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.

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.

Determination of fungal succession during municipal solid waste composting using a cloning-based analysis.

AIMS: The microbiota at industrial full-scale composting plants has earlier been fragmentarily studied with molecular methods. Here, fungal communities from different stages of a full-scale and a pilot-scale composting reactors were studied before and after wood ash amendment. METHODS AND RESULT: The portion of fungal biomass, determined using phospholipid fatty acid analysis, varied between 6.3% and 38.5% in different composting phases. The fungal internal transcribed spacer (ITS) area was cloned and sequenced from 19 samples representing different stages of the composting processes. Altogether 2986 sequenced clones were grouped into 166 phylotypes from which 35% had a close match in the sequence databases. The fungal communities of the samples were related with the measured environmental variables in order to identify phylotypes typical of certain composting conditions. The fungal phylotypes could be grouped into those that dominated the mesophilic low pH initial phases (sequences similar to genera Candida, Pichia and Dipodascaceae) and those found mostly or exclusively in the thermophilic phase (sequences clustering to Thermomyces, Candida and Rhizomucor), but a few were also present throughout the whole process. CONCLUSIONS: The community composition was found to vary between suboptimally and optimally operating processes. In addition, there were differences in fungal communities between processes of industrial and pilot scale. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study reveal the fungal diversity with molecular methods in industrial composting process. This is also one of the first studies conducted with samples from an industrial biowaste composting process.

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.

Immunocytochemical localization of HrpA and HrpZ supports a role for the Hrp pilus in the transfer of effector proteins from Pseudomonas syringae pv. tomato across the host plant cell wall.

The Hrp pilus, composed of HrpA subunits, is an essential component of the type III secretion system in Pseudomonas syringae. We used electron microscopy (EM) and immunocytochemistry to examine production of the pilus in vitro from P. syringae pv. tomato strain DC3000 grown under hrp-inducing conditions on EM grids. Pili, when labeled with antibodies to HrpA, developed rapidly in a nonpolar manner shortly after the detection of the hrpA transcript and extended up to 5 microm into surrounding media. Structures at the base of the pilus were clearly differentiated from the basal bodies of flagella. The HrpZ protein, also secreted via the type III system, was found by immunogold labeling to be associated with the pilus in vitro. Accumulation and secretion of HrpA and HrpZ were also examined quantitatively after the inoculation of wild-type DC3000 and hrpA and hrpZ mutants into leaves of Arabidopsis thaliana. The functional pilus crossed the plant cell wall to generate tracks of immunogold labeling for HrpA and HrpZ. Mutants that produced HrpA but did not assemble pili were nonpathogenic, did not secrete HrpA protein, and were compromised for the accumulation of HrpZ. A model is proposed in which the rapidly elongating Hrp pilus acts as a moving conveyor, facilitating transfer of effector proteins from bacteria to the plant cytoplasm across the formidable barrier of the plant cell wall.

Type III secretion contributes to the pathogenesis of the soft-rot pathogen Erwinia carotovora: partial characterization of the hrp gene cluster.

The virulence of soft-rot Erwinia species is dependent mainly upon secreted enzymes such as pectinases, pectin lyases, and proteases that cause maceration of plant tissue. Some soft-rot Erwinia spp. also harbor genes homologous to the hypersensitive reaction and pathogenesis (hrp) gene cluster, encoding components of the type III secretion system. The hrp genes are essential virulence determinants for numerous nonmacerating gram-negative plant pathogens but their role in the virulence of soft-rot Erwinia spp. is not clear. We isolated and characterized 11 hrp genes of Erwinia carotovora subsp. carotovora. Three putative sigmaL-dependent Hrp box promoter sequences were found. The genes were expressed when the bacteria were grown in Hrp-inducing medium. The operon structure of the hrp genes was determined by mRNA hybridization, and the results were in accordance with the location of the Hrp boxes. An E. carotovora strain with mutated hrcC, an essential hrp gene, was constructed. The hrcC- strain was able to multiply and cause disease in Arabidopsis, but the population kinetics were altered so that growth was delayed during the early stages of infection.

Characterization of type IV pilus genes in Pseudomonas syringae pv. tomato DC3000.

