Hydrolase and plastic-degrading microbiota explain degradation of polyethylene terephthalate microplastics during high-temperature composting

This research aims to explore the degradation properties of polyethylene terephthalate (PET) by PET hydrolase (WCCG) in high-temperature composting and its impact on microbial communities. PET degradation, composting parameters and microbial communities were assessed in 220 L sludge composters with PET and WCCG using high-throughput sequencing. Results showed that WCCG addition led to a deceleration of the humification process and a reduction in the relative abundance of thermophilic genera. Potential PET degrading microbiota, e.g. Acinetobacter, Bacillus, were enriched in the plastisphere in the composters where PET reduced by 26 % without WCCG addition. The external introduction of the WCCG enzyme to compost predominantly instigates a chemical reaction with PET, concurently curtailing the proliferation of plastic-degrading bacteria, leading to a 35 % degradation of PET. Both the WCCG enzyme and the microbiota associated with plastic-degradation showed the potential for reducing PET, offering a novel method for mitigating pollution caused by environmental microplastics.

Bioremediation of contaminated soil and groundwater by in situ biostimulation

Bioremediation by in situ biostimulation is an attractive alternative to excavation of contaminated soil. Many in situ remediation methods have been tested with some success; however, due to highly variable results in realistic field conditions, they have not been implemented as widely as they might deserve. To ensure success, methods should be validated under site-analogous conditions before full scale use, which requires expertise and local knowledge by the implementers. The focus here is on indigenous microbial degraders and evaluation of their performance. Identifying and removing biodegradation bottlenecks for degradation of organic pollutants is essential. Limiting factors commonly include: lack of oxygen or alternative electron acceptors, low temperature, and lack of essential nutrients. Additional factors: the bioavailability of the contaminating compound, pH, distribution of the contaminant, and soil structure and moisture, and in some cases, lack of degradation potential which may be amended with bioaugmentation. Methods to remove these bottlenecks are discussed. Implementers should also be prepared to combine methods or use them in sequence. Chemical/physical means may be used to enhance biostimulation. The review also suggests tools for assessing sustainability, life cycle assessment, and risk assessment. To help entrepreneurs, decision makers, and methods developers in the future, we suggest founding a database for otherwise seldom reported unsuccessful interventions, as well as the potential for artificial intelligence (AI) to assist in site evaluation and decision-making.

High-volume evacuation mitigates viral aerosol spread in dental procedures

Dental healthcare personnel (DHCP) are subjected to microbe-containing aerosols and splatters in their everyday work. Safer work conditions must be developed to ensure the functioning of the healthcare system. By simulating dental procedures, we aimed to compare the virus-containing aerosol generation of four common dental instruments, and high-volume evacuation (HVE) in their mitigation. Moreover, we combined the detection of infectious viruses with RT-qPCR to form a fuller view of virus-containing aerosol spread in dental procedures. The air-water syringe produced the highest number of aerosols. HVE greatly reduced aerosol concentrations during procedures. The air-water syringe spread infectious virus-containing aerosols throughout the room, while other instruments only did so to close proximity. Additionally, infectious viruses were detected on the face shields of DHCP. Virus genomes were detected throughout the room with all instruments, indicating that more resilient viruses might remain infectious and pose a health hazard. HVE reduced the spread of both infectious viruses and viral genomes, however, it did not fully prevent them. We recommend meticulous use of HVE, a well-fitting mask and face shields in dental procedures. We advise particular caution when operating with the air-water syringe. Due to limited repetitions, this study should be considered a proof-of-concept report.

Nutritional additives dominance in driving the bacterial communities succession and bioremediation of hydrocarbon and heavy metal contaminated soil microcosms

Soil quality and microbial diversity are essential to the health of ecosystems. However, it is unclear how the use of eco-friendly natural additives can improve the quality and microbial diversity of contaminated soils. Herein, we used high-throughput 16 S rDNA amplicon Illumina sequencing to evaluate the stimulation and development of microbial diversity and concomitant bioremediation in hydrocarbon (HC) and heavy metal (HM)-rich waste disposal site soil when treated with meat and bone meal (MBM), cyclodextrin (Cdx), and MBM and cyclodextrin mixture (Cdx MBM) over a period of 3 months. Results showed that natural additive treatments significantly increased the soil bacterial diversity (higher Shannon index, Simpson index and evenness) in a time-dependent manner, with Cdx eliciting the greatest enhancement. The two additives influenced the bacterial community succession patterns differently. MBM, while it enhanced the enrichment of specific genera Chitinophaga and Terrimonas, did not significantly alter the total bacterial community. In contrast, Cdx or Cdx MBM promoted a profound change of the bacteria community over time, with the enrichment of the genera Parvibaculum, Arenimonas and unclassified Actinobacteria. These results provide evidence on the involvement of the two natural additives in coupling HC and HM bioremediation and bacterial community perturbations, and thus illustrates their potential application in ecologically sound bioremediation technologies for contaminated soils.

Combining Phi6 as a surrogate virus and computational large-eddy simulations to study airborne transmission of SARS-CoV-2 in a restaurant

COVID-19 has highlighted the need for indoor risk-reduction strategies. Our aim is to provide information about the virus dispersion and attempts to reduce the infection risk. Indoor transmission was studied simulating a dining situation in a restaurant. Aerosolized Phi6 viruses were detected with several methods. The aerosol dispersion was modeled by using the Large-Eddy Simulation (LES) technique. Three risk-reduction strategies were studied: (1) augmenting ventilation with air purifiers, (2) spatial partitioning with dividers, and (3) combination of 1 and 2. In all simulations infectious viruses were detected throughout the space proving the existence long-distance aerosol transmission indoors. Experimental cumulative virus numbers and LES dispersion results were qualitatively similar. The LES results were further utilized to derive the evolution of infection probability. Air purifiers augmenting the effective ventilation rate by 65% reduced the spatially averaged infection probability by 30%-32%. This relative reduction manifests with approximately 15 min lag as aerosol dispersion only gradually reaches the purifier units. Both viral findings and LES results confirm that spatial partitioning has a negligible effect on the mean infection-probability indoors, but may affect the local levels adversely. Exploitation of high-resolution LES jointly with microbiological measurements enables an informative interpretation of the experimental results and facilitates a more complete risk assessment.

