The functional role of temperate forest understorey vegetation in a changing world.

Temperate forests cover 16% of the global forest area. Within these forests, the understorey is an important biodiversity reservoir that can influence ecosystem processes and functions in multiple ways. However, we still lack a thorough understanding of the relative importance of the understorey for temperate forest functioning. As a result, understoreys are often ignored during assessments of forest functioning and changes thereof under global change. We here compiled studies that quantify the relative importance of the understorey for temperate forest functioning, focussing on litter production, nutrient cycling, evapotranspiration, tree regeneration, pollination and pathogen dynamics. We describe the mechanisms driving understorey functioning and develop a conceptual framework synthesizing possible effects of multiple global change drivers on understorey-mediated forest ecosystem functioning. Our review illustrates that the understorey's contribution to temperate forest functioning is significant but varies depending on the ecosystem function and the environmental context, and more importantly, the characteristics of the overstorey. To predict changes in understorey functioning and its relative importance for temperate forest functioning under global change, we argue that a simultaneous investigation of both overstorey and understorey functional responses to global change will be crucial. Our review shows that such studies are still very scarce, only available for a limited set of ecosystem functions and limited to quantification, providing little data to forecast functional responses to global change.

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 (NaMnO(4)) 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 NaMnO(4) 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 NaMnO(4) 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 NaMnO(4) 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.

Comparison of the host specificities of two bacteroidales quantitative PCR assays used for tracking human fecal contamination.

The sewage-associated real-time quantitative PCR (qPCR) assays BacHum and HF183 SYBR were compared for specificity against local fecal sources. Both assays were equally sensitive to sewage, but BacHum showed substantially more false-positive results for cat, dog, gull, and raccoon feces.

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.

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.

Sewage exfiltration as a source of storm drain contamination during dry weather in urban watersheds.

Separating storm drains and sanitary sewers is expected to control sewage pollution, for example, from combined sewer overflows, and to reduce excessive stormwater flow to wastewater treatment plants. However, sewage contamination has been found in such separated storm drain systems in urban areas during dry-weather flow. To determine whether transmission of sewage is occurring from leaking sanitary sewers directly to leaking separated storm drains, field experiments were performed in three watersheds in Santa Barbara, CA. Areas with high and low risks for sewage exfiltration into storm drains were identified, and rhodamine WT (RWT) dye pulses were added to the sanitary sewers. RWT was monitored in nearby storm drain manholes using optical probes set up for unattended continuous monitoring. Above-background RWT peaks were detected in storm drains in high-risk areas, and multiple locations of sewage contamination were found. Sewage contamination during the field studies was confirmed using the human-specific Bacteroidales HF183 and Methanobrevibacter smithii nifH DNA markers. This study is the first to provide direct evidence that leaking sanitary sewers can directly contaminate nearby leaking storm drains with untreated sewage during dry weather and suggests that chronic sanitary sewer leakage contributes to downstream fecal contamination of coastal beaches.

Application of an integrated community analysis approach for microbial source tracking in a coastal creek.

High fecal indicator bacterial (FIB) concentrations signal urban coastal water quality impairments that can threaten public health. However, FIB (total and fecal coliform plus Enterococcus sp.) concentrations are not specific to human waste, and thus, microbial source tracking (MST) is employed to assess public health risks and remediation alternatives. Currently, water quality diagnosis requires several simultaneous MST assays. Relatively unexplored is a community analysis approach for MST where the overall microbial community composition is compared, through multivariate analysis, to link sources and sinks of microbial pollution. In this research, an urban coastal creek and drain sampling transect, previously diagnosed as human-waste-contaminated, were evaluated for bacterial community composition relative to fecal sources; a laboratory spiking study was also performed to assess method sensitivity and specificity. Multivariate statistical analysis of community profiles clearly distinguished different fecal sources, indicated a high sensitivity for sewage spikes, and confirmed creek contamination sources. This work demonstrates that molecular microbial community analysis combined with appropriate multivariate statistical analyses is an effective addition to the MST tool box.

Evaluation of chemical, molecular, and traditional markers of fecal contamination in an effluent dominated urban stream.

In this paper we present a quantitative sanitary survey of the Middle Santa Ana River, in southern California, utilizing a variety of source tracking tools, including traditional culture-dependent fecal markers (Enterococcus and Escherichia coli by IDEXX), speciation of enterococci isolates, culture-independent fecal markers (human-specific HF183 Bacteroides and Enterococcus by quantitative polymerase chain reaction, qPCR), and chemical markers of sewage and wastewater (nutrients, enantiomeric fraction (EF) of propranolol and ethylenediaminetetraacetic acid). To facilitate comparison of these different methods, data are interpreted in a loading (i.e., mass per time) framework that enables a quantitative apportionment of fecal markers and nutrients to specific source waters in the Middle Santa Ana River. Multiple lines of evidence support the hypothesis that Enterococcus in the Middle Santa Ana River originates primarily from in situ growth in streambed sediments, not from significant and persistent sources of untreated human waste. The EF of propranolol of tertiary treated wastewater effluent is in the range (0.42 to 0.71) previously reported for raw sewage, making EF of propranolol an unsuitable marker for fecal pollution, at least at this site. The human fecal marker HF183 Bacteroides was detected at a few sites, although not in a source of disinfected and tertiary treated wastewater effluent. Based on the results presented here and prior experience at other sites in southern California, HF183 Bacteroides would appear to be a candidate marker of fecal contamination for inland waters, although more qPCR measurements in disinfected wastewater effluent are needed to account for variations due to treatment plant performance and other factors. More generally, our results support the notion that regrowth of fecal indicator bacteria (FIB) in river sediments may lead to a decoupling between FIB and pathogen concentrations in the water column and thus limit the utility of FIB as an indicator of recreational waterborne illness in inland waters.

Forest fragmentation modulates effects of tree species richness and composition on ecosystem multifunctionality.

Forest fragments in highly disturbed landscapes provide important ecosystem services ranging from acting as biodiversity reservoir to providing timber or regulating hydrology. Managing the tree species richness and composition of these fragments to optimize their functioning and the deliverance of multiple ecosystem services is of great practical relevance. However, both the strength and direction of tree species richness and tree species composition effects on forest ecosystem multifunctionality may depend on the landscape context in which these forest remnants are embedded. Taking advantage of an observatory network of 53 temperate forest plots varying in tree species richness, tree species composition, and fragmentation intensity we measured 24 ecosystem functions spanning multiple trophic levels and analyzed how tree species diversity-multifunctionality relationships changed with fragmentation intensity. Our results show that fragmentation generally increases multifunctionality and strengthens its positive relationship with diversity, possibly due to edge effects. In addition, different tree species combinations optimize functioning under different fragmentation levels. We conclude that management and restoration of forest fragments aimed at maximizing ecosystem multifunctionality should be tailored to the specific landscape context. As forest fragmentation will continue, tree diversity will become increasingly important to maintain forest functioning.

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.

Degradation of isobutanal at high loading rates in a compost biofilter.

Biofiltration has been increasingly used for cleaning waste gases, mostly containing low concentrations of odorous compounds. To expand the application area of this technology, the biofiltration of higher pollutant loading rates has to be investigated. This article focuses on the biodegradation of isobutanal (IBAL) in a compost biofilter (BF) at mass loading rates between 211 and 4123 g/m3/day (30-590 ppm(v)). At mass loading rates up to 785 g/m3/day, near 100% removal efficiencies could be obtained. However, after increasing the loading rate to 1500-1900 g/m3/ day, the degradation efficiency decreased to 62-98%. In addition, a pH decrease and production of isobutanol (IBOL) and isobutyric acid (IBAC) were observed. This is the first report showing that an aldehyde can act as electron donor as well as acceptor in a BF. To study the effects of pH, compost moisture content, and electron acceptor availability on the biofiltration of IBAL, IBOL, and IBAC, additional batch and continuous experiments were performed. A pH of 5.2 reduced the IBAL degradation rate and inhibited the IBOL degradation, although adaptation of the microorganisms to low pH was observed in the BFs. IBAC was not degraded in the batch experiments. High moisture content (51%) initially had no effect on the IBOL production, although it negatively affected the IBAL elimination increasingly during a 21-day time-course experiment. In batch experiments, the reduction of IBAL to IBOL did not decrease when the amount of available electron acceptors (oxygen or nitrate) was increased. The IBAL removal efficiency at higher loading rates was limited by a combination of nutrient limitation, pH decrease, and dehydration, and the importance of each limiting factor depended on the influent concentration.

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 alpha-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.

Storm drains are sources of human fecal pollution during dry weather in three urban southern California watersheds.

Coastal urbanized areas in Southern California experience frequent beach water quality warnings in summer due to high concentrations of fecal indicator bacteria (FIB). Remediation can be difficult, as sources are often unknown. During two summers, we sampled three urbanized watersheds in Santa Barbara, CA at sites with historically high FIB concentrations to determine if human fecal matter was influencing water quality. By quantification of a human-specific Bacteroides marker (HBM), human waste was evidenced throughout both transects, and concentrations were highest in the discharges of several flowing storm drains. The HBM concentrations in storm drain discharges varied by up to 5 orders of magnitude on the same day. While the exact points of entry into the storm drain systems were not definitively determined, further inspection of the drain infrastructure suggested exfiltrating sanitary sewers as possible sources. The HBM and FIB concentrations were not consistently correlated, although the exclusive occurrence of high HBM concentrations with high FIB concentrations warrants the use of FIB analyses for a first tier of sampling. The association of human fecal pollution with dry weather drainage could be a window into a larger problem for other urbanized coastal areas with Mediterranean-type climates.

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 H(2)S and in a control biofilter without H(2)S loading. During the first 81 days of the experiment, the H(2)S removal efficiencies always exceeded 93% at loading rates between 4.1 and 30 g m(-3) h(-1). Afterwards, the H(2)S removal efficiency decreased to values between 44 and 71%. RNA-based DGGE analysis showed that H(2)S 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 H(2)S-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 H(2)S-degrading biofilter. The decreasing H(2)S removal efficiencies near the end of the experiment were not accompanied by a substantial change of the DGGE patterns. Therefore, the decreased H(2)S 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.