Many strains of Pseudomonas syringae produce retractile pili that act as receptors for lytic bacteriophage phi 6. As these are also characteristics of type IV pili, it was postulated that P. syringae may possess genes for type IV pilus biogenesis. A cosmid clone bank of P. syringae pv. tomato DC3000 genomic DNA was used to complement a mutant of Pseudomonas aeruginosa defective in the PilD (XcpA) prepilin peptidase gene by selection for restoration of extracellular protein secretion, a function also known to require PilD. A cosmid able to complement this mutant was also able to complement mutations in the pilB and pilC genes, suggesting that, if the organization of these genes is similar to that of P. aeruginosa, the cosmid may contain the P. syringae pilA. This was confirmed by sequencing a region from this plasmid that was shown to hybridize at low stringency to the P. aeruginosa pilA gene. The deduced P. syringae PilA polypeptide possesses the characteristic properties of the type IV pilins. Heterologous expression of the P. syringae pilA in P. aeruginosa was also shown, conferring not only phi 6 phage sensitivity to P. aeruginosa pilA mutants but also sensitivity to PO4, a lytic bacteriophage specific for the pilus of P. aeruginosa. This suggests that additional components might be present in the mature pilus of P. aeruginosa that are the true receptors for this phage. Chromosomal mutations in P. syringae pv. tomato DC3000 pilA and pilD genes were shown to abolish its sensitivity to bacteriophage phi 6. To determine the importance of P. syringae pilus in plant leaf interactions, these mutations were tested under laboratory and field conditions. Although little effect was seen on pathogenicity, culturable leaf-associated population sizes of the pilA mutant were significantly different from those of the wild-type parent. In addition, the expression of the DC3000 pilA gene appears to contribute to the UV tolerance of P. syringae and may play a role in survival on the plant leaf surface.

Cloning of cmpE, a plasmid-borne catechol 2,3-dioxygenase-encoding gene from the aromatic- and chloroaromatic-degrading Pseudomonas sp. HV3.

Pseudomonas sp. strain HV3 degrades aromatics and chloroaromatics. It harbours a mega-plasmid, designated pSKY4, from which the gene cmpE, encoding a catechol 2,3-dioxygenase (C23O) catalyzing the conversion of catechol to 2-hydroxymuconic semialdehyde, was cloned and sequenced. The deduced amino acid (aa) sequence shows the highest homology, 52%, to the deduced aa sequences of xylE1 and dmpB. The deduced 307-aa sequence of cmpE contains the extradiol ring-cleavage signature in the same position as other 307-aa C23O-encoding genes.

Repeated sequences isolated from Bordetella pertussis induce DNA rearrangements and deletions at high frequency.

Two repeated sequences (RS) from Bordetella pertussis were cloned in Escherichia coli and sequenced. The RS, called RSBP1 and RSBP3, are highly homologous to other B. pertussis RS. The recombinant plasmids containing RSBP1 and RSBP3 or transposon-like structures of these elements were not stable but segregated plasmids with deletions or rearranged DNA. RS of B. pertussis seem to be able to stimulate both intra- and inter-genomic RecA-independent recombination events. In at least one case, the observed deletion had occurred precisely between the RS terminus and a site with sequence homology to the terminus. The high frequency rearrangements associated with the RS imply that the RS are transposable elements.

Purified HrpA of Pseudomonas syringae pv. tomato DC3000 reassembles into pili.

Pseudomonas syringae pv. tomato DC3000 produces Hrp pili under inducing in vitro conditions. A preparation of partially purified extracellular filaments contains HrpA, flagellin and some minor contaminants. HrpA was separated from the major contaminant, the flagellin, by gel filtration to a fraction containing HrpA as well as its three N-terminally truncated forms. These were further separated by two steps of reversed phase chromatography. HrpA and its degradation products were each shown to reassemble into filament structures after denaturation and renaturation showing that HrpA alone is sufficient for formation of filament structures.

Novel organization of catechol meta-pathway genes in Sphingomonas sp. HV3 pSKY4 plasmid.