Meat and bone meal stimulates microbial diversity and suppresses plant pathogens in asparagus straw composting

Meat and bone meal (MBM), as slaughterhouse waste, is a potential biostimulating agent, but its efficiency and reliability in composting are largely unknown. To access the MBM application to the composting process of asparagus straw rice, we followed the composting process for 60 days in 220-L composters and another 180 days in 20-L buckets in treatments applied with MBM or urea. The microbial succession was investigated by high-throughput sequencing. Compared with urea treatments, MBM addition stabilized pH and extended the thermophilic phase for 7 days. The germination index of MBM treatments was 24.76% higher than that of urea treatments. MBM also promoted higher microbial diversity and shifted community compositions. Organic matter and pH were the most significant factors that influence the bacterial and fungal community structure. At the genus level, MBM enriched relative abundances of organic matter-degrading bacteria (Alterococcus) and lignocellulose-degrading fungi (Trichoderma), as well as lignocellulolytic enzyme activities. Notably, MBM addition decreased sum abundances of plant pathogenic fungi of Phaeoacremonium, Acremonium, and Geosmithia from 17.27 to 0.11%. This study demonstrated the potential of MBM as an effective additive in asparagus straw composting, thus providing insights into the development of new industrial aerobic fermentation.

Natural additives contribute to hydrocarbon and heavy metal co-contaminated soil remediation

A biological treatment method was tested in laboratory conditions for the removal of hydrocarbons contained in a waste disposal soil sample consisting of excavated sandy soil from a former fueling station. Two fractions of hydrocarbons were quantified by GC-FID: diesel (C₁₀-C₂₁) and lubricant oil (C₂₂-C₄₀). Meat and bone meal (MBM, 1% w/w) was used as a bio-stimulant agent for soil organisms. Cyclodextrin, an oligosaccharide produced from starch by enzymatic conversion, was also used to assess its ability to improve the bioavailability/biodegradability of hydrocarbons in the soil. Parameters such as temperature, pH, water content and aeration (O₂ availability) were monitored and optimized to favor degradation processes. Two different experimental tests were prepared: one to measure the degradation of hydrocarbons; the other to monitor the mobility of some elements in the soil and in the leachate produced by watering with tap water. Soil samples treated with MBM and cyclodextrin showed, over time, a greater removal of the more persistent hydrocarbon fraction (lubricant oil). MBM-treated soils underwent a faster hydrocarbon removal kinetic, especially in the first treatment period. However, the final hydrocarbon concentrations are comparable in all treatments, including control. Over time, the effect of cyclodextrin on hydrocarbon degradation seemed to be relevant. MBM-treated soils sequestered lead in the very first weeks. These results highlight the intrinsic capacity of soil, and its indigenous microbial communities, to degrade petroleum hydrocarbons and suggest that MBM-induced bioremediation is a promising, environmentally friendly technology which should be considered when dealing with hydrocarbon/heavy metal co-contaminated soils.

Dataset on bio-stimulation experiments for the removal of hydrocarbons and the monitoring of certain elements in a contaminated soil

Meat and Bone Meal (MBM) and β-cyclodextrin were added to a soil sample co-contaminated by hydrocarbons (diesel fraction C₁₀-C₂₁ and lubricant oil fraction C₂₂-C₄₀) and heavy metals to promote soil remediation. The pilot study was conducted in the laboratory, maintaining optimal conditions (i.e., temperature, pH, water content, soil aeration) to facilitate hydrocarbon biodegradation. Two different experimental tests were prepared: one for the analysis of hydrocarbons in soil, the other to monitor the dynamics of some elements of interest. For the first test, the two hydrocarbon fractions in the soil were quantified separately by GC-FID, following the ISO 16703:2004(E) standard protocol. Sampling and analysis were done every two weeks, for three consecutive months. For the second test (dynamics of certain elements in the soil), soil and leachate samples were analyzed by ICP-MS after appropriate pretreatment steps.

In situ electrokinetic (EK) remediation of the total and plant available cadmium (Cd) in paddy agricultural soil using low voltage gradients at pilot and full scales

Electrokinetic (EK) remediation has been widely studied at laboratory scales. However, field-scale research is far less. In this study, a 14-day EK remediation was carried out, in a field pilot (4 m²) test and a full-scale (200 m²) application for the first time, in a cadmium (Cd) contaminated paddy agricultural field near a mining area. A low voltage of 20 V was applied at both scales; voltage gradient was 20 V m^-1 and 4 V m^-1 at the pilot and full scales, respectively. Samples were taken from near the anode and cathode, and in the middle of the electric field, in the soil layers 0-10 cm, 10-20 cm, and 40-50 cm. After the EK remediation, a significant portion of the total Cd was removed in all the layers at the pilot scale, by 87%, 72%, and 54% from the top down, but only in the 0-10 cm layer at the full scale by 74%. As for the plant available (exchangeable and soluble) Cd, significant removal (64%) was only observed in the 0-10 cm layer at the pilot scale. The percentage reduction of the electrical conductivity and removal efficiency of the total Cd was higher near the anode than the cathode. The soil pH was elevated near the cathode but stayed below pH 6 due to the sufficient supply of lactic acid. After the EK remediation, the concentration of the total Cd dropped below the hazard threshold, i.e. 0.4 mg (kg dry wt soil)^-1 for agricultural paddy fields in China. A total energy of 2 kW·h and 0.6 kW·h was consumed at the pilot and full scales, respectively. This study showed a successful in situ EK remediation of Cd contaminated paddy agricultural soil, especially in the surface layer, with low voltage and energy demand.

In situ bioremediation of Fenton's reaction-treated oil spill site, with a soil inoculum, slow release additives, and methyl-β-cyclodextrin

A residential lot impacted by spills from a leaking light heating oil tank was treated with a combination of chemical oxidation and bioremediation to avoid technically challenging excavation. The tank left emptied in the ground was used for slow infiltration of the remediation additives to the low permeability, clayey soil. First, hydrogen peroxide and citrate chelate was added for Fenton's reaction-based chemical oxidation, resulting in a ca. 50% reduction from the initial 25,000 mg/kg average oil concentration in the soil below the tank. Part of this was likely achieved through mobilization of oily soil into the tank, which was beneficial in regards to the following biological treatment. By first adding live bacteria in a soil inoculum, and then oxygen and nutrients in different forms, an approximately 90% average reduction was achieved. To further enhance the effect, methyl-β-cyclodextrin surfactant (CD) was added, resulting finally in a 98% reduction from the initial average level. The applicability of the surfactant was based on laboratory-scale tests demonstrating that CD promoted oil degradation and, unlike pine soap, was not utilized by the bacteria as a carbon source, and thus inhibiting degradation of oils regardless of the positive effect on biological activity. The effect of CD on water solubility for different hydrocarbon fractions was tested to serve as the basis for risk assessment requirements for authorizing the use of the surfactant at the site.

