The abundance of health-associated bacteria is altered in PAH polluted soils-Implications for health in urban areas?

Long-term exposure to polyaromatic hydrocarbons (PAHs) has been connected to chronic human health disorders. It is also well-known that i) PAH contamination alters soil bacterial communities, ii) human microbiome is associated with environmental microbiome, and iii) alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health. The rationale behind our study was to increase understanding and potentially facilitate reconsidering factors that lead to health disorders in areas characterized by PAH contamination. Large containers filled with either spruce forest soil, pine forest soil, peat, or glacial sand were left to incubate or contaminated with creosote. Biological degradation of PAHs was monitored using GC-MS, and the bacterial community composition was analyzed using 454 pyrosequencing. Proteobacteria had higher and Actinobacteria and Bacteroidetes had lower relative abundance in creosote contaminated soils than in non-contaminated soils. Earlier studies have demonstrated that an increase in the abundance of Proteobacteria and decreased abundance of the phyla Actinobacteria and Bacteroidetes are particularly associated with adverse health outcomes and immunological disorders. Therefore, we propose that pollution-induced shifts in natural soil bacterial community, like in PAH-polluted areas, can contribute to the prevalence of chronic diseases. We encourage studies that simultaneously address the classic "adverse toxin effect" paradigm and our novel "altered environmental microbiome" hypothesis.

Soil microbial communities are shaped by vegetation type and park age in cities under cold climate.

Soil microbes play a key role in controlling ecosystem functions and providing ecosystem services. Yet, microbial communities in urban green space soils remain poorly characterized. Here we compared soil microbial communities in 41 urban parks of (i) divergent plant functional types (evergreen trees, deciduous trees and lawn) and (ii) different ages (constructed 10, ∼50 and >100 years ago). These microbial communities were also compared to those in 5 control forests in southern Finland. Our results indicate that, despite frequent disturbances in urban parks, urban soil microbes still followed the classic patterns typical of plant-microbe associations in natural environments: both bacterial and fungal communities in urban parks responded to plant functional groups, but fungi were under tighter control of plants than bacteria. We show that park age shaped the composition of microbial communities, possibly because vegetation in old parks have had a longer time to modify soil properties and microbial communities than in young parks. Furthermore, control forests harboured distinct but less diverse soil microbial communities than urban parks that are under continuous anthropogenic disturbance. Our results highlight the importance of maintaining a diverse portfolio of urban green spaces and plant communities therein to facilitate complex microbial communities and functions in urban systems.

Analyses of Sporocarps, Morphotyped Ectomycorrhizae, Environmental ITS and LSU Sequences Identify Common Genera that Occur at a Periglacial Site.

Periglacial substrates exposed by retreating glaciers represent extreme and sensitive environments defined by a variety of abiotic stressors that challenge organismal establishment and survival. The simple communities often residing at these sites enable their analyses in depth. We utilized existing data and mined published sporocarp, morphotyped ectomycorrhizae (ECM), as well as environmental sequence data of internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal RNA gene to identify taxa that occur at a glacier forefront in the North Cascades Mountains in Washington State in the USA. The discrete data types consistently identified several common and widely distributed genera, perhaps best exemplified by Inocybe and Laccaria. Although we expected low diversity and richness, our environmental sequence data included 37 ITS and 26 LSU operational taxonomic units (OTUs) that likely form ECM. While environmental surveys of metabarcode markers detected large numbers of targeted ECM taxa, both the fruiting body and the morphotype datasets included genera that were undetected in either of the metabarcode datasets. These included hypogeous (Hymenogaster) and epigeous (Lactarius) taxa, some of which may produce large sporocarps but may possess small and/or spatially patchy genets. We highlight the importance of combining various data types to provide a comprehensive view of a fungal community, even in an environment assumed to host communities of low species richness and diversity.

Layer of organic pine forest soil on top of chlorophenol-contaminated mineral soil enhances contaminant degradation.

Chlorophenols, like many other synthetic compounds, are persistent problem in industrial areas. These compounds are easily degraded in certain natural environments where the top soil is organic. Some studies suggest that mineral soil contaminated with organic compounds is rapidly remediated if it is mixed with organic soil. We hypothesized that organic soil with a high degradation capacity even on top of the contaminated mineral soil enhances degradation of recalcitrant chlorophenols in the mineral soil below. We first compared chlorophenol degradation in different soils by spiking pristine and pentachlorophenol-contaminated soils with 2,4,6-trichlorophenol in 10-L buckets. In other experiments, we covered contaminated mineral soil with organic pine forest soil. We also monitored in situ degradation on an old sawmill site where mineral soil was either left intact or covered with organic pine forest soil. 2,4,6-Trichlorophenol was rapidly degraded in organic pine forest soil, but the degradation was slower in other soils. If a thin layer of the pine forest humus was added on top of mineral sawmill soil, the original chlorophenol concentrations (high, ca. 70 µg g(-1), or moderate, ca. 20 µg g(-1)) in sawmill soil decreased by >40 % in 24 days. No degradation was noticed if the mineral soil was kept bare or if the covering humus soil layer was sterilized beforehand. Our results suggest that covering mineral soil with an organic soil layer is an efficient way to remediate recalcitrant chlorophenol contamination in mineral soils. The results of the field experiment are promising.