Sphingomonas sp. strain HV3 (formerly Pseudomonas sp. HV3), which degrades aromatics and chloroaromatics, harbors a mega-plasmid, pSKY4. A sequenced 4 kb fragment of the plasmid reveals a novel gene organization for catechol meta-pathway genes. The putative meta operon starts with the cmpF gene encoding a 2-hydroxymuconic semialdehyde hydrolase. The gene has a 6 bp overlap with the previously characterized ring-cleavage gene, catechol 2,3-dioxygenase, cmpE. Downstream of cmpE is a 429 bp open reading frame of unknown function. Gene cmpC, encoding a 2-hydroxymuconic semialdehyde dehydrogenase, starts 44 bp further downstream. It has the highest homology to 2-hydroxymuconic semialdehyde dehydrogenases of dmp and xyl pathways and to XylC from the marine oligotroph Cycloclasticus oligotrophus. The gene organization is different from other known meta pathways. This is the first report of organization of plasmid-encoded meta-pathway genes in the genus Sphingomonas.

Construction and Use of Broad Host Range Mercury and Arsenite Sensor Plasmids in the Soil Bacterium Pseudomonas fluorescens OS8.

We have generated new sensors for the specific detection and studies of bioavailability of metals by engineering Pseudomonas fluorescens with reporter gene systems. One broad host range mercury (pTPT11) and two arsenite (pTPT21 and pTPT31) sensor plasmids that express metal presence by luminescence phenotype were constructed and transferred into Escherichia coli DH5a and Pseudomonas fluorescens OS8. The maximal induction was reached after 2 h of incubation in metal solutions at room temperature (22 degrees C). In optimized conditions the half maximal velocity of reaction was achieved at acidic pH using a d-luciferin substrate concentration that was nearly sixfold lower for P. fluorescens OS8 than for E. coli DH5a. When using a luciferin concentration (150 mM) that was optimal for E. coli the luminescence declined rapidly in the case of Pseudomonas, for which the substrate level 25 mM gave a stable reading between about 20 min and 3 h. The ability of the strain OS8 to quantitatively detect specific heavy metals in spiked soil and soil extracts is as good, or even better in being a real-time reporter system, than that of a traditional chemical analysis. The Pseudomonas strain used is an isolate from pine rhizosphere in oil and heavy metal contaminated soil. It is also a good humus soil colonizer and is therefore a good candidate for measuring soil heavy metal bioavailability.

Evaluation of the Galega-Rhizobium galegae system for the bioremediation of oil-contaminated soil.

The bioremediation potential of a nitrogen-fixing leguminous plant, Galega orientalis, and its microsymbiont Rhizobium galegae was evaluated in BTX (benzene, toluene, xylene)-contaminated soils in microcosm and mesocosm scale. To measure the intrinsic tolerance of the organisms to m-toluate, a model compound representing BTX, G. orientalis and R. galegae were cultivated under increasing concentrations of m-toluate alone and in association with Pseudomonas putida pWWO, a bacterial strain able to degrade toluene-derived compounds. The test plants and rhizobia remained viable in m-toluate concentrations as high as 3000 ppm. Plant growth was inhibited in concentrations higher than 500 ppm, but restituted when plants were transferred into m-toluate-free medium. Nodulation was blocked under the influence of m-toluate, but was restored after the plants were transferred into the non-contaminated media. In the mesocosm assay the Galega plants showed good growth, nodulation and nitrogen fixation, and developed a strong rhizosphere in soils contaminated with oil or spiked with 2000 ppm m-toluate. Thus, this legume system has good potential for use on oil-contaminated sites

Assessing sediment toxicity and arsenite concentration with bacterial and traditional methods.

Three sediment samples LP (pool where logs are stored), LF (brook through landfill area), KN (Kaskesniemi) which is in Lake Pyhäselkä downstream from the mill, were taken from an old sawmill area and one from the unpolluted Lake Höytiäinen. The arsenite concentration was measured by GFAAS and two arsenite biosensing bacterial strains Pseudomonas fluorescens OS8 (pTPT31) and Escherichia coli MC1061 (pTOO31). The toxicity of sediment and pore water samples was determined by using luminescent bacteria (Flash test) and, further, whole sediment toxicity was measured using 10 days growth test and 50 days emergency test with midges (Chironomus riparius). With the flash test a lowered EC50 value was found only in sediment LF (EC50=0.17 v/v%). The Flash test indicated that all sediment samples taken from the sawmill area were highly toxic to bacteria, whereas growth and the emergence of chironomids showed no effects in other samples than LF. The midges tolerate well the contaminated environment. In contrast, bioavailability of arsenite of sediment samples KN and LF was quite high determined using the biosensor-strains in a direct contact assay. The bioavailable fraction of sediment LP was 6-10% out of the total arsenite concentration obtained with GFAAS (0.46-0.77 microg g-1 dw). The results show that the choice of analysis method grossly affects the outcome without any of the method giving an incorrect result. Different methods measure different parameters of a toxic sample and can thus be used to complement each other.

Means to improve the effect of in situ bioremediation of contaminated soil: an overview of novel approaches.

Different aspects of bacterial degradation of organic contaminants in soil, and how to improve the efficiency and reproducibility is discussed in this review. Although bioremediation in principle includes the use of any type of organism in improving the condition of a contaminated site, most commonly bacteria are the degraders and other organisms, such as soil animals or plant roots, play a role in dissemination of bacteria and, indirectly, plasmids between bacteria, and in providing nutrients and co-substrates for the bacteria active in the degradation process. There are a number of different procedures that have been tested more-or-less successfully in attempts to improve reliability, cost efficiency and speed of bioremediation. The methods range from minimal intervention, such as mere monitoring of intrinsic bioremediation, through in situ introduction of nutrients and/or bacterial inocula or improvement of physico-chemical conditions, all the way to excavation followed by on site or ex situ composting in its different varieties. In the past the rule has been that more intervention (leading to higher costs) has been more reliable, but novel ideas are continuously tried out, both as a means to come up with new truly functional applications and also as a line of studies in basic soil microbial ecology. Both approaches generate valuable information needed when predicting outcome of remediation activities, evaluating environmental risks, deciding on cleaning-up approaches, etc. The emphasis of this review is to discuss some of the novel methods for which the value has not been clearly shown, but that in our view merit continued studies and efforts to make them work, separately or in combination.

Use of a by-product of peat excavation, cotton grass fibre, as a sorbent for oil-spills.

The sorbents used to collect oil in case of oil-spills are mostly synthetic, which limits the possibilities of their disposal. We studied the absorption capacities and rates of cotton grass fibre, a by-product of peat excavation, and cotton grass mats for several oil types and compared them with a synthetic, commercially available oil sorbent. We found cotton grass fibre to have superior absorption properties: Cotton grass sorbent absorbed oil approximately two to three times as much, and two to three times as fast as the synthetic one. Cotton grass fibre absorbed no measurable amount of water in the conditions used in the tests making it ideal for absorbing oil from the surface of water. In removing diesel oil from the surface of water, the efficiency was over 99% up to an absorbing factor of 20 times its own weight. The biodegradable cotton grass fibre proved to be an effective oil sorbent with low raw-material costs.

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.

Microbially treated peat-cellulose fabric as a biodegradable oil-collection cloth.

The aim of this work was to study the use of a fully biodegradable peat-cellulose fabric as a first aid in collecting and removing spilled oil. The fabric itself was made from entirely biodegradable natural components. Another aspect investigated was whether drying microbial suspension--specifically enriched for the degradation of oil hydrocarbons while maintaining a high survival rate and rapid initial growth--to the fabric would improve the degradation of absorbed oil along with the fabric. The results show that the oil absorption capacity of the biodegradable fabric was comparable to commercial products, and that the oil absorbed to the fabric degraded readily when incubated at various conditions. The microbial inoculum enhanced the degradation rate to some degree in sand, but in garden soil no significant difference existed. It was concluded that an oily fabric can be disposed of by biodegradation, e.g., by composting, but that a microbial inoculum is not essential for this purpose.

The causal agent of halo blight in bean, Pseudomonas syringae pv. phaseolicola, attaches to stomata via its pili.

The phytopathogenic pseudomonad Pseudomonas syringae pv. phaseolicola causes halo blight of bean (Phaseolus vulgaris L.). Initiation of infection depends on the ability of the cells to adhere to the target cell surface. P. syringae pv. phaseolicola expresses pili, which are the receptors of the lipid-containing dsRNA bacteriophage phi 6. phi 6-resistant bacterial strains can be divided into different piliation types. It was possible to show that the adhesion of the bacteria onto plant cell surface was dependent on the pili. Non-piliated bacterial stains showed a much lower adherence to the leaf surface than strains expressing phi 6 specific pili. Scanning electron microscopy showed that the piliated bacteria attached to the leaf surface at the site of stomata. Non-piliated bacteria were evenly distributed on the leaf surface. All bacterial strains used in this study were capable of causing halo blight if injected into the plant. If the bacteria were sprayed on the plants, followed by spraying of sterile buffer, only piliated bacteria caused symptoms.