Simulation of Microbial Response to Accidental Diesel Spills in Basins Containing Brackish Sea Water and Sediment

The brackish Baltic Sea is under diesel oil pollution risk due to heavy ship traffic. The situation is exasperated by densely distributed marinas and a vigorous although seasonal recreational boating. The seasonality and physical environmental variations hamper the monitoring of microbial communities in response to diesel oil spills. Hence, an 8-week simulation experiment was established in metal basins (containing 265 L sea water and 18 kg quartz sand or natural shore sand as the littoral sediment) to study the effect of accidental diesel oil spills on microbial communities. Our results demonstrated that microbial communities in the surface water responded to diesel oil contamination, whereas those in the littoral sediment did not, indicating that diesel oil degradation mainly happened in the water. Diesel oil decreased the abundance of bacteria and fungi, but increased bacterial diversity in the water. Time was the predominant driver of microbial succession, attributable to the adaption strategies of microbes. Bacteria were more sensitive to diesel oil contamination than fungi and archaea. Diesel oil increased relative abundances of bacterial phyla, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Flavobacteriia and Cytophagia, and fungal phylum Ascomycota in the surface water. Overall, this study improves the understanding of the immediate ecological impact of accidental diesel oil contamination, providing insights into risk management at the coastal area.

Yard vegetation is associated with gut microbiota composition

Gut microbes play an essential role in the development and functioning of the human immune system. A disturbed gut microbiota composition is often associated with a number of health disorders including immune-mediated diseases. Differences in host characteristics such as ethnicity, living habit and diet have been used to explain differences in the gut microbiota composition in inter-continental comparison studies. As our previous studies imply that daily skin contact with organic gardening materials modify gut microflora, here we investigated the association between living environment and gut microbiota in a homogenous western population along an urban-rural gradient. We obtained stool samples from 48 native elderly Finns in province Häme in August and November 2015 and identified the bacterial phylotypes using 16S rRNA Illumina MiSeq sequencing. We assumed that yard vegetation and land cover classes surrounding homes explain the stool bacterial community in generalized linear mixed models. Diverse yard vegetation was associated with a reduced abundance of Clostridium sensu stricto and an increased abundance of Faecalibacterium and Prevotellaceae. The abundance of Bacteroides was positively and strongly associated with the built environment. Exclusion of animal owners did not alter the main associations. These results suggest that diverse vegetation around homes is associated with health-related changes in gut microbiota composition. Manipulation of the garden diversity, possibly jointly with urban planning, is a promising candidate for future intervention studies that aim to maintain gut homeostasis.

Fenton's reaction-based chemical oxidation in suboptimal conditions can lead to mobilization of oil hydrocarbons but also contribute to the total removal of volatile compounds

Fenton's reaction-based chemical oxidation is in principle a method that can be utilized for all organic fuel residues thus making it a potential all-purpose, multi-contaminant, in situ application for cases in which storage and distribution of different types of fuels have resulted in contamination of soil or groundwater. Since peroxide breakdown reactions are also expected to lead to a physical transport of the target compound, this secondary physical removal, or rebound concentrations related to it, is prone to be affected by the chemical properties of the target compound. Also, since soil conditions are seldom optimal for Fenton's reaction, the balance between chemical oxidation and transport may vary. In this study, it was found that, with a high enough hydrogen peroxide concentration (5 M), methyl tert-butyl ether-spiked groundwater could be treated even under suboptimal conditions for chemical mineralization. In these cases, volatilization was not only contributing to the total removal but also leading to rebound effects similar to those associated with air sparging techniques. Likewise for diesel, temporal transport from soil to the aqueous phase was found to lead to false positives that outweighed the actual remediation effect through chemical mineralization.

Meat and bone meal as a novel biostimulation agent in hydrocarbon contaminated soils

Soil contamination with diesel oil is frequent and methods to improve remediation of diesel oil contaminated soils are urgently needed. The aim of the current study was to assess the potential of meat and bone meal (MBM) as a biostimulation agent to enhance diesel oil degradation in contaminated soils collected from southern Finland. MBM (2% w/w) increased oil degradation in soils when compared to natural attenuation. The increase was comparable to soils treated with a traditional fertilizer (urea). Soil pH increased rapidly in urea treated soil but remained at the level of natural attenuation in MBM treated soil, suggesting that in large-scale experiments MBM treated soils avoid the usual negative impact of urea on soil pH and ultimately microbial degradation. These results indicate that MBM addition enhances diesel oil degradation, and that MBM speeds up ex situ bioremediation of oil contaminated soils.

Influence of long term nitrogen limitation on lipid, protein and pigment production of Euglena gracilis in photoheterotrophic cultures

Nitrogen limitation is considered a good strategy for enhancement of algal lipid production while conversely N repletion has been shown to result in biomass rich in proteins. In this study, the influence of long-term N limitation on Euglena gracilis fatty acid (FA), protein, chlorophyll a, and carotenoid concentrations was studied in N limited cultures. Biomass composition was analyzed from three-time points from N starved late stationary phase cultures, exposed to three different initial N concentrations in the growth medium. Total lipid content increased under N limitation in ageing cultures, but the low N content and prolonged cultivation time resulted in the formation of a high proportion of saturated FAs. Furthermore, growth as well as the production of proteins, chlorophyll a and carotenoids were enhanced in higher N concentrations and metabolism of these cellular components stayed stable during the stationary growth phase. Our findings showed that a higher N availability and a shorter cultivation time is a good strategy for efficient E. gracilis biomass production, regardless of whether the produced biomass is intended for maximal recovery of polyunsaturated FAs, proteins, or photosynthetic pigments. Additionally, we showed an increase of neoxanthin, β-carotene, and diadinoxanthin as a response to higher N availability.

Successful aerobic bioremediation of groundwater contaminated with higher chlorinated phenols by indigenous degrader bacteria

The xenobiotic priority pollutant pentachlorophenol has been used as a timber preservative in a polychlorophenol bulk synthesis product containing also tetrachlorophenol and trichlorophenol. Highly soluble chlorophenol salts have leaked into groundwater, causing severe contamination of large aquifers. Natural attenuation of higher-chlorinated phenols (HCPs: pentachlorophenol + tetrachlorophenol) at historically polluted sites has been inefficient, but a 4-year full scale in situ biostimulation of a chlorophenol-contaminated aquifer by circulation and re-infiltration of aerated groundwater was remarkably successful: pentachlorophenol decreased from 400 μg L^-1 to <1 μg L^-1 and tetrachlorophenols from 4000 μg L^-1 to <10 μg L^-1. The pcpB gene, the gene encoding pentachlorophenol hydroxylase - the first and rate-limiting enzyme in the only fully characterised aerobic HCP degradation pathway - was present in up to 10% of the indigenous bacteria already 4 months after the start of aeration. The novel quantitative PCR assay detected the pcpB gene in situ also in the chlorophenol plume of another historically polluted aquifer with no remediation history. Hotspot groundwater HCPs from this site were degraded efficiently during a 3-week microcosm incubation with one-time aeration but no other additives: from 5400 μg L^-1 to 1200 μg L^-1 and to 200 μg L^-1 in lightly and fully aerated microcosms, respectively, coupled with up to 2400% enrichment of the pcpB gene. Accumulation of lower-chlorinated metabolites was observed in neither in situ remediation nor microcosms, supporting the assumption that HCP removal was due to the aerobic degradation pathway where the first step limits the mineralisation rate. Our results demonstrate that bacteria capable of aerobic mineralisation of xenobiotic pentachlorophenol and tetrachlorophenol can be present at long-term polluted groundwater sites, making bioremediation by simple aeration a viable and economically attractive alternative.

Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials

Background

Polycyclic aromatic hydrocarbons (PAHs) accumulate in urban soils, and PAH contamination can change soil microbial community composition. Environmental microbiota is associated with human commensal microbiota, immune system and health. Therefore, studies investigating the degradation of PAHs, and the consequences of soil pollution on microbial communities in urban landscaping materials, are crucial.

Methods

Four landscaping materials (organic matter 1, 2, 13 and 56%) were contaminated with PAHs commonly found at urban sites (phenanthrene, fluoranthene, pyrene, chrysene and benzo(b)fluoranthene) in PAH concentrations that reflect urban soils in Finland (2.4 µg g ^-1 soil dry weight). PAHs were analyzed initially and after 2, 4, 8 and 12 weeks by gas chromatography-mass spectrometry. Half-lives of PAHs were determined based on 12-weeks degradation. Bacterial communities were analyzed at 1 and 12 weeks after contamination using Illumina MiSeq 16S rRNA gene metabarcoding.

Results

Half-lives ranged from 1.5 to 4.4 weeks for PAHs with relatively low molecular weights (phenanthrene, fluoranthene and pyrene) in landscaping materials containing 1–2% organic matter. In contrast, in materials containing 13% and 56% organic matter, the half-lives ranged from 2.5 to 52 weeks. Shorter half-lives of phenanthrene and fluoranthene were thus associated with low organic matter content. The half-life of pyrene was inversely related to the relative abundance of Beta-, Delta- and Gammaproteobacteria, and diversity of Bacteroidetes and Betaprotebacteria. Compounds with higher molecular weights followed compound-specific patterns. Benzo(b)fluoranthene was resistant to degradation and half-life of chrysene was shorter when the relative abundance of Betaproteobacteria was high. Temporal microbiota changes involved increase in the relative abundance of Deltaproteobacteria and decrease in genera Flavobacterium and Rhodanobacter. Exposure to PAHs seems to adjust microbial community composition, particularly within class Beta- and Deltaproteobacteria.

Conclusions

In this study, PAH degradation depended on the organic matter content and bacterial community composition of landscaping materials. Contamination seems to alter bacterial community composition in landscaping materials depending on material type. This alteration includes changes in bacterial phyla associated with human health and immune system. This may open new possibilities for managing urban environments by careful selection of landscaping materials, to benefit health and wellbeing.

Assessing toxicity of metal contaminated soil from glassworks sites with a battery of biotests

The present study addresses toxicological properties of metal contaminated soils, using glassworks sites in south-eastern Sweden as study objects. Soil from five selected glassworks sites as well as from nearby reference areas were analysed for total and water-soluble metal concentrations and general geochemical parameters. A battery of biotests was then applied to assess the toxicity of the glassworks soil environments: a test of phytotoxicity with garden cress (Lepidium sativum); the BioTox™ test for toxicity to bacteria using Vibrio fischeri; and analyses of abundancies and biomass of nematodes and enchytraeids. The glassworks- and reference areas were comparable with respect to pH and the content of organic matter and nutrients (C, N, P), but total metal concentrations (Pb, As, Ba, Cd and Zn) were significantly higher at the former sites. Higher metal concentrations in the water-soluble fraction were also observed, even though these concentrations were low compared to the total ones. Nevertheless, toxicity of the glassworks soils was not detected by the two ex situ tests; inhibition of light emission by V. fischeri could not be seen, nor was an effect seen on the growth of L. sativum. A decrease in enchytraeid and nematode abundance and biomass was, however, observed for the landfill soils as compared to reference soils, implying in situ toxicity to soil-inhabiting organisms. The confirmation of in situ bioavailability and negative effects motivates additional studies of the risk posed to humans of the glassworks villages.

Distribution of Archaeal Communities along the Coast of the Gulf of Finland and Their Response to Oil Contamination

The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the archaeal core species network plausibly revealed resilience and the potential for oil degradation. Halobacteriaceae and putative cytochrome P450 pathways were significantly enriched in the oil-contaminated littoral sediment. The archaeal taxa formed highly interconnected and interactive networks, in which Halobacteriaceae, Thermococcus, and methanogens were the main components, implying a potential relevant trophic connection between hydrocarbon degradation, methanogenesis, sulfate reduction, and/or fermentative growth.

Effect of Silene vulgaris and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil

In this study, we analysed the impact of heavy metals and plant rhizodeposition on the structure of indigenous microbial communities in rhizosphere and bulk soil that had been exposed to heavy metals for more than 150 years. Samples of the rhizosphere of Silene vulgaris and non-rhizosphere soils 250 and 450 m from the source of emission that had different metal concentrations were collected for analyses. The results showed that soils were collected 250 m from the smelter had a higher number of Cd-resistant CFU compared with the samples that were collected from 450 m, but no significant differences were observed in the number of total and oligotrophic CFU or the equivalent cell numbers between rhizosphere and non-rhizosphere soils that were taken 250 and 450 m from the emitter. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of the denaturing gradient gel electrophoresis (DGGE) profiles, as well as a cluster analysis that was generated on the phospholipid fatty acid (PLFA) profiles, showed that the bacterial community structure of rhizosphere soils depended more on the plant than on the distance and metal concentrations. The sequencing of the 16S rDNA fragments that were excised from the DGGE gel revealed representatives of the phyla Bacteroidetes, Acidobacteria, Gemmatimonadetes, Actinobacteria and Betaproteobacteria in the analysed soil with a predominance of the first three groups. The obtained results demonstrated that the presence of S. vulgaris did not affect the number of CFUs, except for those of Cd-resistant bacteria. However, the presence of S. vulgaris altered the soil bacterial community structure, regardless of the sampling site, which supported the thesis that plants have a higher impact on soil microbial community than metal contamination.

