Temporal and Spatial Variation of Methylmercury in Sediments in the Second Songhua River,China

The methylmercury (MeHg) content in the Second Songhua River was investigated in this study. Compared with the former data, the following trends in temporal variation were observed. The MeHg content decreased in relation to the distance from the pollution source in 1977; it showed a decline in 1983 after the pollution source had been shut off for one year and continued to decline from 1983 to 1991 when the Second Songhua River was in a cleansing period. The MeHg content in most segments investigated in this study was higher than in 1991. Along the river, sediment samples were collected from the Baishan Segment to the Sifangtai Segment, and from the surface to the underlying layer to check the vertical trend. The MeHg content was high in the segments upstream due to the gold mines existing, with highest content in the Toudaogou Segment (10.0 ng/g). The MeHg content declined from the Jiapigou Segment (6.2 ng/g) to the Hongshi Segment (0.69 ng/g), and it gradually increased from the Hongshi Segment (0.69 ng/g) to the Hadawan Segment (1.8 ng/g). It was still lower than upstream. The MeHg content gradually decreased from the Hadawan Segment to the Zhaoyuan Segment. However, there was no clear trend from the Zhaoyuan Segment to the Sifangtai Segment, where the order of the MeHg content was the Sanzhan Segment > the Sifangtai Segment > the Zhaoyuan Segment > the Laozhou Segment. The vertical variation in sediments showed that the MeHg content in the surface layer was higher than in the underlying layer in all segments with the exception of the Hongshi Segment and the Zhaoyuan Segment. The pollution index of MeHg content in the Second Songhua River was also discussed.     

Spatial and Temporal Variation of Enterobacter Genotypes in Sediments and the Underlying Hyporheic Zone of an Agricultural Stream

Population studies of enteric bacteria in an agriculturally impacted stream (Ledbetter Creek, Murray, Kentucky, USA) were conducted over a period of 2 years. Total number of bacteria, cultivated heterotrophic aerobic bacteria, and enteric bacteria showed significant differences between winter and summer. The cultivated numbers of heterotrophic aerobic bacteria and enteric bacteria were significantly more abundant in summer than in winter. The abundance of enteric bacteria was 12.9% in an upwelling zone and 9.8% in a downwelling zone in summer. Most of the enteric bacterial strains isolated on MacConkey agar were assigned to Enterobacter cloacae and E. agglomerans by API 20E and an analysis of the restriction patterns produced by amplified DNA coding for 16S rRNA (ARDRA) with the enzyme Hpa II. E. cloacae and E. agglomerans genotypes isolated from three hyporheic and gravel bar depth intervals (0-10 cm, 15-25 cm, and 30-40 cm) in summer and fall showed significant spatial variation and were heterogeneously distributed along the stream. Temperature, inorganic nutrients, and occurrence of anoxic zones affected the distribution of enteric bacteria. These techniques can be used as a model to monitor shifts among different species in the stream ecosystem.     

Interactions between Benthic Copepods,Bacteria and Diatoms Promote Nitrogen Retention in Intertidal Marine Sediments

The present study aims at evaluating the impact of diatoms and copepods on microbial processes mediating nitrate removal in fine-grained intertidal sediments. More specifically, we studied the interactions between copepods, diatoms and bacteria in relation to their effects on nitrate reduction and denitrification. Microcosms containing defaunated marine sediments were subjected to different treatments: an excess of nitrate, copepods, diatoms (Navicula sp.), a combination of copepods and diatoms, and spent medium from copepods. The microcosms were incubated for seven and a half days, after which nutrient concentrations and denitrification potential were measured. Ammonium concentrations were highest in the treatments with copepods or their spent medium, whilst denitrification potential was lowest in these treatments, suggesting that copepods enhance dissimilatory nitrate reduction to ammonium over denitrification. We hypothesize that this is an indirect effect, by providing extra carbon for the bacterial community through the copepods'' excretion products, thus changing the C/N ratio in favour of dissimilatory nitrate reduction. Diatoms alone had no effect on the nitrogen fluxes, but they did enhance the effect of copepods, possibly by influencing the quantity and quality of the copepods'' excretion products. Our results show that small-scale biological interactions between bacteria, copepods and diatoms can have an important impact on denitrification and hence sediment nitrogen fluxes.     