The fate of lead at abandoned and active shooting ranges in a boreal pine forest.

Changes in leaching, availability, bioaccumulation, and vertical distribution of lead (Pb) in soil 20 years after the cessation of shooting activity were studied by comparing three pine forest sites in southern Finland: an active shooting range, an abandoned shooting range, and a noncontaminated control site. At both shooting ranges, shooting activity had lasted for 20 years, but it had taken place 20 years earlier at the abandoned range. Up to 4 kg m(-2) of Pb pellets had accumulated in the soil at both shooting ranges, and extremely high Pb concentrations, reaching 50,000 mg kg(-1) , were detected in the organic soil layer. Elevated Pb concentrations were also found in leachate waters and in the biota. Concentrations of Pb in the top organic soil layer and in some of the biota were lower at the abandoned shooting range, which can be taken as a sign of starting recovery of the forest ecosystem. However, the concentration of water-extractable Pb had not decreased in the topsoil, possibly indicating the release of Pb from decaying litter. Deeper in the organic soil layer, weathering of Pb pellets enhanced Pb availability and leaching, indicating an increased risk of groundwater contamination over time at shooting sites located above aquifers.

Responses of fungal and plant communities to partial humus removal in mid-boreal N-enriched forests.

Partial removal of the forest humus layer was performed in nitrogen-enriched urban Scots pine forest stands in the northern Finland in order to improve soil conditions for ectomycorrhizal (ECM) fungi, important symbionts of trees. Aboveground part of understory vegetation and the uppermost half of the humus layer were removed (REMOVAL treatment) from sample plots in six urban and eight rural reference forest sites at the beginning of the 2001 growing season. During the seasons 2001-2005, we inventoried sporocarp production of ECM and saprophytic fungi, and in 2003 the recovery of understory vegetation. The REMOVAL treatment resulted in a higher number of fruiting ECM species and sporocarps than controls at the rural, but not at urban sites. The sporocarp number of saprophytic fungi declined in the REMOVAL subplots at the urban sites. The recovery of bryophytes and lichens in the REMOVAL treatment was slow at both the urban and rural sites, whereas Vaccinium dwarf shrub cover, and herb and grass cover returned rapidly at the urban sites. We conclude that the partial vegetation and humus layer removal as a tool to promote the reproduction of ECM fungal species is limited in the boreal urban forests.

Natural attenuation is enhanced in previously contaminated and coniferous forest soils.

PURPOSE: Prevalence of organic pollutants or their natural analogs in soil is often assumed to lead to adaptation in the bacterial community, which results in enhanced bioremediation if the soil is later contaminated. In this study, the effects of soil type and contamination history on diesel oil degradation and bacterial adaptation were studied. METHODS: Mesocosms of mineral and organic forest soil (humus) were artificially treated with diesel oil, and oil hydrocarbon concentrations (GC-FID), bacterial community composition (denaturing gradient gel electrophoresis, DGGE), and oil hydrocarbon degraders (DGGE + sequencing of 16S rRNA genes) were monitored for 20 weeks at 16°C. RESULTS: Degradation was advanced in previously contaminated soils as compared with pristine soils and in coniferous organic forest soil as compared with mineral soil. Contamination affected bacterial community composition especially in the pristine mineral soil, where diesel addition increased the number of strong bands in the DGGE gel. Sequencing of cloned 16S rRNA gene fragments and DGGE bands showed that potential oil-degrading bacteria were found in mineral and organic soils and in both pristine and previously contaminated mesocosms. Fast oil degradation was not associated with the presence of any particular bacterial strain in soil. CONCLUSIONS: We demonstrate at the mesocosm scale that previously contaminated and coniferous organic soils are superior environments for fast oil degradation as compared with pristine and mineral soil environments. These results may be utilized in preventing soil pollution and planning soil remediation.

EcM fungal community structure, but not diversity, altered in a Pb-contaminated shooting range in a boreal coniferous forest site in Southern Finland.

