Operational and microbiological aspects of a bioaugmented two-stage biotrickling filter removing hydrogen sulfide and dimethyl sulfide

A two-stage biotrickling filter was developed for removing dimethyl sulfide (DMS) and hydrogen sulfide (H2S). The first biotrickling filter (ABF) was inoculated with Acidithiobacillus thiooxidans and operated without pH control, while the second biotrickling filter (HBF) was inoculated with Hyphomicrobium VS and operated at neutral pH. High DMS elimination capacities were observed in the HBF (8.2 g DMS m(-3) h(-1) at 90% removal efficiency) after 2 days. Maximal observed elimination capacities were 83 g H2S m(-3) h(-1) (100% removal efficiency) and 58 g DMS m(-3) h(-1) (88% removal efficiency) for the ABF and the HBF, respectively. The influence of a decreasing empty bed residence time (120 down to 30 sec) and the robustness of the HBF towards changing operational parameters (low pH, starvation, and DMS and H2S peak loadings) were investigated. Suboptimal operational conditions rapidly resulted in lower DMS removal efficiencies, but recovery of the HBF was mostly obtained within a few days. The H2S removal efficiency in the ABF, however, was not influenced by varying operational conditions. In both reactors, microbial community dynamics of the biofilm and the suspended bacteria were investigated, using denaturing gradient gel electrophoresis (DGGE). After a period of gradual change, a stable microbial community was observed in the HBF after 60 days, although Hyphomicrobium VS was not the dominant microorganism. In contrast, the ABF biofilm community was stable from the first day and only a limited bacterial diversity was observed. The planktonic microbial community in the HBF was very different from that in the biofilm.     

How tree species identity and diversity affect light transmittance to the understory in mature temperate forests

Light is a key resource for plant growth and is of particular importance in forest ecosystems, because of the strong vertical structure leading to successive light interception from canopy to forest floor. Tree species differ in the quantity and heterogeneity of light they transmit. We expect decreases in both the quantity and spatial heterogeneity of light transmittance in mixed stands relative to monocultures, due to complementarity effects and niche filling. We tested the degree to which tree species identity and diversity affected, via differences in tree and shrub cover, the spatiotemporal variation in light availability before, during, and after leaf expansion. Plots with different combinations of three tree species with contrasting light transmittance were selected to obtain a diversity gradient from monocultures to three species mixtures. Light transmittance to the forest floor was measured with hemispherical photography. Increased tree diversity led to increased canopy packing and decreased spatial light heterogeneity at the forest floor in all of the time periods. During leaf expansion, light transmittance did differ between the different tree species and timing of leaf expansion might thus be an important source of variation in light regimes for understory plant species. Although light transmittance at the canopy level after leaf expansion was not measured directly, it most likely differed between tree species and decreased in mixtures due to canopy packing. A complementary shrub layer led, however, to similar light levels at the forest floor in all species combinations in our plots. Synthesis. We find that a complementary shrub layer exploits the higher light availability in particular tree species combinations. Resources at the forest floor are thus ultimately determined by the combined effect of the tree and shrub layer. Mixing species led to less heterogeneity in the amount of light, reducing abiotic niche variability.     

Characterization of Coastal Urban Watershed Bacterial Communities Leads to Alternative Community-Based Indicators

Background

Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring.

Methodology/Principal Findings

Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and α-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC∶A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies.

Conclusions/Significance

This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.     

The Influence of In Situ Chemical Oxidation on Microbial Community Composition in Groundwater Contaminated with Chlorinated Solvents

In situ chemical oxidation with permanganate has become an accepted remedial treatment for groundwater contaminated with chlorinated solvents. This study focuses on the immediate and short-term effects of sodium permanganate (NaMnO₄) on the indigenous subsurface microbial community composition in groundwater impacted by trichloroethylene (TCE). Planktonic and biofilm microbial communities were studied using groundwater grab samples and reticulated vitreous carbon passive samplers, respectively. Microbial community composition was analyzed by terminal restriction fragment length polymorphism and a high-density phylogenetic microarray (PhyloChip). Significant reductions in microbial diversity and biomass were shown during NaMnO₄ exposure, followed by recovery within several weeks after the oxidant concentrations decreased to <1 mg/L. Bray–Curtis similarities and nonmetric multidimensional scaling showed that microbial community composition before and after NaMnO₄ was similar, when taking into account the natural variation of the microbial communities. Also, 16S rRNA genes of two reductive dechlorinators (Desulfuromonas spp. and Sulfurospirillum spp.) and diverse taxa capable of cometabolic TCE oxidation were detected in similar quantities by PhyloChip across all monitoring wells, irrespective of NaMnO₄ exposure and TCE concentrations. However, minimal biodegradation of TCE was observed in this study, based on oxidized conditions, concentration patterns of chlorinated and nonchlorinated hydrocarbons, geochemistry, and spatiotemporal distribution of TCE-degrading bacteria.     

