Influence of Nutrient Inputs, Hexadecane, and Temporal Variations on Denitrification and Community Composition of River Biofilms

Biofilms were cultivated on polycarbonate strips in rotating annular reactors using South Saskatchewan River water during the fall of 1999 and the fall of 2001, supplemented with carbon (glucose), nitrogen (NH₄Cl), phosphorus (KH₂PO₄), or combined nutrients (CNP), with or without hexadecane, a model compound representing aliphatic hydrocarbons used to simulate a pollutant. In fall 1999 and fall 2001, comparable denitrification activities and catabolic potentials were observed in the biofilms, implying that denitrifying populations showed similar activity patterns and catabolic potentials during the fall from year to year in this river ecosystem, when environmental conditions were similar. Both nirS and nirK denitrification genes were detected by PCR amplification, suggesting that both denitrifying bacterial subpopulations can potentially contribute to total denitrification. Between 91.7 and 99.8% of the consumed N was emitted in the form of N₂, suggesting that emission of N₂O, a major potent greenhouse gas, by South Saskatchewan River biofilms is low. Denitrification was markedly stimulated by the addition of CNP, and nirS and nirK genes were predominant only in the presence of CNP. In contrast, individual nutrients had no impact on denitrification and on the occurrence of nirS and nirK genes detected by PCR amplification. Similarly, only CNP resulted in significant increases in algal and bacterial biomass relative to control biofilms. Biomass measurements indicated a linkage between autotrophic and heterotrophic populations in the fall 1999 biofilms. Correlation analyses demonstrated a significant relationship (P ≤ 0.05) between the denitrification rate and the biomass of algae and heterotrophic bacteria but not cyanobacteria. At the concentration assessed (1 ppb), hexadecane partially inhibited denitrification in both years, slightly more in the fall of 2001. This study suggested that the response of the anaerobic heterotrophic biofilm community may be cyclic and predictable from year to year and that there are interactive effects between nutrients and the contaminant hexadecane.     

Diversity and Seasonal Changes of Uncultured Planctomycetales in River Biofilms

Cell counts of planctomycetes showed that there were high levels of these organisms in the summer and low levels in the winter in biofilms grown in situ in two polluted rivers, the Elbe River and the Spittelwasser River. In this study 16S rRNA-based methods were used to investigate if these changes were correlated with changes in the species composition. Planctomycete-specific clone libraries of the 16S rRNA genes found in both rivers showed that there were seven clusters, which were distantly related to the genera Pirellula, Planctomyces, and Gemmata. The majority of the sequences from the Spittelwasser River were affiliated with a cluster related to Pirellula, while the majority of the clones from the Elbe River fell into three clusters related to Planctomyces and one deeply branching cluster related to Pirellula. Some clusters also contained sequences derived from freshwater environments worldwide, and the similarities to our biofilm clones were as high as 99.8%, indicating the presence of globally distributed freshwater clusters of planctomycetes that have not been cultivated yet. Community fingerprints of planctomycete 16S rRNA genes were generated by temperature gradient gel electrophoresis from Elbe River biofilm samples collected monthly for 1 year. Sixteen bands were identified, and for the most part these bands represented organisms related to the genus Planctomyces. The fingerprints showed that there was strong seasonality of most bands and that there were clear differences in the summer and the winter. Thus, seasonal changes in the abundance of Planctomycetales in river biofilms were coupled to shifts in the community composition.     

The Effects of Nitrogen Supply and Defoliation on the Seasonal Internal Cycling of Nitrogen in Molinia caerulea

Plants of Molinia caerulea were grown in pots for two seasonsat two levels of nitrogen (N) supply and two levels of defoliation.All N supplied was enriched with ¹⁵N in the first season andwas at natural abundance in the second season. This allowedthe contribution of remobilization from overwintering storesto be discriminated from current root uptake in supplying Nfor new shoot growth in the second season. The effects of Nsupply and defoliation upon the internal cycling of N in M.caerulea were quantified. N was remobilized from both roots and basal internodes to supportnew shoot, especially leaf, growth in spring. Roots suppliedmore N than basal internodes. Since the remobilization mainlyoccurred before the onset of root N uptake, internal cyclingwas important for the earliest period of shoot growth. An increasedN supply increased the amount of N remobilized to new shootgrowth, however, the proportion of N remobilized from overwinteringstores was independent of N supply. Defoliation increased theamount of N remobilized from the roots, and had no effect onthe ¹⁵N content of basal internodes of plants receiving a lowsupply of N. Remobilization of N from leaves of undefoliatedplants occurred later in the season. Remobilization from leavessupplied flowers in plants receiving a low N supply and bothflowers and new basal internodes in plants receiving a higherN supply. Key words: Molinia caerulea, internal cycling, nitrogen, defoliation     

