial abundance in the sediments. Viral abundance differed significantly among the surface sediment samples taken at different bottom depths and among samples taken at different depths of the water column. Viral abundance also varied significantly between the oxic and anoxic zones of the water column and the sediments. The virus-to-bacteria ratio varied greatly among the different sediment sites but not among depths in the water column. Viral abundance in the water column was related to bacterial abundance and chlorophyll concentration, whereas viruses in the sediments were most abundant in sediments with high organic matter content. Elevated viral abundance and their erratic distribution in the sediments suggest that viruses might play an important role in sediment microbial dynamics. Correspondence to: Roxane Maranger     

Physical and biological parameters that determine the fate of p-chlorophenol in laboratory test systems.

Shake-flask and microcosm studies were conducted to determine the fate of para-chlorophenol (p-CP) in water and sediment systems and the role of sediment and nonsediment surfaces in the biodegradation process. Biodegradation of p-CP in estuarine water samples in shake flasks was slow over incubation periods of 300 h. The addition of detrital sediment resulted in immediate and rapid degradation evidenced by the production of 14CO2 from [14C]p-CP. The addition of sterile sediment, glass beads, or sand resulted in approximately four to six times more CO2 evolution than observed in the water alone. Densities of p-CP-degrading bacteria associated with the detrital sediment were 100 times greater than those enumerated in water. Bacteria in the water and associated with the sediment after preexposure of both water and sediment of p-CP demonstrated enhanced biodegradation. In some microcosms, p-CP was degraded completely in the top 1.0 cm of intact sediment beds. Sediment reworking activities by benthic invertebrates from one site were sufficient to mix p-CP deep into the sediment bed faster than biodegradation or molecular diffusion. p-CP was persistent at lower depths of the sediment, possibly a result of reduced oxygen conditions preventing aerobic biodegradation.     

Physical and biological parameters that determine the fate of p-chlorophenol in laboratory test systems

Shake-flask and microcosm studies were conducted to determine the fate of para-chlorophenol (p-CP) in water and sediment systems and the role of sediment and nonsediment surfaces in the biodegradation process. Biodegradation of p-CP in estuarine water samples in shake flasks was slow over incubation periods of 300 h. The addition of detrital sediment resulted in immediate and rapid degradation evidenced by the production of 14CO2 from [14C]p-CP. The addition of sterile sediment, glass beads, or sand resulted in approximately four to six times more CO2 evolution than observed in the water alone. Densities of p-CP-degrading bacteria associated with the detrital sediment were 100 times greater than those enumerated in water. Bacteria in the water and associated with the sediment after preexposure of both water and sediment of p-CP demonstrated enhanced biodegradation. In some microcosms, p-CP was degraded completely in the top 1.0 cm of intact sediment beds. Sediment reworking activities by benthic invertebrates from one site were sufficient to mix p-CP deep into the sediment bed faster than biodegradation or molecular diffusion. p-CP was persistent at lower depths of the sediment, possibly a result of reduced oxygen conditions preventing aerobic biodegradation.     

The effect of current velocity and sediment on the drift of the mayfly Ephemerella subvaria Mcdunnough

SUMMARY. Experiments conducted in an artificial stream showed that significantly more nymphs drifted from an inorganic substrate at a mean current velocity of 28.5 cm s⁻¹ than at 18.5 cm s⁻¹. Drift density, however, was not affected. Disproportionately large numbers of nymphs drifted while current velocities were being increased from 18.5 to 28.5 cm s⁻¹.
Both drift numbers and drift density were greater in turbid water, after the addition of large amounts of inorganic sediment, than under clear-flowing conditions during dark periods but not in the light. The interaction of increasing current velocity and sediment levels resulted in a significantly greater number of drifting nymphs under lighted conditions.
Minor spates which do not seriously disturb the stream bed may initiate significant increases in macroinvertebrate drift.     