Cultivation-independent analysis of bacteria in IDEXX Quanti-Tray/2000 fecal indicator assays

Monitoring microbiological water quality is important for protecting water resources and the health of swimmers. Routine monitoring relies on cultivating fecal indicator bacteria (FIB), frequently using defined substrate technology. Defined substrate technology is designed to specifically enrich for FIB, but a complete understanding of the assay microbiology requires culture-independent analysis of the enrichments. This study aimed to identify bacteria in positive wells of Colilert and Enterolert Quanti-Tray/2000 (IDEXX Laboratories) FIB assays in environmental water samples and to quantify the degree of false-positive results for samples from an urban creek by molecular methods. Pooled Escherichia coli- and Enterococcus-positive Quanti-Tray/2000 enrichments, either from urban creek dry weather flow or municipal sewage, harbored diverse bacterial populations based on 16S rRNA gene sequences and terminal restriction fragment length polymorphism analyses. Target taxa (coliforms or enterococci) and nontarget taxa (Vibrio spp., Shewanella spp., Bacteroidetes, and Clostridium spp.) were identified in pooled and individual positive Colilert and Enterolert wells based on terminal restriction fragments that were in common with those generated in silico from clone sequences. False-positive rates of between 4 and 23% occurred for the urban creek samples, based on the absence of target terminal restriction fragments in individual positive wells. This study suggests that increased selective inhibition of nontarget bacteria could improve the accuracy of the Colilert and Enterolert assays.     

Interaction between cartilage oligomeric matrix protein and extracellular matrix protein 1 mediates endochondral bone growth

In an effort to define the biological functions of COMP, a functional genetic screen was performed. This led to the identification of extracellular matrix protein 1 (ECM1) as a novel COMP-associated partner. COMP directly binds to ECM1 both in vitro and in vivo. The EGF domain of COMP and the C-terminus of ECM1 mediate the interaction between them. COMP and ECM1 colocalize in the growth plates in vivo. ECM1 inhibits chondrocyte hypertrophy, matrix mineralization, and endochondral bone formation, and COMP overcomes the inhibition by ECM1. In addition, COMP-mediated neutralization of ECM1 inhibition depends on their interaction, since COMP largely fails to overcome the ECM1 inhibition in the presence of the EGF domain of COMP, which disturbs the association of COMP and ECM1. These findings provide the first evidence linking the association of COMP and ECM1 and the biological significance underlying the interaction between them in regulating endochondral bone growth.     

H2S degradation is reflected by both the activity and composition of the microbial community in a compost biofilter

In this study, 16S rRNA- and rDNA-based denaturing gradient gel electrophoresis (DGGE) were used to study the temporal and spatial evolution of the microbial communities in a compost biofilter removing H₂S and in a control biofilter without H₂S loading. During the first 81 days of the experiment, the H₂S removal efficiencies always exceeded 93% at loading rates between 4.1 and 30 g m⁻³ h⁻¹. Afterwards, the H₂S removal efficiency decreased to values between 44 and 71%. RNA-based DGGE analysis showed that H₂S loading to the biofilter increased the stability of the active microbial community but decreased the activity-based diversity and evenness. The most intense band in both the RNA- and DNA-based DGGE patterns of the H₂S-degrading biofilter represented the sulfur oxidizing bacterium Thiobacillus thioparus. This suggested that T. thioparus constituted a major part of the bacterial community and was an important primary degrader in the H₂S-degrading biofilter. The decreasing H₂S removal efficiencies near the end of the experiment were not accompanied by a substantial change of the DGGE patterns. Therefore, the decreased H₂S removal was probably not caused by a failing microbiology but rather by a decrease of the mass transfer of substrates after agglutination of the compost particles.     