Influences of Infaunal Burrows on the Community Structure and Activity of Ammonia-Oxidizing Bacteria in Intertidal Sediments

Influences of infaunal burrows constructed by the polychaete (Tylorrhynchus heterochaetus) on O₂ concentrations and community structures and abundances of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in intertidal sediments were analyzed by the combined use of a 16S rRNA gene-based molecular approach and microelectrodes. The microelectrode measurements performed in an experimental system developed in an aquarium showed direct evidence of O₂ transport down to a depth of 350 mm of the sediment through a burrow. The 16S rRNA gene-cloning analysis revealed that the betaproteobacterial AOB communities in the sediment surface and the burrow walls were dominated by Nitrosomonas sp. strain Nm143-like sequences, and most of the clones in Nitrospira-like NOB clone libraries of the sediment surface and the burrow walls were related to the Nitrospira marina lineage. Furthermore, we investigated vertical distributions of AOB and NOB in the infaunal burrow walls and the bulk sediments by real-time quantitative PCR (Q-PCR) assay. The AOB and Nitrospira-like NOB-specific 16S rRNA gene copy numbers in the burrow walls were comparable with those in the sediment surfaces. These numbers in the burrow wall at a depth of 50 to 55 mm from the surface were, however, higher than those in the bulk sediment at the same depth. The microelectrode measurements showed higher NH₄⁺ consumption activity at the burrow wall than those at the surrounding sediment. This result was consistent with the results of microcosm experiments showing that the consumption rates of NH₄⁺ and total inorganic nitrogen increased with increasing infaunal density in the sediment. These results clearly demonstrated that the infaunal burrows stimulated O₂ transport into the sediment in which otherwise reducing conditions prevailed, resulting in development of high NH₄⁺ consumption capacity. Consequently, the infaunal burrow became an important site for NH₄⁺ consumption in the intertidal sediment.     

Rapid Assessment of Intertidal Wetland Sediments

Urbanization of coastal areas poses a severe threat to ecologically valuable intertidal wetlands. This paper presents a pragmatic approach called Rapid Assessment for Intertidal Wetland Sediments (RAITWS) for evaluating the sediment quality of intertidal wetlands. RAITWS involves construction of reference groups, selection of a subset of environmental variables, matching of test sites to reference groups, prediction of the benthic fauna community structure (e.g. of macroinvertebrates) at test sites, evaluation of the Observation to Expectation ratio (O/E ratio), quantification of environmental variables with series of dynamic numerical models, and interpretation of the O/E findings. The proposed method extends the existing rapid biological assessment approach from static to dynamic applications. In particular, RAITWS provides a fast method of assessing intertidal wetland sites which are undergoing ecological change due to nearby coastal development.     

Denitrification in San Francisco Bay Intertidal Sediments

The acetylene block technique was employed to study denitrification in intertidal estuarine sediments. Addition of nitrate to sediment slurries stimulated denitrification. During the dry season, sediment-slurry denitrification rates displayed Michaelis-Menten kinetics, and ambient NO₃⁻ + NO₂⁻ concentrations (≤26 μM) were below the apparent K_m (50 μM) for nitrate. During the rainy season, when ambient NO₃⁻ + NO₂⁻ concentrations were higher (37 to 89 μM), an accurate estimate of the K_m could not be obtained. Endogenous denitrification activity was confined to the upper 3 cm of the sediment column. However, the addition of nitrate to deeper sediments demonstrated immediate N₂O production, and potential activity existed at all depths sampled (the deepest was 15 cm). Loss of N₂O in the presence of C₂H₂ was sometimes observed during these short-term sediment incubations. Experiments with sediment slurries and washed cell suspensions of a marine pseudomonad confirmed that this N₂O loss was caused by incomplete blockage of N₂O reductase by C₂H₂ at low nitrate concentrations. Areal estimates of denitrification (in the absence of added nitrate) ranged from 0.8 to 1.2 μmol of N₂ m⁻² h⁻¹ (for undisturbed sediments) to 17 to 280 μmol of N₂ m⁻² h⁻¹ (for shaken sediment slurries).     