Limited reduction of ferrihydrite encrusted by goethite in freshwater sediment

Many physical and chemical processes control the extent of Fe(III) oxyhydroxide reduction by dissimilatory Fe(III)‐reducing bacteria. The surface precipitation of secondary Fe minerals on Fe(III) oxyhydroxides limits the extent of microbial Fe(III) reduction, but this phenomenon has not yet been observed in nature. This paper reports the observation of secondary Fe‐mineral (goethite) encrustation on ferrihydrite surface within freshwater sediment up to 10 cm deep. The sediment surface was characterized by the predominance of ferrihydrites with biogenic stalks and sheaths. An Fe(II)‐oxidizing bacterium (Gallionellaceae) was detected by 16S rRNA gene analysis at sediment depths of 1 and 2 cm. Fe²⁺ concentration in the sediment pore water was relatively higher at 2–4 cm depths. The 16S rRNA genes affiliated with dissimilatory Fe(III)‐reducing bacteria were detected at 1, 2, and 4 cm depths. The results of the Fe K‐edge extended X‐ray absorption fine structure (EXAFS) analysis suggested the presence of goethite and siderite at depths below 3 cm. However, the change in the Fe‐mineral composition was restricted to sediment depths between 3 and 4 cm, despite the presence of abundant ferrihydrite at depths below 4 cm. An increase in CH₄ concentration was observed at deeper than 6 cm. Stable isotopic analysis of CH₄ in the pore water indicated that acetoclastic CH₄ occurred at depths below 7 cm. Transmission electron microscope observations suggested the presence of goethite and siderite on stalks and sheaths at depths below 3 cm. Results from conversion electron yield EXAFS analysis suggested that goethite dominated at 10 cm depth, thereby indicating that ferrihydrite was encrusted by goethite at this depth. Moreover, the incomplete reduction of ferrihydrite below depths of 4 cm was not due to the lack of organic carbon, but was possibly due to the surface encrustation of goethite on ferrihydrite.     

Distribution of viral abundance in the reef environment of Key Largo, Florida.

The distribution of viral and microbial abundance in the Key Largo, Fla., reef environment was measured. Viral abundance was measured by transmission electron microscope direct counts and plaque titer on specific bacterial hosts in water and sediment samples from Florida Bay (Blackwater Sound) and along a transect from Key Largo to the outer edge of the reef tract in Key Largo Sanctuary. Water column viral direct counts were highest in Blackwater Sound of Florida Bay (1.2 x 10(7) viruses per ml), decreased to the shelf break (1.7 x 10(6) viruses per ml), and were inversely correlated with salinity (r = -0.97). Viral direct counts in sediment samples ranged from 1.35 x 10(8) to 5.3 x 10(8)/cm(3) of sediment and averaged nearly 2 orders of magnitude greater than counts in the water column. Viral direct counts (both sediment and water column measurements) exceeded plaque titers on marine bacterial hosts (Vibrio natriegens and others) by 7 to 8 orders of magnitude. Water column viral abundance did not correlate with bacterial direct counts or chlorophyll a measurements, and sediment viral parameters did not correlate with water column microbial, viral, or salinity data. Coliphage, which are indicators of fecal pollution, were detected in two water column samples and most sediment samples, yet their concentrations were relatively low (<2 to 15/liter for water column samples, and <2 to 108/cm(3) of sediment). Our findings indicate that viruses are abundant in the Key Largo environment, particularly on the Florida Bay side of Key Largo, and that processes governing their distribution in the water column (i.e., salinity and freshwater input) are independent of those governing their distribution in the sediment environment.     

黄河三角洲滨岸潮滩湿地碱蓬对水沙条件及氮输入的适应性

调水调沙工程的实施为黄河三角洲带来大量淡水恢复退化湿地的同时,也改变了湿地的水沙状况并带来大量的外源物质。本研究采用3因素4水平的正交试验,以黄河口滨岸潮滩湿地典型的先锋物种碱蓬为研究对象,探讨了其对淹水深度、泥沙埋深及外源氮输入的适应机制。结果表明: 泥沙埋深对碱蓬叶片蛋白含量及超氧化物歧化酶(SOD)活性的影响较大;氮输入对过氧化物酶(POD)活性的影响较大,而3种处理对过氧化氢酶(CAT)活性的影响无显著差异。淹水深度对叶、茎及总干重具有显著影响,且随淹水深度的增加呈现减小趋势,最大值(25.70、40.86、69.73 g)均出现在2 cm淹水处理;而氮输入及泥沙埋深对碱蓬干重的影响不显著。极差分析表明,淹水深度对碱蓬叶、茎、根及总干重的影响最为显著,其次为氮输入和泥沙埋深,2 cm淹水深度+12 cm埋深深度+9 g·m^-2氮输入量最有利于碱蓬的生长。可见,淹水深度的变化对碱蓬的生长起到决定性的作用,在调水调沙等工程的实施过程中应注重淹水深度的把控。     

Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments

The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66 degrees S, 143 degrees E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15 degrees C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.     