Seasonal and Spatial Controls over Nutrient Cycling in a Pacific Northwest Prairie

West Coast prairies in the US are an endangered ecosystem, and effective conservation will require an understanding of how changing climate will impact nutrient cycling and availability. We examined how seasonal patterns and micro-heterogeneity in edaphic conditions (% moisture, total organic carbon, % clay, pH, and inorganic nitrogen and phosphorus) control carbon, nitrogen, and phosphorus cycling in an upland prairie in western Oregon, USA. Across the prairie, we collected soils seasonally and measured microbial respiration, net nitrogen mineralization, net nitrification, and phosphorus availability under field conditions and under experimentally varied temperature and moisture treatments. The response variables differed in the degree of temperature and moisture limitation within seasons and how these factors varied across sampling sites. In general, we found that microbial respiration was limited by low soil moisture year-round and by low temperatures in the winter. Net nitrogen mineralization and net nitrification were never limited by temperature, but both were limited by excessive soil moisture in winter, and net nitrification was also inhibited by low soil moisture in the summer. Factors that enhanced microbial respiration tended to decrease soil phosphorus availability. Edaphic factors explained 76% of the seasonal and spatial variation in microbial respiration, 35% of the variation in phosphorus availability, and 29% of the variation in net nitrification. Much of the variation in net nitrogen mineralization remained unexplained (R ² = 0.19). This study, for the first time, demonstrates the complex seasonal controls over nutrient cycling in a Pacific Northwest prairie.     

Cytokine Degradation by Biofilms of Porphyromonas gingivalis

The aim of this study was to determine whether biofilms of Porphyromonas gingivalis could proteolytically degrade the cytokines interleukin (IL)-1β, IL-6, or IL-1 receptor antagonist (IL-1ra). Biofilms were grown on membrane filters on the surface of Wilkins-Chalgren blood agar. The biofilms were removed from the plates, and solutions containing 2.5 μg/ml of each cytokine were added. Following incubation for up to 4.0 h, supernatants from the biofilms were subjected to SDS-PAGE. The separated proteins were transferred by Western blotting to PVDF membranes and probed with peroxidase-conjugated antibodies recognizing both the intact cytokines and their degradation products. After 2 h, no intact IL-1β, IL-6, or IL-1ra were detectable. Cytokine proteolysis also occurred in the presence of horse serum. These results demonstrate that biofilm-grown P. gingivalis can degrade both pro- and anti-inflammatory cytokines and so may be able to perturb cytokine networks in vivo by eliminating cytokines from the local environment. Received: 12 August 1997 / Accepted: 15 October 1997     

The Effects of a Bacillus Biosurfactant on Methanogenic Hexadecane Degradation

The effects of microbially produced biosurfactants on hydrocarbon degradation have been examined previously by other researchers. However, almost all of these studies were conducted using rhamnolipid biosurfactants produced by various Pseudomonas species under aerobic conditions. The purpose of this study was to elucidate the effects of various levels of the Bacillus sp. JF2 lipopeptide biosurfactant on the degradation of hexadecane under methanogenic conditions. Hexadecane degradation did increase significantly when levels below critical micelle concentration of the pre-purified biosurfactant were added. However, at levels above this amount of biosurfactant, degradation of hexadecane appeared to be inhibited. The terminal electron accepting process, methanogenesis, was stimulated by surfactant addition. A review of the published literature revealed a wide variety of results, some which are similar to, but many that differ from those reported here. However, the results from this study were reproducible. Although there is no clear explanation for these results, more research on the effect of biosurfactants produced by Gram positive bacteria on the biodegradation of hydrocarbons is needed, as well as further studies under anaerobic conditions.     