The Fate of Nitrate in Intertidal Permeable Sediments

Coastal zones act as a sink for riverine and atmospheric nitrogen inputs and thereby buffer the open ocean from the effects of anthropogenic activity. Recently, microbial activity in sandy permeable sediments has been identified as a dominant source of N-loss in coastal zones, namely through denitrification. Some of the highest coastal denitrification rates measured so far occur within the intertidal permeable sediments of the eutrophied Wadden Sea. Still, denitrification alone can often account for only half of the substantial nitrate (NO₃ ⁻) consumption. Therefore, to investigate alternative NO₃ ⁻ sinks such as dissimilatory nitrate reduction to ammonium (DNRA), intracellular nitrate storage by eukaryotes and isotope equilibration effects we carried out ¹⁵NO₃ ⁻ amendment experiments. By considering all of these sinks in combination, we could quantify the fate of the ¹⁵NO₃ ⁻ added to the sediment. Denitrification was the dominant nitrate sink (50–75%), while DNRA, which recycles N to the environment accounted for 10–20% of NO₃ ⁻ consumption. Intriguingly, we also observed that between 20 and 40% of ¹⁵NO₃ ⁻ added to the incubations entered an intracellular pool of NO₃ ⁻ and was subsequently respired when nitrate became limiting. Eukaryotes were responsible for a large proportion of intracellular nitrate storage, and it could be shown through inhibition experiments that at least a third of the stored nitrate was subsequently also respired by eukaryotes. The environmental significance of the intracellular nitrate pool was confirmed by in situ measurements which revealed that intracellular storage can accumulate nitrate at concentrations six fold higher than the surrounding porewater. This intracellular pool is so far not considered when modeling N-loss from intertidal permeable sediments; however it can act as a reservoir for nitrate during low tide. Consequently, nitrate respiration supported by intracellular nitrate storage can add an additional 20% to previous nitrate reduction estimates in intertidal sediments, further increasing their contribution to N-loss.     

Characterization of beta-Glucosidase Activity in Intertidal Marine Sediments

Glycoside derivatives of 4-methylumbelliferone (MUF) were used to characterize the polysaccharidase enzyme systems present in sediments from an intertidal mud flat. The formation of highly fluorescent MUF on hydrolysis of the various glycosides was determined at low substrate concentrations (<1 muM) and with short incubation periods (>5 min). The hydrolysis of MUF-beta-d-glucose in sediments from depth intervals of 0 to 2 cm was insensitive to the presence of oxygen, dissolved sulfide, and iron; magnesium and calcium were stimulatory, however. A pronounced temperature optimum was observed at 40 degrees C, a salinity optimum at 30 per thousand, and a pH optimum at 8.5. Rates of hydrolysis were completely inhibited by the addition of mercuric chloride and sodium azide, but only partially inhibited by toluene and the specific beta-glucosidase inhibitor delta-1,5-gluconolactone. The response to delta-1,5-gluconolactone suggested that about 50% of the observed hydrolysis of MUF-beta-d-glucoside was due to exo- and endoglucanases. A wide variety of hydrolytic activities was observed, with at least some nonspecificity occurring in the case of MUF-beta-d-fucoside. Depth profiles indicated maximal activity in surface sediments with a rapid decline below 2 cm. MUF-glycosides provided a convenlent tool for initial analyses of the dynamics and controls of polymer hydrolysis in marine sediments.     

Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters

Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4–5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.     

Spatial and Temporal Distribution of Two Diazotrophic Bacteria in the Chesapeake Bay

The aim of this study was to initiate autecological studies on uncultivated natural populations of diazotrophic bacteria by examining the distribution of specific diazotrophs in the Chesapeake Bay. By use of quantitative PCR, the abundance of two nifH sequences (907h22 and 912h4) was quantified in water samples collected along a transect from the head to the mouth of the Chesapeake Bay during cruises in April and October 2001 and 2002. Standard curves for the quantitative PCR assays demonstrated that the relationship between gene copies and cycle threshold was linear and highly reproducible from 1 to 10⁷ gene copies. The maximum number of 907h22 gene copies detected was approximately 140 ml⁻¹ and the maximum number of 912h4 gene copies detected was approximately 340 ml⁻¹. Sequence 912h4 was most abundant at the mouth of the Chesapeake Bay, and in general, its abundance increased with increasing salinity, with the highest abundances observed in April 2002. Overall, the 907h22 phylotype was most abundant at the mid-bay station. Additionally, 907h22 was most abundant in the April samples from the mid-bay and mouth of the Chesapeake Bay. Despite the fact that the Chesapeake Bay is rarely nitrogen limited, our results show that individual nitrogen-fixing bacteria have distinct nonrandom spatial and seasonal distributions in the Chesapeake Bay and are either distributed by specific physical processes or adapted to different environmental niches.     

Spatial and Temporal Variation in Hydrochory in Amazonian Floodplain Forest1

ABSTRACT The hypothesis that water depth, plant species, and the presence of submerged substrates influence seed dispersal by water was tested in a whitewater tributary of the Tocantins River of the Amazon Basin. Seed dispersal was greatest when water depth was greatest, which occurred during the new moon. Seeds of buoyant species with smaller seeds required less water for dispersal than large seeded species. Submerged objects reduced the distance dispersed but not the probability of dispersal.     