Culturing of Selenastrum on diluted composting fluids; conversion of waste to valuable algal biomass in presence of bacteria

Growth and fatty acid production of microalga Selenastrum sp. with associated bacteria was studied in lab-scale experiments in three composting leachate liquids. Nutrient reduction in cultures was measured at different initial substrate strengths. A small, pilot-scale photobioreactor (PBR) was used to verify lab-scale results. Similar growth conditions supported growth of both Selenastrum and bacteria. CO₂ feed enhanced the production of biomass and lipids in PBR (2.4gL^-1 and 17% DW) compared to lab-scale (0.1-1.6gL^-1 and 4.0-6.5% DW) experiments. Also prolonged cultivation time increased lipid content in PBR. At both scales, NH₄-N with an initial concentration of ca. 40mgL^-1 was completely removed from the biowaste leachate. In lab-scale, maximal COD reduction was over 2000mgL^-1, indicating mixotrophic growth of Selenastrum. Co-cultures are efficient in composting leachate liquid treatment, and conversion of waste to biomass is a promising approach to improve the bioeconomy of composting plants.

Treatment of municipal wastewater in full-scale on-site sand filter reduces BOD efficiently but does not reach requirements for nitrogen and phosphorus removal

A traditional sand filter for treatment of household wastewater was constructed in the fall of 2012 at Biolinja 12, Turku, Finland. Construction work was led and monitored by an authorized wastewater treatment consultant. The filter was placed on a field bordered by open ditches from all sides in order to collect excess rain and snowmelt waters. The filter was constructed and insulated from the environment so that all outflowing water was accounted for. Untreated, mainly municipal, wastewater from Varissuo suburb was pumped from a sewer separately via three septic tanks (volume = 1 m³ each) into the filters. Normally, wastewater was distributed to ground filters automatically according to pre-programmed schedule. Initially, the daily flow was 1200 L day^-1 to reflect the average organic load of a household of five persons (load: ca 237 g day^-1 BOD; 73 g day^-1 total N; and 10.4 g day^-1 total P). Later in the test, the flow rate was decreased first to 900 and then to 600 L day^-1 to better reflect the average volume produced by five persons. Volumes of inlet wastewater as well as treated water were monitored by magnetic flow meters. Samples were withdrawn from the inlet water, from the water entering the filters after the third septic tank, and from the outflowing water. After an initial adaption time, the reductions in BOD and chemical oxygen demand were constantly between 92 and 98%, showing that the biological degradation process in the filters functioned optimally and clearly comply with the national and EU standards. The reduction in total nitrogen and total phosphorus, however, reached required levels only during the first months of testing, apparently when buildup of microbial biomass was still ongoing. After this initial period of 3 months showing satisfactory reduction levels, the reduction of total nitrogen varied between 5 and 25% and total phosphorus mostly between 50 and 65%. Nitrification was efficient in the filter, but as indicated by high nitrate levels and poor nitrogen reductions, denitrification was inefficient or absent. During the winter period, the temperature in the filter dropped to near freezing, but at all time points, the flow of water was unaffected by freezing. During snowmelt and heavy rain, occasional flooding was observed. Such situations may lead to dilution rather than purification of the wastewater. In conclusion, the sand filter tested worked well for reduction of the organic load in municipal wastewater but failed to sufficiently reduce nitrogen and phosphorus levels.

Biodegration of BPA and HHCB from Waste Water by Multi-Stage Biofilm Processes

The removal of bisphenol A and 1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta[γ]2-benzopyran (HHCB), which both are widely used chemicals and known endocrine disrupters, was studied applying two biofilm processes. One of the processes was a rotating bed biofilm process (RBBR) in which waste water and small plastic pieces were rotated in cylindrical reactors by air supply. The plastic pieces served as a carrier material for biofilm as the other process, fixed bed reactor (FBR) applied wood chips. RBBR was fed with municipal waste water and FBR with artificial gray water. Preliminary results show that both experiment setups remove efficiently BOD, COD and suspended solids from waste water. BPA and HHCB were added to municipal waste water and artificial gray water to study their removal in RBBR and FBR. In RBBR, BPA removal was 10 – 29 % in the first stage and 68 – 83 % in the second stage. HHCB was removed 3 – 4 % in the first stage and 70 – 79 % in the second stage of RBBR. In FBR, the first stage removed 31 – 97 % of BPA and the second stage 80 – 100 %. 84 – 95 % and 96 – 99 % of HHCB was removed in the first and second stage, respectively. However, the percentage of removed BPA and HHCB decreased over the course of time, which refers to adsorption and saturation of BPA and HHCB to wood chips at the beginning of BPA and HHCB addition. The experiments will be continued and adaptation of microbial is expected in the latter stages of the setups. Denaturing gradient gel electrophoresis is applied to study differences in bacteria and fungi diversities in different steps of the multi-stage RBBR and FBR. In future, also 454 pyrosequencing will be applied.

Biostimulation proved to be the most efficient method in the comparison of in situ soil remediation treatments after a simulated oil spill accident

The use of in situ techniques in soil remediation is still rare in Finland and most other European countries due to the uncertainty of the effectiveness of the techniques especially in cold regions and also due to their potential side effects on the environment. In this study, we compared the biostimulation, chemical oxidation, and natural attenuation treatments in natural conditions and pilot scale during a 16-month experiment. A real fuel spill accident was used as a model for experiment setup and soil contamination. We found that biostimulation significantly decreased the contaminant leachate into the water, including also the non-aqueous phase liquid (NAPL). The total NAPL leachate was 19 % lower in the biostimulation treatment that in the untreated soil and 34 % lower in the biostimulation than oxidation treatment. Soil bacterial growth and community changes were first observed due to the increased carbon content via oil amendment and later due to the enhanced nutrient content via biostimulation. Overall, the most effective treatment for fresh contaminated soil was biostimulation, which enhanced the biodegradation of easily available oil in the mobile phase and consequently reduced contaminant leakage through the soil. The chemical oxidation did not enhance soil cleanup and resulted in the mobilization of contaminants. Our results suggest that biostimulation can decrease or even prevent oil migration in recently contaminated areas and can thus be considered as a potentially safe in situ treatment also in groundwater areas.