Contribution of food availability to the more rapid growth of the scallop, Euvola ziczac (Pteroida, Pectinidae) in bottom than in suspended culture

We conducted a 5-month experiment at Turpialito in the Golfo de Cariaco, Venezuela, to examine whether the previously reported more rapid growth of scallop Euvola ziczac in bottom compared to suspended culture can be attributed to more abundant or higher quality food resources near the sediment/water interface. The various body components (shell, muscle, digestive gland, gonad and remaining tissues) increased in size at a much greater rate for scallops maintained on the bottom, in partly buried cages at 5 m in depth, than in cages suspended at the same depth in the water column. Furthermore, survival was greater on the bottom. Food abundance and quality were examined by analyzing the seston collected in sediment traps at the sediment/water interface in the vicinity of the bottom cages and next to the suspended cages. Phytoplankton abundance (chlorophyll a) and the proportion of various fatty acids in the lipid fraction of the seston were similar on the bottom and in suspension. However, sestonic protein, lipid and carbohydrate levels, and the estimated energetic content of the seston, were higher on the bottom than in suspension, and probably contributed to the greater growth on the bottom. As the increase in the energetic content of the seston on the bottom compared to in suspension was less than the increase in growth (biomass) on the bottom compared to in suspension, and the evidence showed in previous studies above the negative influence of fouling and wave action in suspended culture, we conclude that the more rapid growth of Euvola ziczac in bottom than suspended culture is principally due to stress relative to suspended culture system.     

Temperature limitation of methanogenesis in aquatic sediments.

Microbial methanogenesis was examined in sediments collected from Lake Mendota, Wisconsin, at water depths of 5, 10, and 18 m. The rate of sediment methanogenesis was shown to vary with respect to sediment site and depth, sampling date, in situ temperature, and number of methanogens. Increased numbers of methanogenic bacteria and rates of methanogenesis correlated with increased sediment temperature during seasonal change. The greatest methanogenic activity was observed for 18-m sediments throughout the sampling year. As compared with shallower sediments, 18-m sediment was removed from oxygenation effects and contained higher amounts of ammonia, carbonate, and methanogenic bacteria, and the population density of methanogens fluctuated less during seasonal change. Rates of methanogenesis in 18-m sediment cores decreased with increasing sediment depth. The optimum temperature, 35 to 42 C, for sediment methanogenesis was considerably higher than the maximum observed in situ temperature of 23 C. The conversion of H2 and [14C]carbonate to [14C]methane displayed the same temperature optimum when these substrates were added to sediments. The predominant methanogenic population had simple nutritional requirements and were metabolically active at 4 to 45 C. Hydrogen oxidizers were the major nutritional type of sediment methanogens; formate and methanol fermentors were present, but acetate fermentors were not observed. Methanobacterium species were most abundant in sediments although Methanosarcina, Methanococcus, and Methanospirillum species were observed in enrichment cultures. A chemolithotropic species of Methanosarcina and Methanobacterium was isolated in pure culture that displayed temperature optima above 30 C and had simple nutritional requirements.     

Coexistence of Microaerophilic,Nitrate-Reducing,and Phototrophic Fe(II) Oxidizers and Fe(III) Reducers in Coastal Marine Sediment

Iron is abundant in sediments, where it can be biogeochemically cycled between its divalent and trivalent redox states. The neutrophilic microbiological Fe cycle involves Fe(III)-reducing and three different physiological groups of Fe(II)-oxidizing microorganisms, i.e., microaerophilic, anoxygenic phototrophic, and nitrate-reducing Fe(II) oxidizers. However, it is unknown whether all three groups coexist in one habitat and how they are spatially distributed in relation to gradients of O₂, light, nitrate, and Fe(II). We examined two coastal marine sediments in Aarhus Bay, Denmark, by cultivation and most probable number (MPN) studies for Fe(II) oxidizers and Fe(III) reducers and by quantitative-PCR (qPCR) assays for microaerophilic Fe(II) oxidizers. Our results demonstrate the coexistence of all three metabolic types of Fe(II) oxidizers and Fe(III) reducers. In qPCR, microaerophilic Fe(II) oxidizers (Zetaproteobacteria) were present with up to 3.2 × 10⁶ cells g dry sediment⁻¹. In MPNs, nitrate-reducing Fe(II) oxidizers, anoxygenic phototrophic Fe(II) oxidizers, and Fe(III) reducers reached cell numbers of up to 3.5 × 10⁴, 3.1 × 10², and 4.4 × 10⁴ g dry sediment⁻¹, respectively. O₂ and light penetrated only a few millimeters, but the depth distribution of the different iron metabolizers did not correlate with the profile of O₂, Fe(II), or light. Instead, abundances were homogeneous within the upper 3 cm of the sediment, probably due to wave-induced sediment reworking and bioturbation. In microaerophilic Fe(II)-oxidizing enrichment cultures, strains belonging to the Zetaproteobacteria were identified. Photoferrotrophic enrichments contained strains related to Chlorobium and Rhodobacter; the nitrate-reducing Fe(II) enrichments contained strains related to Hoeflea and Denitromonas. This study shows the coexistence of all three types of Fe(II) oxidizers in two near-shore marine environments and the potential for competition and interrelationships between them.     