Risky Business: Temporal and Spatial Variation in Preindustrial Dryland Agriculture

Traditional dryland agriculture in the Pacific island was often labor-intensive and risky, yet settlement and farming in dry areas played an important role in the development of Polynesian societies. We investigate how temporal and spatial climatic fluctuations shape variation in agricultural production across dryland landscapes. We use a model that couples plant growth, climate, and soil organic matter dynamics, together with data from Kohala, Hawai'i, to understand how temperature, rainfall, nitrogen availability, and cropping activity interact to determine yield dynamics through time and space. Due to these interactions, the statistical characterization of rainfall alone is a poor characterization of agricultural yield. Using a simple linear model of human population dynamics, we show that the observed yield variation can affect long-term population growth substantially. Our approach to analyzing spatial and temporal fluctuations in food supply, and to interpreting the population consequences of these fluctuations, provides a quantitative evaluation of agricultural risk and human carrying capacity in dry regions.     

Substrates for Sulfate Reduction and Methane Production in Intertidal Sediments

The activity of and potential substrates for methane-producing bacteria and sulfate-reducing bacteria were examined in marsh, estuary, and beach intertidal sediments. Slow rates of methane production were detected in all sediments, although rates of sulfate reduction were 100- to 1,000-fold higher. After sulfate was depleted in sediments, the rates of methane production sharply increased. The addition of methylamine stimulated methanogenesis in the presence of sulfate, and [¹⁴C]methylamine was rapidly converted to ¹⁴CH₄ and ¹⁴CO₂ in freshly collected marsh sediment. Acetate, hydrogen, or methionine additions did not stimulate methanogenesis. [methyl-¹⁴C]methionine and [2-¹⁴C]acetate were converted to ¹⁴CO₂ and not to ¹⁴CH₄ in fresh sediment. No reduction of ¹⁴CO₂ to ¹⁴CH₄ occurred in fresh sediment. Molybdate, an inhibitor of sulfate reduction, inhibited [2-¹⁴C]acetate metabolism by 98.5%. Fluoracetate, an inhibitor of acetate metabolism, inhibited sulfate reduction by 61%. These results suggest that acetate is a major electron donor for sulfate reduction in marine sediments. In the presence of high concentrations of sulfate, methane may be derived from novel substrates such as methylamine.     

Spatial and Temporal Variation of Macroinvertebrate Drift in Two Neotropical Streams1

The detection of spatial variation in macroinvertebrate drift depends on the spatial scale of investigation in streams of the La Selva Biological Station, Costa Rica. Drift samples were taken in a spatially nested design, with two streams, two reaches per stream, two riffles per reach, and four replicate samples per riffle. Drift showed little variation among streams, but varied significantly at the scales of reach and riffle, with variation among samples also high. In addition, sampling took place at two temporal scales: diel and at two different periods that differed in rainfall conditions. Drift diel periodicity was a clear pattern, while only density of individuals varied among sampling periods. This is the first study of macroinvertebrate drift at multiple spatial scales, despite the recognition that multi‐scale studies are essential for a more complete understanding of community patterns and processes.     

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.     

Spatial and Temporal Variation in the Ant Occupants of a Facultative Ant-Plant1

Striking variation in ant occupation of a facultative ant-plant, Conostegia setosa (Melastomataceae), was found at three scales: local spatial, geographic, and temporal. C. setosa provides housing for ants and grows in groups of stems (clones). The ant occupants of 14 C. setosa clones were censused four times over a 14-mo period at the La Selva Biological Station, Costa Rica, and twice over a 9-mo period at the Nusagandi Station, Panama. Twelve facultative ant species occupied C. setosa stems at La Selva, compared to six facultative and one obligate species at Nusagandi. Occupancy (as % of stems ever occupied/clone) was higher at Nusagandi (median = 89%) compared to La Selva (65%). Occupancy varied among clones at La Selva but not at Nusagandi. C. setosa clones differed between sites, with larger clones and more small stems/clone at La Selva. Occupancy was influenced by clone structure; larger clones contained more ant species at both sites and had lower occupancy at La Selva. Occupancy was highest in larger stems and lowest in small stems at both sites. Temporally, percent occupation/clone did not differ among censuses at either site, but overall occupancy was lower in the dry season at La Selva. Turnover in ant occupants was higher at La Selva than at Nusagandi. The variation observed in this study is likely due to a number of factors, including differences between sites in plant population structure and history, differences between and within sites in ant faunas and their nesting requirements, and changes over space and time in microclimatic variables. Such high variation at multiple scales draws attention to the importance of long-term comparative studies of facultative animal-plant interactions.     

Spatial and Temporal Variation of Archaeal,Bacterial and Fungal Communities in Agricultural Soils

Background

Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time.

Methodology/Principal Findings

In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal β-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal β-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers.

Conclusions

Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.     

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.