Rhizospheric Bacterial Strain Brevibacterium casei MH8a Colonizes Plant Tissues and Enhances Cd, Zn, Cu Phytoextraction by White Mustard

Environmental pollution by heavy metals has become a serious problem in the world. Phytoextraction, which is one of the plant-based technologies, has attracted the most attention for the bioremediation of soils polluted with these contaminants. The aim of this study was to determine whether the multiple-tolerant bacterium, Brevibacterium casei MH8a isolated from the heavy metal-contaminated rhizosphere soil of Sinapis alba L., is able to promote plant growth and enhance Cd, Zn, and Cu uptake by white mustard under laboratory conditions. Additionally, the ability of the rifampicin-resistant spontaneous mutant of MH8a to colonize plant tissues and its mechanisms of plant growth promotion were also examined. In order to assess the ecological consequences of bioaugmentation on autochthonous bacteria, the phospholipid fatty acid (PLFA) analysis was used. The MH8a strain exhibited the ability to produce ammonia, 1-amino-cyclopropane-1-carboxylic acid deaminase, indole 3-acetic acid and HCN but was not able to solubilize inorganic phosphate and produce siderophores. Introduction of MH8a into soil significantly increased S. alba biomass and the accumulation of Cd (208%), Zn (86%), and Cu (39%) in plant shoots in comparison with those grown in non-inoculated soil. Introduced into the soil, MH8a was able to enter the plant and was found in the roots and leaves of inoculated plants thus indicating its endophytic features. PLFA analysis revealed that the MH8a that was introduced into soil had a temporary influence on the structure of the autochthonous bacterial communities. The plant growth-promoting features of the MH8a strain and its ability to enhance the metal uptake by white mustard and its long-term survival in soil as well as its temporary impact on autochthonous microorganisms make the strain a suitable candidate for the promotion of plant growth and the efficiency of phytoextraction.

Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes

Over 258 Mt of solid waste are generated annually in Europe, a large fraction of which is biowaste. Sewage sludge is another major waste fraction. In this study, biowaste and sewage sludge were co-digested in an anaerobic digestion reactor (30% and 70% of total wet weight, respectively). The purpose was to investigate the biogas production and methanogenic archaeal community composition in the anaerobic digestion reactor under meso- (35-37 °C) and thermophilic (55-57 °C) processes and an increasing organic loading rate (OLR, 1-10 kg VS m(-3) d(-1)), and also to find a feasible compromise between waste treatment capacity and biogas production without causing process instability. In summary, more biogas was produced with all OLRs by the thermophilic process. Both processes showed a limited diversity of the methanogenic archaeal community which was dominated by Methanobacteriales and Methanosarcinales (e.g. Methanosarcina) in both meso- and thermophilic processes. Methanothermobacter was detected as an additional dominant genus in the thermophilic process. In addition to operating temperatures, the OLRs, the acetate concentration, and the presence of key substrates like propionate also affected the methanogenic archaeal community composition. A bacterial cell count 6.25 times higher than archaeal cell count was observed throughout the thermophilic process, while the cell count ratio varied between 0.2 and 8.5 in the mesophilic process. This suggests that the thermophilic process is more stable, but also that the relative abundance between bacteria and archaea can vary without seriously affecting biogas production.

Effect of temperature on the reductive dechlorination of 1,2,3,4-tetrachlorodibenzofuran in anaerobic PCDD/F-contaminated sediments

The effect of temperature on the reductive dechlorination in sediments of the PCDD/F-contaminated Kymijoki River, Finland was assessed with 1,2,3,4-tetrachlorodibenzofuran (1,2,3,4-TeCDF) at various temperatures and with co-amendment of 2,3,4,6-tetrachlorophenol (2,3,4,6-TeCP) in laboratory microcosms. The dechlorination rate of 1,2,3,4-TeCDF increased with incubation temperature, with TeCDF half-lives of 2.1 y at 21°C, 3.9 y at 15°C, and 19.0 y at 4°C. Co-amendment with 2,3,4,6-TeCP reduced the TeCDF half-life to 1.8 y at 21°C. 1,2,3,4-TeCDF was dechlorinated mainly in the lateral position to 1,3,4-TrCDF and then to 1,3-DiCDF over 29 months, but incubation temperature affected the relative molar ratios of the dechlorination products. The abundance of the Dehalococcoides-like Chloroflexi community did not substantially change in microcosms over 24 months incubation at the different temperatures. The dechlorination activity of 1,2,3,4-TeCDF was significantly limited at lower temperatures, which should be considered in predicting the environmental fate of aged PCDD/Fs in sediments of the Kymijoki River.

Changes in TcpA gene frequency explain 2,4,6-trichlorophenol degradation in mesocosms

Soils are often polluted by chlorophenols in timber production areas in the northern hemisphere. The tcpA gene encodes the first step of 2,4,6-trichlorophenol (246-TCP) degradation. We tested tcpA gene frequency in three natural pristine soils with different 246-TCP degradation capacity. Gene tcpA frequency increased more in spiked than non-spiked 10-L pails containing coniferous humus soil with high degradation capacity, in contrast to soils where degradation was slower. As the soil in each mesocosm originated from a spatially separate field plot, changes in tcpA gene frequency affected 246-TCP degradation over a range of soil origins. This indicates that the abundance of and changes in tcpA gene frequency could be utilized in estimating the efficacy of natural attenuation and biostimulation treatments in controlled conditions.

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.

Effects of pH and microbial composition on odour in food waste composting

A major problem for composting plants is odour emission. Slow decomposition during prolonged low-pH conditions is a frequent process problem in food waste composting. The aim was to investigate correlations between low pH, odour and microbial composition during food waste composting. Samples from laboratory composting experiments and two large scale composting plants were analysed for odour by olfactometry, as well as physico-chemical and microbial composition. There was large variation in odour, and samples clustered in two groups, one with low odour and high pH (above 6.5), the other with high odour and low pH (below 6.0). The low-odour samples were significantly drier, had lower nitrate and TVOC concentrations and no detectable organic acids. Samples of both groups were dominated by Bacillales or Actinobacteria, organisms which are often indicative of well-functioning composting processes, but the high-odour group DNA sequences were similar to those of anaerobic or facultatively anaerobic species, not to typical thermophilic composting species. High-odour samples also contained Lactobacteria and Clostridia, known to produce odorous substances. A proposed odour reduction strategy is to rapidly overcome the low pH phase, through high initial aeration rates and the use of additives such as recycled compost.

Increasing lake water and sediment oxygen levels using slow release peroxide

The sediment and hypolimnion of many Finnish lakes suffer from anoxia due to increasing nutrient loading. The aim of this research was to develop a method for increasing the oxygen level using granulated calcium peroxide (CaO₂) as a slow oxygen releasing compound. This compound releases oxygen (O₂) in a reaction with water during 5 to 7 months. The method was tested in both laboratory and field conditions. In the field test granulated CaO₂ were then spread manually from a rowing boat over the whole surface of the test pond. The granules sink onto and into the sediment. No mixing was needed. The dissolved oxygen concentration increased significantly during a laboratory experiment with a CaO₂ amendment of 75 g m⁻² and in a pond experiment with a CaO₂ amendment of 50 g m⁻². In the pond experiment, the effect was visible for the entire 40-week experiment. In the laboratory, the abundance of aerobic bacteria increased in the sediment after CaO₂ addition, while the pond experiment gave more mixed results. The organic matter content of the sediment did not change during the experiment in the control pond, but decreased from 18% to 4% in the pond with the CaO₂ amendment. This was possibly due to enhanced microbial activity in the test pond. Although the results show improved oxygen concentrations and effects on the sediment organic matter following CaO₂ amendment, the usability of this method in larger lakes remains to be tested.

Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation

BACKGROUND

Microbial anaerobic digestion (AD) is used as a waste treatment process to degrade complex organic compounds into methane. The archaeal and bacterial taxa involved in AD are well known, whereas composition of the fungal community in the process has been less studied. The present study aimed to reveal the composition of archaeal, bacterial and fungal communities in response to increasing organic loading in mesophilic and thermophilic AD processes by applying 454 amplicon sequencing technology. Furthermore, a DNA microarray method was evaluated in order to develop a tool for monitoring the microbiological status of AD.

RESULTS

The 454 sequencing showed that the diversity and number of bacterial taxa decreased with increasing organic load, while archaeal i.e. methanogenic taxa remained more constant. The number and diversity of fungal taxa increased during the process and varied less in composition with process temperature than bacterial and archaeal taxa, even though the fungal diversity increased with temperature as well. Evaluation of the microarray using AD sample DNA showed correlation of signal intensities with sequence read numbers of corresponding target groups. The sensitivity of the test was found to be about 1%.

CONCLUSIONS

The fungal community survives in anoxic conditions and grows with increasing organic loading, suggesting that Fungi may contribute to the digestion by metabolising organic nutrients for bacterial and methanogenic groups. The microarray proof of principle tests suggest that the method has the potential for semiquantitative detection of target microbial groups given that comprehensive sequence data is available for probe design.

Biogasification of biowaste and sewage sludge--measurement of biogas quality

Biogas quality, the presence of some trace components (siloxanes, sulfur compounds, volatile organic compounds, VOCs) in biogas, is in a decisive role when determining the biogas utilization and the purification requirements and equipments. In the present work, the effects of process changes related to reactor loading variations on the concentrations of selected trace compounds in biogas were studied. Source separated biowaste and sewage sludge were co-digested in a mesophilic pilot reactor (200 L) for four months during which the organic load was stepwise increased. The results showed that the process worked steadily up to the load of 8 kgVS m(-3)d(-1). Also the community composition of methanogenic archae stayed largely unaffected by the load increase, and was at all stages typical for a mesophilic biogasification process. Gaseous concentrations of siloxanes, hydrogen sulfide and most VOCs remained at a constant low level, showing no sensitivity to variations in the load and related process changes. However, the total siloxane concentration in the biogas was dependent on feed quality, and the detected concentrations require removal prior to use in turbines or fuel cells. Otherwise, after the removal of siloxanes, the biogas studied in this work is well applicable in various electricity production options, like in gas engines, turbines, microturbines and fuel cells.

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.

Evolution of clostridia and streptomycetes in full-scale composting facilities and pilot drums equipped with on-line temperature monitoring and aeration

The evolution of sporulating bacteria in full-scale composting facilities with online temperature monitoring has been poorly studied, although organic matter recycling increases. We analysed Clostridium perfringens and sulphite-reducing clostridia (SRC) by cultivation, and streptomycetes by real-time PCR in five full-scale, temperature-monitored and aerated composting processes, and two pilot-scale drum composters. Facilities composted woodchips, sawdust, peat, or bark amended sludge or source-separated biowaste. Streptomycetes genes of 0.21-110×10(7)copies/g feed increased fast to 0.019-33×10(9)copies/g, and then were equal or decreased. SRC of 0.06-2.2×10(7)cfu/g feed decreased to 0-600 cfu/g, with re-growth in two facilities. End products were clean of C. perfringens, detected in sludge composts. Although processes contained large quantities of spore-forming bacteria, in the best facilities end products had the high quality. Temperature (>55°C,>2d) was not related to the end compost quality, but relations between waste and bulking agent qualities, aeration, and processing time should be better controlled.

Wood ash for application in municipal biowaste composting

This study aimed to clarify the impacts of pH control by wood ash amendment on biowaste composting processes. To achieve this, fresh source separated municipal biowaste was mixed with low doses (2-8% wt/vol) of wood ash and processed in a pilot and large-scale composting systems. The results indicated a correlation between a low initial pH and delay in the early rise of the process temperature. Wood ash elevated the composting temperatures and pH, and stimulated the mineralisation both in the pilot scale and the industrial large-scale processes. According to the results addition of amounts of 4-8% wood ash is sufficient for efficient biowaste composting process and yields a safe end product. However, to minimise the environmental risk for heavy metal contamination, and meet the criteria for the limit values of the impurities in wood ash, strict quality control of the applied wood ashes should be implemented.

Functional mapping of harpin HrpZ of Pseudomonas syringae reveals the sites responsible for protein oligomerization, lipid interactions and plant defence induction

Harpin HrpZ is one of the most abundant proteins secreted through the pathogenesis-associated type III secretion system of the plant pathogen Pseudomonas syringae. HrpZ shows membrane-binding and pore-forming activities in vitro, suggesting that it could be targeted to the host cell plasma membrane. We studied the native molecular forms of HrpZ and found that it forms dimers and higher order oligomers. Lipid binding by HrpZ was tested with 15 different membrane lipids, with HrpZ interacting only with phosphatidic acid. Pore formation by HrpZ in artificial lipid vesicles was found to be dependent on the presence of phosphatidic acid. In addition, HrpZ was able to form pores in vesicles prepared from Arabidopsis thaliana plasma membrane, providing evidence for the suggested target of HrpZ in the host. To map the functions associated with HrpZ, we constructed a comprehensive series of deletions in the hrpZ gene derived from P. syringae pv. phaseolicola, and studied the mutant proteins. We found that oligomerization is mainly mediated by a region near the C-terminus of the protein, and that the same region is also essential for membrane pore formation. Phosphatidic acid binding seems to be mediated by two regions separate in the primary structure. Tobacco, a nonhost plant, recognizes, as a defence elicitor, a 24-amino-acid HrpZ fragment which resides in the region indispensable for the oligomerization and pore formation functions of HrpZ.