Nitrogen and Carbohydrate Metabolism of Japanese Mint as Affected by Phosphorus Deficiency and Seasonal Variations

The paper presents effects of phosphorus deficiency and seasonal variations on nitrogen and carbohydrate metabolism of Japanese mint (Mentha arvensis L. var. piperascens, Holmes). Mint plants were grown in sand cultures under full nutrition and under phosphorus deficiency conditions during winter and summer. Various nitrogen and sugar fractions were determined in the component parts at specified periods of growth stages. Phosphorus deficiency disturbed the nitrogen metabolism at the stages for amide and amino acid formation, which resulted in an accumulation of carbohydrates. The content of total soluble and total nitrogen was higher and that of insoluble nitrogen was lower in summer as compared with winter plants. Of the soluble fractions, the ammonia, amide and nitrate nitrogen were higher and the ‘rest’ nitrogen lower in winter plants. Nitrate formed the highest bulk of the pool of soluble nitrogen in winter, whereas in summer ‘rest’ nitrogen was most abundant. The content of total sugar in winter plants far exceeded that of summer plants, which was wholly due to increase in sucrose content. Glucose was the predominant reducing sugar in both seasons. However, the summer plants were richer in glucose than those from the winter.     

The Effects of a Bacillus Biosurfactant on Methanogenic Hexadecane Degradation

The effects of microbially produced biosurfactants on hydrocarbon degradation have been examined previously by other researchers. However, almost all of these studies were conducted using rhamnolipid biosurfactants produced by various Pseudomonas species under aerobic conditions. The purpose of this study was to elucidate the effects of various levels of the Bacillus sp. JF2 lipopeptide biosurfactant on the degradation of hexadecane under methanogenic conditions. Hexadecane degradation did increase significantly when levels below critical micelle concentration of the pre-purified biosurfactant were added. However, at levels above this amount of biosurfactant, degradation of hexadecane appeared to be inhibited. The terminal electron accepting process, methanogenesis, was stimulated by surfactant addition. A review of the published literature revealed a wide variety of results, some which are similar to, but many that differ from those reported here. However, the results from this study were reproducible. Although there is no clear explanation for these results, more research on the effect of biosurfactants produced by Gram positive bacteria on the biodegradation of hydrocarbons is needed, as well as further studies under anaerobic conditions.     

Biogeochemical Contributions of Tree Islands to Everglades Wetland Landscape Nitrogen Cycling During Seasonal Inundation

In the Florida Everglades, tree islands are conspicuous heterogeneous elements in the herbaceous wetland landscape. We characterized the biogeochemical role of a seasonally flooded tree island during wet season inundation, specifically examining hydrologically mediated flows of nitrogen (N) and N retention by the tree island. We estimated ecosystem N standing stocks and fluxes, soil and litter N transformation rates, and hydrologic fluxes of N to quantify the net ecosystem N mass flux. Results showed that hydrologic sources of N were dominated by surface water loads of nitrate (NO₃) and ammonium (NH₄). Nitrate immobilization by soils and surficial leaf litter was an important sink for surface water dissolved inorganic N (DIN). We estimated that the net annual DIN retention by a seasonally flooded tree island was 20.5 ± 5.0 g m⁻² during wet season inundation. Based on the estimated tree island surface water DIN loading rate, a seasonally flooded tree island retained 76% of imported DIN. As such, seasonally flooded tree islands have the potential to retain 55% of DIN entering the marsh landscape via upstream canal overland flow in the wet season. By increasing reactive surface area and DOC availability, we suggest that tree islands promote convergence of elements that enhance DIN retention. Tree islands of this region are thus important components of landscape-scale restoration efforts that seek to reduce sources of anthropogenic DIN to downstream estuaries.     

农业生态系统养分循环研究概况

营养物质循环作为农业生态系统的主要过程及基本功能,是系统生产力及持久性的决定因素,也对生物圈化学环境有重大影响。早在本世纪初,人们就从植物营养生理的角度开始了营养物质循环平衡的研究［１］。１９５５年Ａｌｉｓｏｎ将系统和整体的观点引入生态系统物质循环的...     