Phospholipid Scramblase 1 Is Secreted by a Lipid Raft-dependent Pathway and Interacts with the Extracellular Matrix Protein 1 in the Dermal Epidermal Junction Zone of Human Skin

We examined the interaction of ECM1 (extracellular matrix protein 1) using yeast two-hybrid screening and identified the type II transmembrane protein, PLSCR1 (phospholipid scramblase 1), as a binding partner. This interaction was then confirmed by in vitro and in vivo co-immunoprecipitation experiments, and additional pull-down experiments with GST-tagged ECM1a fragments localized this interaction to occur within the tandem repeat region of ECM1a. Furthermore, immunohistochemical staining revealed a partial overlap of ECM1 and PLSCR1 in human skin at the basal epidermal cell layer. Moreover, in human skin equivalents, both proteins are expressed at the basal membrane in a dermal fibroblast-dependent manner. Next, immunogold electron microscopy of ultrathin human skin sections showed that ECM1 and PLSCR1 co-localize in the extracellular matrix, and using antibodies against ECM1 or PLSCR1 cross-linked to magnetic immunobeads, we were able to demonstrate PLSCR1-ECM1 interaction in human skin extracts. Furthermore, whereas ECM1 is secreted by the endoplasmic/Golgi-dependent pathway, PLSCR1 release from HaCaT keratinocytes occurs via a lipid raft-dependent mechanism, and is deposited in the extracellular matrix. In summary, we here demonstrate that PLSCR1 interacts with the tandem repeat region of ECM1a in the dermal epidermal junction zone of human skin and provide for the first time experimental evidence that PLSCR1 is secreted by an unconventional secretion pathway. These data suggest that PLSCR1 is a multifunctional protein that can function both inside and outside of the cell and together with ECM1 may play a regulatory role in human skin.     

Terrestrial Sources Homogenize Bacterial Water Quality During Rainfall in Two Urbanized Watersheds in Santa Barbara, CA

Microbiological contamination from runoff is a human health concern in urbanized coastal environments, but the contamination sources are often unknown. This study quantified fecal indicator bacteria and compared the distributions of human-specific genetic markers and bacterial community composition during dry and wet weather in urban creeks draining two neighboring watersheds in Santa Barbara, CA. In a prior study conducted during exclusively dry weather, the creeks were contaminated with human waste as indicated by elevated numbers of the human-specific Bacteroidales marker HF183 (Sercu et al. in Environ Sci Technol 43:293-298, 2009). During the storm, fecal indicator bacterial numbers and loads increased orders of magnitude above dry weather conditions. Moreover, bacterial community composition drastically changed during rainfall and differed from dry weather flow by (1) increased bacterial diversity, (2) reduced spatial heterogeneity within and between watersheds, and (3) clone library sequences more related to terrestrial than freshwater taxa. Finally, the spatial patterns of human-associated genetic markers (HF183 and Methanobrevibacter smithii nifH gene) changed during wet weather, and the contribution of surface soils to M. smithii nifH gene detection was suspected. The increased fecal indicator bacteria numbers during wet weather were likely associated with terrestrial sources, instead of human waste sources that dominated during dry weather flow.     

Flowering phenology and reproduction of a forest understorey plant species in response to the local environment

Temperate forest understorey plants are subjected to a strong seasonality in their optimal growing conditions. In winter and early spring, low temperatures are suboptimal for plant growth while light becomes limited later in spring season. We can thus expect that differences in plant phenology in relation to spatiotemporal environmental variation will lead to differences in reproductive output, and hence selection. We specifically studied whether early flowering, a paradoxical pattern that is observed in many plant species, is an adaptive strategy, and whether selection for early flowering was confounded with selection for flower duration or was attributable to environmental variables. We used Geum urbanum as a study species to investigate the effect of relevant environmental factors on the species’ flowering phenology and the consequences for plant reproductive output. We monitored the phenology of four to six plants in each of ten locations in a temperate deciduous forest (Belgium). We first quantified variation in flowering time within individuals and related this temporal variation to individual flower reproductive output. Then, we studied inter-individual variation here-in and linked this to reproduction at the plant level, hence studying the selection differential. We found that flowering within individual plants of Geum urbanum was spread over a long period from June to October. Reproductive output of individual flowers, measured as total seed mass per flower, declined during the season. We found no indication for selection for early flowering but rather for longer flower duration. Larger plants had an earlier flowering onset and a higher seed mass, which suggests that these factors covary and are condition dependent. None of the studied environmental variables could explain plant size, although soil pH and to a lesser extent light availability had a positive direct effect on seed mass per plant. Finally, we suggest that the high intra-individual variation in flowering time, which might be a risk spreading strategy of the plant in the presence of seed predation, limits the potential for selection on flowering phenology.