Characterisation of source-separated household waste intended for composting

Large-scale composting of source-separated household waste has expanded in recent years in the Nordic countries. One problem can be low pH at the start of the process. Incoming biowaste at four composting plants was characterised chemically, physically and microbiologically. The pH of food waste ranged from 4.7 to 6.1 and organic acid concentration from 24 to 81 mmol kg(-1). The bacterial diversity in the waste samples was high, with all samples dominated by Gammaproteobacteria, particularly Pseudomonas and Enterobacteria (Escherichia coli, Klebsiella, Enterobacter). Lactic acid bacteria were also numerically important and are known to negatively affect the composting process because the lactic acid they produce lowers the pH, inhibiting other bacteria. The bacterial groups needed for efficient composting, i.e. Bacillales and Actinobacteria, were present in appreciable amounts. The results indicated that start-up problems in the composting process can be prevented by recycling bulk material and compost.

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.

Effect of light Sphagnum peat on odour formation in the early stages of biowaste composting

In the present study, we investigated the effects of two bulking materials, Sphagnum peat and pine wood chips, on the early stages of biowaste composting in two pilot-scale processes. Emphasis was placed on studying the formation conditions of malodorous compost gases in the initial phases of the processes. The results showed that gas emission leaving an open windrow and a closed drum composting system contained elevated concentrations of fermentative microbial metabolites when acid Sphagnum peat (pH 3.2) was used as a bulking material. Moreover, the gas emission of the peat amended drum composter contained a high concentration of odour (up to 450,000oum(-3) of air). The highest odour values in the outlet gas of peat amended composts coincided with the elevated concentrations of volatile organic compounds such as acetoin and buthanedion. We conclude that the acidifying qualities of composting substrates or bulking material may intensify odour emission from biowaste composts and prolong the early stages of the composting process.

Bacterial diversity at different stages of the composting process

BACKGROUND

Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA.

RESULTS

Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts.

CONCLUSIONS

Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.

Bacterial diversity at different stages of the composting process

Background

Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA.

Results

Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts.

Conclusions

Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.

Reduction of odorants in swine manure by carbohydrate and bacterial amendments

Malodors from pig manure storage pits are a problem lacking a cost-efficient solution particularly for small pig (Sus domestica) farms. The objective of this study was to reduce emissions of noxious odorants by changing the conditions in the pig manure to favor an altered microbial community. Sugars (maltose, lactose, and saccharose), carbohydrate-rich waste (maltose syrup and wheat flour), and bacterial amendments (Lactobacillus plantarum and L. amylophilus) were tested for their effect on manure pH, bacterial community, and gaseous emissions. In laboratory experiments, a permanent pH reduction was achieved with all carbohydrates when added to a 5% final concentration. Maltose significantly decreased emissions of sulfur-containing compounds, whereas bacterial amendments had little effect on odorants. Lactobacilli were found in manure receiving carbohydrate amendments alone, but Clostridiales, Bacteroidetes, and Enterobacteriaceae were observed in all treatments (including the control). At the mesocosm (60 L) level, maltose syrup and wheat flour amendments caused clear pH reductions in manure, whereas L. plantarum and L. amylophilus had no additional effect. The addition of maltose syrup and wheat flour to a manure storage pit (600 m(3)) lowered the pH slightly. When the manure was spread onto the fields, the observed reduction in odor was found to be reversible, and the release of malodors was delayed rather than eliminated. We conclude that these methods require further development to produce a reliable technical application.

Universal ligation-detection-reaction microarray applied for compost microbes

BACKGROUND

Composting is one of the methods utilised in recycling organic communal waste. The composting process is dependent on aerobic microbial activity and proceeds through a succession of different phases each dominated by certain microorganisms. In this study, a ligation-detection-reaction (LDR) based microarray method was adapted for species-level detection of compost microbes characteristic of each stage of the composting process. LDR utilises the specificity of the ligase enzyme to covalently join two adjacently hybridised probes. A zip-oligo is attached to the 3'-end of one probe and fluorescent label to the 5'-end of the other probe. Upon ligation, the probes are combined in the same molecule and can be detected in a specific location on a universal microarray with complementary zip-oligos enabling equivalent hybridisation conditions for all probes. The method was applied to samples from Nordic composting facilities after testing and optimisation with fungal pure cultures and environmental clones.

RESULTS

Probes targeted for fungi were able to detect 0.1 fmol of target ribosomal PCR product in an artificial reaction mixture containing 100 ng competing fungal ribosomal internal transcribed spacer (ITS) area or herring sperm DNA. The detection level was therefore approximately 0.04% of total DNA. Clone libraries were constructed from eight compost samples. The LDR microarray results were in concordance with the clone library sequencing results. In addition a control probe was used to monitor the per-spot hybridisation efficiency on the array.

CONCLUSION

This study demonstrates that the LDR microarray method is capable of sensitive and accurate species-level detection from a complex microbial community. The method can detect key species from compost samples, making it a basis for a tool for compost process monitoring in industrial facilities.

Atrazine and terbutryn degradation in deposits from groundwater environment within the boreal region in Lahti, Finland

The degradation of pesticides atrazine and terbutryn was investigated under aerobic and anaerobic conditions in the northern boreal region subsurface deposits and sterilized controls from the depths of 6.3-21.0 m below the surface and 1.2-16.9 m below the groundwater table. During 1.3-1.7 years of laboratory incubation, atrazine degradation under aerobic conditions varied from rapid (half-live 38 days) to no degradation. Anaerobically, atrazine half-lives were 430-829 days. Organic matter, nitrogen, and lead in deposits correlated positively with the atrazine concentration in groundwater. Aerobic and anaerobic terbutryn half-lives were 193-644 and 266-400 days, respectively. Microbial aerobic atrazine and terbutryn degradation was confirmed in the deep deposits near the water table. Under aerobic conditions, the high amounts of Cr, Mn, Ni, and Zn in deposits decreased the chemical degradation of terbutryn.

Effects of differing temperature management on development of Actinobacteria populations during composting

Actinobacteria are believed to play a major role in organic matter degradation and humification processes in composts. In this study, the effects of different temperature regimes on the succession of Actinobacteria populations during composting were investigated in a laboratory reactor. Phospholipid fatty acid (PLFA) was used to investigate quantitative changes in the overall microbial biomass and community structure, and in the size of Actinobacteria populations. Qualitative changes were determined using PCR-DGGE (denaturing gradient gel electrophoresis) and sequencing of 16S rRNA genes with Actinobacteria-specific primers. The peak in total microbial biomass was roughly twice as high and delayed in trials where the maximum temperature was 40 degrees C, compared to those where it was 55 or 67 degrees C. There was a shift from members of Corynebacterium, Rhodococcus and Streptomyces at the onset to species of thermotolerant Actinobacteria in the cooling phase, e.g. Saccharomonospora viridis, Thermobifida fusca and Thermobispora bispora. In conclusion, temperature was an important selective factor for the development of Actinobacteria populations in composts, and they constituted a substantial part of the community in the later compost stages.