Effects of CO2 enrichment on mineral accumulation and nitrogen relations in a submersed macrophyte

1. Six- to eight-week greenhouse experiments with independent control of pH and dissolved CO₂ evaluated the potential for CO₂ enrichment to stimulate the accumulation of Al, Fe, P and N in shoots of Vallisneria americana , particularly at pH 5. These minerals were provided only as they occurred in natural lake sediments.
2. The effect of CO₂ enrichment at pH 5 v pH 7.3 on growth and tissue N concentration was also determined.
3. CO₂ enrichment at pH 5 effected 5.5- and 7-fold increases in total shoot accumulation of Al and Fe, respectively. In a two-way factorial experiment, CO₂ enrichment yielded 6- to 11-fold greater total shoot P accumulation in plants grown on less and more fertile sediments, respectively.
4. In a three-way factorial experiment, CO₂ enrichment stimulated Vallisneria growth, especially at pH 5, and resulted in a 31–58% reduction in tissue [N] for different pH × sediment combinations. These are greater reductions than previously reported. It also increased total shoot N accumulation up to 6-fold, and there were significant interactions with pH and sediment source: the CO₂ enrichment effect on shoot N accumulation was greater at pH 5 than at pH 7.3, and it was greater with the more fertile sediment at pH 5.
5. Water chemistry (pH and/or [CO₂]) and sediment fertility thus both indirectly influenced the accumulation of sediment-derived minerals in macrophyte shoots within the water column.     

Effects of CO2 enrichment on mineral accumulation and nitrogen relations in a submersed macrophyte

1. Six- to eight-week greenhouse experiments with independent control of pH and dissolved CO₂ evaluated the potential for CO₂ enrichment to stimulate the accumulation of Al, Fe, P and N in shoots of Vallisneria americana , particularly at pH 5. These minerals were provided only as they occurred in natural lake sediments.
2. The effect of CO₂ enrichment at pH 5 v pH 7.3 on growth and tissue N concentration was also determined.
3. CO₂ enrichment at pH 5 effected 5.5- and 7-fold increases in total shoot accumulation of Al and Fe, respectively. In a two-way factorial experiment, CO₂ enrichment yielded 6- to 11-fold greater total shoot P accumulation in plants grown on less and more fertile sediments, respectively.
4. In a three-way factorial experiment, CO₂ enrichment stimulated Vallisneria growth, especially at pH 5, and resulted in a 31–58% reduction in tissue [N] for different pH × sediment combinations. These are greater reductions than previously reported. It also increased total shoot N accumulation up to 6-fold, and there were significant interactions with pH and sediment source: the CO₂ enrichment effect on shoot N accumulation was greater at pH 5 than at pH 7.3, and it was greater with the more fertile sediment at pH 5.
5. Water chemistry (pH and/or [CO₂]) and sediment fertility thus both indirectly influenced the accumulation of sediment-derived minerals in macrophyte shoots within the water column.     

杭州西湖水域微生物的生态调查

对杭州西湖水域微生物生态调查结果表明:(1)有机营养型细菌在富营养化程度较重的岳湖分布较多,而无机营养型细菌在水质较好的小南湖丰度较大;(2)许多微生物类群在温度较高的季节数量反而较少;(3)西湖经综合治理后,异养型细菌和大肠菌群数量有显着减少,但近年又有增加的趋势;(4)西湖水体中的微生物以假单胞菌属的细菌较多,而底泥中芽孢杆菌属的细菌占优势。       

Prokaryotic Metabolic Activity and Community Structure in Antarctic Continental Shelf Sediments

The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66°S, 143°E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15°C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.     

Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment

Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for Archaea. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802-805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the genera Desulfonema, Desulfococcus, and Desulfosarcina. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin.