Jukka Kurola

University of Helsinki, Helsinki, Uusimaa, Finland

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Publications (19)40.55 Total impact

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    ABSTRACT: The present study aimed to investigate microbial communities in seven Indian composts and their potential for biocontrol of Fusarium oxysporum f. sp. lycopersici. In addition, identification of bioactive substances in disease suppressive composts was also attempted. Composts were chosen based on disease suppressiveness and subjected to molecular microbial analyses. Total genomic DNA from the composts was extracted and amplified with polymerase chain reaction using primers targeting the 18S rRNA and 16S rRNA genes of fungi and bacteria, respectively. Denaturing gradient gel electrophoresis (DGGE) fingerprinting and DNA sequencing were used to identify the fungal and bacterial targets. Phylogenetic analysis of the fungal 18S rRNA ITS gene sequences showed that phylum Ascomycota was dominant in all composts, while in the bacterial 16S rRNA gene sequences, the phylum Proteobacteria was dominant. Some fungi in disease suppressive composts grouped phylogenetically close to F. oxysporum. Bacterial sequences with close similarity (>95% identity) with Actinobacterium showed a strong presence only in disease suppressive composts. Disease suppressive composts formed a separate group in the cluster analysis of 18S rRNA ITS and 16S rRNA gene sequences. Gas chromatography-time of flight-mass spectrometry was performed with compost extracts to determine if bioactive substances were present in disease suppressive composts. The analysis of compost organic matter showed a negative association of disease suppressiveness with phloroglucinol, sitosterol, and monoenoic fatty acid, while cholesterol and certain organic acids were positively associated with suppressiveness.
    No preview · Article · Apr 2016 · Compost science & utilization
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    ABSTRACT: The use of compost of varied origins for the management of plant disease has been reported all over the world for decades, and microorganisms are suggested to be one of the driving forces. In this study, composts produced during two successive years were mixed with peat at 1:4 v/v ratios, and screened for cucumber Pythium disease suppression in two experiments in 2009. Nine composts were selected based on their suppressive effects against Pythium on cucumber plants, and thereafter were subjected to molecular analyses. The aim of this study was to compare the bacterial and fungal communities present in strongly-suppressive and non- or weakly-suppressive composts, in an effort to identify bacterial and fungal groups associated with Pythium disease suppression. The total genomic DNA from the composts was extracted and amplified using primers targeting 16S rRNA and ITS rRNA genes of bacteria and fungi, respectively, prior to 454 sequencing. Sequencing results indicated the potential roles of bacterial Acidobacteria Gp14 and fungal Cystobasidiomycetes in the suppression of Pythium wilt disease, due to their presence and absence in composts with strong and lower/absent disease suppression ability, respectively. The abundance of Actinobacteria was associated positively with suppressiveness. Phosphorus concentration was the only abiotic factor that was associated with suppressiveness: a negative correlation was found in both experiments. These results indicate that certain bacterial and fungal groups can potentially suppress Pythium wilt while the abiotic conditions might be less important.
    Full-text · Article · Aug 2015 · Applied Soil Ecology
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    ABSTRACT: 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.
    Full-text · Article · May 2014 · Journal of Environmental Management
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    ABSTRACT: Cells are the basic functional units in forest ecosystems. Plants have strong cell wall, formed by cellulose and lignin. Cell membrane isolates the cell from its surroundings, starch acts as storage and enzymes enable synthesis of new compounds. Membrane pumps allow penetration of cell membrane and pigments capture of light energy. We call enzymes, membrane pumps and pigments as functional substances. The biochemical regulation system changes the concentrations and activities of the functional substances: In summer, metabolism is very active, but in winter, vegetation is dormant and tolerates low temperatures. The action of the biochemical regulation system generates emergent regularities in the functional substances, called the state of the functional substances. The effect of environmental factors on metabolism is built in the complex chain of enzymes, membrane pumps and pigments, acting in each metabolic task. The process-specific state of functional substances and the environmental factors determine the rate of each metabolic process. Microbes have dominating role in the soil. Together with soil fauna, microbes break down macromolecules with extracellular enzymes to small molecules that can penetrate the microbial cell membrane through membrane pumps. The microbial metabolism utilises the small carbon-rich molecules for the energy needs, growth and synthesis of the extracellular enzymes.
    No preview · Chapter · Jan 2013
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    ABSTRACT: Figure of rarefaction curves of Archaea, Bacteria and Fungi in samples M1-M4. (675 KB, PDF) (PDF 674 kb)
    Preview · Dataset · Jun 2012
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    ABSTRACT: Microarray signals of sensitivity tests. Figures showing microarray signals of different concentrations of synthetic template oligos. (47 KB, PDF) (PDF 47 kb)
    Preview · Dataset · Jun 2012
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    ABSTRACT: Sequences of templates used in microarray specificity tests. (40 KB, XLS) (XLS 39 kb)
    Preview · Dataset · Jun 2012
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    ABSTRACT: Example of microarray signals of mismatching probes. Figures showing comparison of microarray signals and sequencing read numbers of two probes aligning with mismatches to groups present in samples M1-M4. (32 KB, PDF) (PDF 32 kb)
    Preview · Dataset · Jun 2012
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    ABSTRACT: 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. 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%. 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.
    Full-text · Article · Jun 2012 · BMC Microbiology
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    ABSTRACT: Microarray signals of specificity tests. Boxplots of signals of each probe in response to artificial target template pools and alignment scores to sequences in the target pool. (273 KB, PDF) (PDF 273 kb)
    Preview · Dataset · Jun 2012
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    ABSTRACT: Sequences of ligation probes. Table containing the probe sequences and target Genbank accession numbers. (39 KB, XLS) (XLS 39 kb)
    Preview · Dataset · Jun 2012
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    ABSTRACT: The aim of the study was to gain a more detailed view of the changes in microbial community structure in boreal forest soil due to lead contamination. The Hälvälä shooting range in southern Finland is heavily polluted by lead. The humus soil microbial community was examined using DNA based methods. To examine the bacterial community a 400 bp section of the 16S rRNA gene was amplified, cloned, and sequenced. For fungi, the internal transcribed spacer (ITS) area was examined. The 917 bacterial sequences grouped into 398 operational taxonomic units (OTUs) at ≥ 97% similarity, while 649 fungal sequences grouped into 155 OTUs at ≥ 99% similarity. No effect of lead was found on bacterial richness or diversity, while fungal richness and diversity were significantly altered. Some OTUs assigned to Basidiomycota were much rarer in the lead contaminated areas while the genus Thelephora was enriched in the lead contaminated soil. This difference between bacterial and fungal responses to lead suggests a difference in the strategy to avoid the contaminant. The analyses performed here do not, however, allow for conclusions regarding mechanisms.
    No preview · Article · Feb 2012 · Boreal Environment Research
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    ABSTRACT: Compost can be considered as a soil conditioner that contributes to soil fertility, structure, porosity, organic matter, water holding capacity, and suppression of soil borne disease in plants. Disease suppression by composts is a fairly recently established alternative use of composts. The interest in suppressive composts has increased due to concern over pesticide use, increasing pesticide resistance, and lack of chemical control against disease or disease resistant plant cultivars. We have carried out a study, the aim of which was to search for disease suppressiveness properties of commercial composts produced in Finland. Twentyone mature composts were screened for their ability to decrease strawberry crown rot caused by Phytophthora cactorum and cucumber wilt disease caused by Pythium sp. The compost raw materials used included municipal sewage sludge, biowaste, cattle, horse or poultry manure, various kinds of garden wastes, and sludge from the paper mill industry. The majority of composts seemed not to affect strawberry crown rot or cucumber wilt disease, but seven composts had distinct suppressiveness capacities in both experiments. Three composts were in common for both experiments. One compost was conducive to disease in both experiments, but it was not the same one in both cases. The results indicated that closed composting systems in tunnels or drums induced suppressiveness better than composting in windrows. Preliminary observations also indicated that suppressiveness capacities were found more commonly in biowaste composts than in composts made from manure. Further studies with several plant pathogens are needed in order to get a more comprehensive picture of the potential use of composts for controlling soil borne plant diseases. Studies on underlying suppressiveness mechanisms, including microbial profiles of suppressive and non-suppressive composts, also need to be carried out.
    No preview · Article · Mar 2011 · Acta horticulturae
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    ABSTRACT: 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.
    No preview · Article · Feb 2011 · Journal of Environmental Management
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    ABSTRACT: 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.
    No preview · Article · Feb 2011 · Bioresource Technology
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    ABSTRACT: 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.
    No preview · Article · May 2010 · Waste Management
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    ABSTRACT: Composting is an aerobic biological process in which solid organic matter is degraded by microorganisms. The microbiology of composting has been of interest for decades, and microbes in composting have been characterized in many types of composing processes using traditional culture-based methods. In recent years, an immense diversity of bacteria, archaea, and fungi has been found to occupy many different habitats using culture-independent molecular biological methods. Molecular methods which can detect both the culturable and non-culturable fractions of the microbial community are under constant development. In this chapter, several new molecular tools for characterising the microbes present in different composting processes are described, and the advantages and limitations of the application of these methods in studying composting microbiology are discussed.
    No preview · Chapter · Jan 2010
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    ABSTRACT: 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. 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. 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. 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.
    Full-text · Article · Jul 2009 · Journal of Applied Microbiology
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    ABSTRACT: The tendency in the paper industry is to close all water loops to save water. This leads to higher process temperatures and may increase the colloidal and dissolved material in the process circulation. Increase of nutrients in the water circuits may favor microbiological growth and fouling. In this paper the chemical and microbial compositions of water circuits and deposits were studied of two closed cycled paper/board mills, one mill totally closed (0 m(3) waste water t(-1)), and the other low discharging (about 4 m(3 )t(-1)). The zero discharge mill accumulated high amounts (>10 g C L(-1)) of organic carbon in the circulation waters, about 40% of which composed of volatile acids (lactic, acetic, propionic and butyric acid). Water contents of sulfate, chloride, sodium and calcium increased to >1 g L(-1) of each. q-PCR targeted on 16S rRNA genes indicated that the bacteria in water circuits were mainly viable cells. In both mills anaerobic growth (10(6)-10(8) CFU mL(-1)) equalled or exceeded aerobic growth, with odor problem but no actual slime problem. The major part (40%) of all identifiable bacterial sequences were closest but yet distant (<96%) to Enterococcus cecorum and in the 4 m(3 )t(-1) discharging mill also Bacillus thermoamylovorans and Bacillus coagulans. Slimes and deposits from the mills contained high amounts, > or =10(8) g(-1), of archaean, but only the genus Methanothrix was identifiable from the cloned sequences. The findings indicate that closing the water circuits strongly limited diversity of the microbiota but allowed efficient mineralization of the dissolved and suspended matter.
    No preview · Article · Oct 2008 · Journal of Industrial Microbiology and Biotechnology
  • Jukka Kurola · Mirja Salkinoja-Salonen
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    ABSTRACT: The effect of temperatures of −2.5 to +20 °C on the biodegradation of concentrations 0.2–50 μg cm−3 of pentachlorophenol (PCP), phenanthrene, pyrene and 2,4,5-trichlorophenol (TCP) was studied in soils sampled from an agricultural field and a relatively pristine forest in Helsinki, Finland. At the temperatures simulating seasonal variation of boreal soil temperatures [Heikinheimo, M., Fougstedt, B., 1992. Statistic of Soil Temperature in Finland. Meteorological Publications 22. Finnish Meteorological Institute, Helsinki, Finland], the response of mineralization of PCP, phenanthrene and 2,4,5-TCP was the most effective in the rhizosphere fraction of the forest humus soil at the substrate concentrations of ⩽5 μg cm−3. In the control incubation, performed at constant temperature of +20 °C, the mineralization yields of the model pollutants were highest in the agricultural soil with the highest applied substrate concentration (50 μg cm−3). The results suggest that the high level of pollutant mineralization at +20 °C resulted from the apparent adaptation of the soil microbial community to the high substrate concentration. No such adaptation occurred when the soils were incubated at temperatures simulating the actual boreal soil temperatures. The present results stress the role of adjusting the incubation conditions to environmentally relevant values, when assessing biodegradation of anthropogenic organic compound in boreal soils.
    No preview · Article · May 2007 · Soil Biology and Biochemistry