Boreal forests contain diverse fungal communities that form essential ectomycorrhizal symbioses with trees. To determine the effects of lead (Pb) contamination on ectomycorrhizal fungal communities associated with the dominant pine (Pinus sylvestris L.), we surveyed sporocarps for 3 years, analyzed morphotyped ectomycorrhizal root tips by direct sequencing, and 454-sequenced fungal communities that grew into in-growth bags during a 2-year incubation at a shooting range where sectors vary in the Pb load. We recorded a total of 32 ectomycorrhizal fungi that formed conspicuous sporocarps, 27 ectomycorrhizal fungal phylotypes from 294 root tips, and 116 ectomycorrhizal fungal operation taxonomic unit (OTUs) from a total of 8194 internal transcribed spacer-2 454 sequences. Our ordination analyses by nonparametric multidimensional scaling (NMS) indicated that the Pb enrichment induced a shift in the ectomycorrhizal community composition. This was visible as indicative trends in the sporocarp and root tip data sets, but was explicitly clear in the communities observed in the in-growth bags. The compositional shift in the ectomycorrhizal community was mainly attributable to an increase in the frequencies of OTUs assigned to genus Thelephora and to a decrease in the OTUs assigned to Pseudotomentella, Suillus, and Tylospora in Pb-contaminated areas when compared with the control. While the compositional shifts are clear, their functional consequences for the dominant trees or soil ecosystem function remain undetermined.

Testing the homogenizing effect of low copper sulfate concentrations on the size distribution of Portulaca oleracea seedlings in vitro.

Traditionally, toxicological bioassays rely upon the differences in mean-based statistical tests between the exposed and unexposed plants, and exceptional plant individuals are treated as statistical outliers. Recently, low toxicant concentrations have been observed to affect gene regulation in exposed plant stands and to change the frequency of the largest individuals even if mean plant size remains unchanged. In this paper, we present the results that the latter phenomenon is not restricted to a single toxicant and plant species. Our data analysis consists of two statistical methods that may be of general interest. We utilized the one-tailed Moses extreme reactions test by comparing exposed groups to control plants with and without the trimming of a certain amount of potential outliers from both treatments compared. We also propose that Mann-Whitney U or other tests at ordinal scale can be utilized to analyze if the largest plant individuals in exposed and control treatments come from a single 'survivor' population. We conclude that the results supported the hypothesis that very low toxicant concentrations may have ecological effects on fast-growing plant species. Finally, we discuss the limitations of the statistical methods currently in use.

Low toxicant concentrations decrease the frequency of fast-growing seedlings at high densities of annual baby's breath (Gypsophila elegans).

Very low toxicant concentrations reduce the frequency of most vital seedlings in dense stands in vitro.

Lead contamination of an old shooting range affecting the local ecosystem--A case study with a holistic approach.

The aim of this case study was to uncover the consequences of lead pellet-derived heavy lead contamination at a cast-off shooting range in southern Finland, covering aspects from soil chemistry and biology up to ecosystem level. The observed changes in the soil properties of the most contaminated areas suggest that the contamination may be disturbing processes of decomposition and nutrient mineralisation. Also two functionally important groups of soil organisms, microbes (as analysed using the PLFA analysis) and enchytraeid worms, were negatively affected by the contamination. Furthermore, there was an indication of reduced pine litter production at the contaminated areas. On the other hand, lead contamination appears not to have affected pine growth or soil-dwelling nematodes and microarthropods, and the general outlook of the whole ecosystem is that of a healthy forest. Thus, the boreal forest ecosystem studied as a whole appears to bear strong resistance to contamination, despite negative effects of lead on many of its components. This resistance may result from e.g. low bioavailability of lead, avoidance of the most contaminated soil horizons and microsites by the organisms, and functional redundancy and development of lead-tolerant populations amongst the organisms. The relative importance of these factors and the mechanisms behind them will be investigated in forthcoming studies.

Interaction modification among decomposers impairs ecosystem processes in lead-polluted soil.

Environmental pollution by toxicants is generally believed to lead both to direct toxic effects and indirect effects via altered species interactions in a stressed community. We examined how contamination of a coniferous forest soil floor by lead (from an abandoned shooting range area) may alter trophic interactions and decomposition processes. We constructed laboratory microcosms containing microbial-based food webs with various trophic structures: microbes alone; microbes with microbivorous-detritivorous enchytraeid worms (Cognettia sphagnetorum, a potential keystone species of boreal forest soil); and microbes, worms, and predatory mites (Lysigamasus spp.) together. The direct toxic effect of lead and the effectiveness of the predators in preying upon the worms were studied in separate experiments. Polluted humic soil (acid-extractable lead concentration was 2,720 +/- 349 mg/kg of dry soil [mean +/- standard error]) was toxic to enchytraeids, and predators effectively reduced worm populations. Positive density-dependent effects of worms on microbes and a trophic cascade from predatory mites to microbes, observed in the unpolluted humus, were not observed in the polluted humus, indicating pollution-induced interaction modification among organisms. Concomitantly, lead pollution altered the process of nutrient mineralization in the humic soil. However, causality and relative importance of direct toxicity and indirect effects of lead on the dynamics of the decomposer food web could not be pointed out. Examination of our results indicates that traditional food web models are incapable of predicting mechanisms that alter dynamics of pollution-stressed belowground food webs.