Nutrient Dynamics of Estuarine Invertebrates Are Shaped by Feeding Guild Rather than Seasonal River Flow

This study aimed to determine the variability of carbon and nitrogen elemental content, stoichiometry and diet proportions of invertebrates in two sub-tropical estuaries in South Africa experiencing seasonal changes in rainfall and river inflow. The elemental ratios and stable isotopes of abiotic sources, zooplankton and macrozoobenthos taxa were analyzed over a dry/wet seasonal cycle. Nutrient content (C, N) and stoichiometry of suspended particulate matter exhibited significant spatio-temporal variations in both estuaries, which were explained by the variability in river inflow. Sediment particulate matter (%C, %N and C:N) was also influenced by the variability in river flow but to a lesser extent. The nutrient content and ratios of the analyzed invertebrates did not significantly vary among seasons with the exception of the copepod Pseudodiaptomus spp. (C:N) and the tanaid Apseudes digitalis (%N, C:N). These changes did not track the seasonal variations of the suspended or sediment particulate matter. Our results suggest that invertebrates managed to maintain their stoichiometry independent of the seasonality in river flow. A significant variability in nitrogen content among estuarine invertebrates was recorded, with highest % N recorded from predators and lowest %N from detritivores. Due to the otherwise general lack of seasonal differences in elemental content and stoichiometry, feeding guild was a major factor shaping the nutrient dynamics of the estuarine invertebrates. The nutrient richer suspended particulate matter was the preferred food source over sediment particulate matter for most invertebrate consumers in many, but not all seasons. The most distinct preference for suspended POM as a food source was apparent from the temporarily open/closed system after the estuary had breached, highlighting the importance of river flow as a driver of invertebrate nutrient dynamics under extreme events conditions. Moreover, our data showed that estuarine invertebrates concentrated C and N between 10–100 fold from trophic level I (POM) to trophic level II (detritivores/deposit feeders) and thus highlighted their importance not only as links to higher trophic level organisms in the food web, but also as providers of a stoichiometrically homeostatic food source for such consumers. As climate change scenarios for the east coast of South Africa predict increased rainfall as a higher number of rainy days and days with higher rainfall, our results suggest that future changes in rainfall and river inflow will have measurable effects on the nutrient content and stoichiometry of food sources and possibly also in estuarine consumers.     

Seasonal Variations of Dissolved Nitrogen and DOC:DON Ratios in an Intermittent Mediterranean Stream

Seasonal variations of dissolved inorganic nitrogen (DIN) (NO₃–N and NH₄–N) and dissolved organic nitrogen (DON) were determined in Fuirosos, an intermittent stream draining an unpolluted Mediterranean forested catchment (10.5 km²) in Catalonia (Spain). The influence of flow on streamwater concentrations and seasonal differences in quality and origin of dissolved organic matter, inferred from dissolved organic carbon to nitrogen ratios (DOC:DON ratios), were examined. During baseflow conditions, nitrate and ammonium had opposite behaviour, probably controlled by biological processes such as vegetation uptake and mineralization activity. DON concentrations did not have a seasonal trend. During storms, nitrate and DON increased by several times but discharge was not a good predictor of nutrient concentrations. DOC:DON ratios in streamwater were around 26, except during the months following drought when DOC:DON ratios ranged between 42 and 20 during baseflow and stormflow conditions, respectively. Annual N export during 2000–2001 was 70 kg km⁻¹ year⁻¹, of which 75% was delivered during stormflow. The relative contribution of nitrogen forms to the total annual export was 57, 35 and 8% as NO₃–N, DON and NH₄–N, respectively.     

Seasonal Retention and Release of Cryptosporidium parvum Oocysts by Environmental Biofilms in the Laboratory

Cryptosporidium is a genus of waterborne protozoan parasites that causes significant gastrointestinal disease in humans. These parasites can accumulate in environmental biofilms and be subsequently released to contaminate water supplies. Natural microbial assemblages were collected each season from an eastern Pennsylvania stream and used to grow biofilms in laboratory microcosms in which influx, efflux, and biofilm retention were determined from daily oocyst counts. For each seasonal biofilm, oocysts attached to the biofilm quickly during oocyst dosing. Upon termination of oocyst dosing, the percentage of oocysts retained within the biofilm decreased to a new steady state within 5 days. Seasonal differences in biofilm retention of oocysts were observed. The spring biofilm retained the greatest percentage of oocysts, followed (in decreasing order) by the winter, summer, and fall biofilms. There was no statistically significant correlation between the percentage of oocysts attached to the biofilm and (i) any measured stream water quality parameter (including temperature, pH, conductivity, and dissolved organic carbon concentration) or (ii) experimental temperature. Seasonal differences in oocyst retention persisted when biofilms were tested with stream water from a different season. These data suggest that seasonal variation in the microbial community and resulting biofilm architecture may be more important to oocyst transport in this stream site than water quality. The biofilm attachment and detachment dynamics of C. parvum oocysts have implications for public health, and the drinking water industry should recognize that the potential exists for pathogen-free water to become contaminated during the distribution process as a result of biofilm dynamics.Cryptosporidium is a genus of waterborne protozoan parasites that cause a gastrointestinal disease in humans (cryptosporidiosis) that can be prolonged and life-threatening for people with compromised immune systems. Recent advances in medical treatment for cryptosporidiosis exist but are not entirely effective for immunocompromised patients (1). In addition, conventional water treatment does not effectively target Cryptosporidium oocysts because the oocysts'' small size (4 to 8 μm) limits the ability of filters to remove them and, more importantly, oocysts are resistant to chlorine (25). Therefore, environmental control of Cryptosporidium is important to protect public health. To determine the risk of human exposure and infection, the fate and transport of Cryptosporidium oocysts in the environment, including biofilms, should be examined.Within the past two decades, biofilms have been recognized as ubiquitous habitats found on most surfaces exposed to water (20, 24). Environmental biofilms can rapidly accumulate pathogens at densities much higher than water column densities, and the potential for gradual or sudden pathogen loss from the biofilm exists long after entrapment (8, 22). Biofilm sloughing events are commonplace, occurring when a biofilm detaches from the substrate to be resuspended as large particles in the water column, and may result in the release of pathogen reservoirs from the biofilm into the water column (8).Biofilms have been identified as a possible contamination source for drinking water supplies, which may lead to infections for which the source cannot be identified (7, 9). An example of the impact of biofilm sloughing events on human health is seen in the cryptosporidiosis outbreak that occurred in Lancashire County, England, in March 2000 (10). After the outbreak, the oocyst source was identified as cattle feces from adjacent farmland that contaminated the drinking water after abnormally heavy rainfall. The water source was subsequently changed to two upland impounding reservoirs containing filtered surface water. However, oocysts persisted in the water distribution system for 19 days, with large peaks associated with major water main disturbance events, including the initial flushing of the system and a burst in the main supply pipe. This persistence of oocysts in the water supply was attributed to the release of oocysts trapped in biofilms on the interior surface of the distribution pipes and may have contributed to additional infections.Several studies have examined pathogen transport dynamics in biofilms using glass or latex beads of various sizes as surrogates for pathogens (5, 8, 16, 17). A few studies examined the attachment of C. parvum oocysts to biofilms but did not use natural microbial assemblages to make the biofilms (3, 23) or quantify how many oocysts attached or sloughed (9, 22). Rogers and Keevil (22) showed that oocysts attached to a biofilm composed of a natural microbial assemblage collected from a reservoir at a concentration of 1,400 oocysts/cm² after the addition of 10⁸ oocysts in 10 ml of sterile water. Dai and Hozalski (3) and Searcy et al. (23) used pure culture biofilms to demonstrate oocyst attachment; however, only Searcy et al. (23) accounted for sloughing, although no oocyst release from the biofilm was seen during the course of their experiments. Helmi et al. (9) noted attachment and detachment of oocysts from a natural biofilm but did not include a quantitative analysis to account for all oocysts in the flow system over time. None of these studies examined pathogen attachment seasonally over the course of a year. Seasonal changes in temperature, precipitation, and water quality (including nutrient availability) may have significant impacts on the microbial composition and functional structure of a biofilm (14). These changes include structural changes in the biofilm thickness and morphology, as well as changes in the water composition and suspended matter. In addition, seasonal changes in stream flow dynamics may alter biofilm composition and morphology, as well as oocyst attachment and release patterns.This study provides novel information about C. parvum oocyst attachment to biofilms grown in the laboratory from natural microbial assemblages collected seasonally (i.e., in January, April, July, and October) from Monocacy Creek in Bethlehem, PA. Previous work (26) showed that (i) a significant fraction of C. parvum oocysts adhered to the surface of experimental biofilms during a 3-day oocyst dosing period, (ii) a portion of the adhered oocysts immediately released from the biofilm, and (iii) a portion of the oocysts remained attached to the biofilm for a period of days after termination of oocyst dosing. Here, we test the hypotheses that (i) oocyst retention by biofilms varies seasonally and (ii) seasonal changes in water quality influence oocyst retention.     

Impact of rpoS Deletion on Escherichia coli Biofilms

Slow growth has been hypothesized to be an essential aspect of bacterial physiology within biofilms. In order to test this hypothesis, we employed two strains of Escherichia coli, ZK126 (ΔlacZ rpoS⁺) and its isogenic ΔrpoS derivative, ZK1000. These strains were grown at two rates (0.033 and 0.0083 h⁻¹) in a glucose-limited chemostat which was coupled either to a modified Robbins device containing plugs of silicone rubber urinary catheter material or to a glass flow cell. The presence or absence of rpoS did not significantly affect planktonic growth of E. coli. In contrast, biofilm cell density in the rpoS mutant strain (ZK1000), as measured by determining the number of CFU per square centimeter, was reduced by 50% (P < 0.05). Deletion of rpoS caused differences in biofilm cell arrangement, as seen by scanning confocal laser microscopy. In reporter gene experiments, similar levels of rpoS expression were seen in chemostat-grown planktonic and biofilm populations at a growth rate of 0.033 h⁻¹. Overall, these studies suggest that rpoS is important for biofilm physiology.     

Effects of Exotic Plant Invasions on Soil Nutrient Cycling Processes

Although it is generally acknowledged that invasions by exotic plant species represent a major threat to biodiversity and ecosystem stability, little attention has been paid to the potential impacts of these invasions on nutrient cycling processes in the soil. The literature on plant–soil interactions strongly suggests that the introduction of a new plant species, such as an invasive exotic, has the potential to change many components of the carbon (C), nitrogen (N), water, and other cycles of an ecosystem. I have reviewed studies that compare pool sizes and flux rates of the major nutrient cycles in invaded and noninvaded systems for invasions of 56 species. The available data suggest that invasive plant species frequently increase biomass and net primary production, increase N availability, alter N fixation rates, and produce litter with higher decomposition rates than co-occurring natives. However, the opposite patterns also occur, and patterns of difference between exotics and native species show no trends in some other components of nutrient cycles (for example, the size of soil pools of C and N). In some cases, a given species has different effects at different sites, suggesting that the composition of the invaded community and/or environmental factors such as soil type may determine the direction and magnitude of ecosystem-level impacts. Exotic plants alter soil nutrient dynamics by differing from native species in biomass and productivity, tissue chemistry, plant morphology, and phenology. Future research is needed to (a) experimentally test the patterns suggested by this data set; (b) examine fluxes and pools for which few data are available, including whole-site budgets; and (c) determine the magnitude of the difference in plant characteristics and in plant dominance within a community that is needed to alter ecosystem processes. Such research should be an integral component of the evaluation of the impacts of invasive species.     

Global Positive Effects of Litter Inputs on Soil Nitrogen Pools and Fluxes

Ecosystems - Soil nitrogen (N) pools and fluxes are strongly influenced by litter inputs in natural ecosystems. However, general responses of soil N pools and fluxes to litter inputs from both...     

Nitrogen Inputs by Marine Vertebrates Drive Abundance and Richness in Antarctic Terrestrial Ecosystems

1. Download : Download high-res image (283KB)
2. Download : Download full-size image

     

Effect of Pristine Multi-Walled Carbon Nanotubes on Formation and Degradation of Bacterial Biofilms

Microbiology - The effect of pristine multi-walled carbon nanotubes (MWCNT) on the biofilms of gram-negative bacteria, typical members of the activated sludge community, and gram-positive...