[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
Microbes at Work, 01/2010: pages 135-151; , ISBN: 978-3-642-04042-9
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
Journal of Industrial Microbiology and Biotechnology 10/2008; 35(10):1165-73. DOI:10.1007/s10295-008-0396-8 · 2.51 Impact Factor
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] ABSTRACT: Chemolithotrophic ammonia-oxidising bacteria (AOB) present in oil-contaminated landfarming soil were studied over two growing seasons in 1999 and 2000. The number of AOB (4-9 x 10(5) cellsg(-1) of dry soil) determined with the quantitative polymerase chain reaction (real-time PCR) and the rate of potential ammonium oxidation (0.05-0.28 microg NO2(-)-N g(-1) of dry soil h(-1)) indicated the presence of stable AOB populations. Denaturing gradient gel electrophoresis (DGGE) profiling and sequence analysis of PCR-amplified AOB 16S rRNA genes showed dominance of Nitrosospira-like sequences in clusters 2 and 3. The present results from the chronically oil-contaminated landfarming soil support the suggested importance of Nitrosospira-like AOB in terrestrial environments.
[Show abstract][Hide abstract] ABSTRACT: A new approach, in which ammonia-oxidizing bacteria (AOB) are entrapped from soil onto cation-exchange membranes, was applied to identify terrestrial AOB by fluorescence in situ hybridization (FISH). An experimental hot spot of ammonia oxidation was developed by establishing a gradient of ammonium substrate (200 to <20 mg NH4+-N l(-1)) diffused through the cation-exchange membranes incubated in soil for 6 months. By this approach we were able to characterise and image indigenous AOB populations growing in heavily oil-polluted soil using FISH and sequence analysis of PCR-amplified 16S rRNA genes, respectively. The FISH results revealed that Nitrosospira-like AOB were dominant on the ammonium-enriched membranes incubated in the soil. Fourteen unique Nitrosospira-like 16S rRNA gene sequences belonging to clusters 2 and 3 were recovered from the soil-incubated membranes and from the soil, suggesting the importance of Nitrosospira-like AOB in the oil-polluted landfarming soil.
[Show abstract][Hide abstract] ABSTRACT: A novel approach allowing on-site high throughput enzyme activity measurements by fluorogenic model substrates was applied to study the functioning of enzymes involved in biochemical cycling of nutrients in boreal forest soil ecosystems. The examined enzymes comprised α-glucosidase, β-glucosidase, β-xylosidase, β-cellobiosidase, N-acetyl-glucosamidase, acetate-esterase, butyrate-esterase, phosphomonoesterase, sulphatase and aminopeptidase, whereby spatial and seasonal variation of their activity was investigated over nine seasons in 2 years. The studied sites of boreal podzolized soil of Pinus sylvestris and Picea abies forest were located in central Finland. Activity of all enzymes except sulphatase was highest in the humus layer in all seasons. Maximum sulphatase activity was located below the humus layer in the soil column. Annual activities of acetate-esterase, butyrate-esterase, β-glucosidase and phosphomonosterase calculated to in situ temperature during the year were 480–700, 690–950, 110–190 and 110–200 mol m−2 year−1, respectively. They were up to 100 fold higher than the other six measured activities. The overall turnover capacity of the enzymes was >1000 mol of ester linked carbon, >700 mols carbon from different carbohydrates, 100–200 mol of ester linked phosphate, 10–40 mol of ester linked sulphate m−2 year−1. Winter time (November–April) contributed from 7 to 32% to the annual turnover capacity indicating important enzyme activities also during a cold period of the year. Clear-cutting of the tree stand did not adversely affect enzyme activities related to the cycling of carbon, nitrogen, sulphur and phosphorus during the year. The pH optimum for hemicellulose and cellulose hydrolysing enzymes was pH 3–4 and the pH optimum of phosphomonoesterase, sulphatase, aminopeptidase and N-acetyl-glucosamidase was 4–5. This shows that the hydrolytic activities were adapted to the acid pH-values of the soils. The soil hydrolytic potential was many fold higher as compared to the actual amount of litter it received in the P. sylvestris and P. abies forests.
[Show abstract][Hide abstract] ABSTRACT: Organic matter degrading microbial activities in economically managed, acid boreal Scots pine forest soils were analysed in different seasons. We observed Q10 values ranging from 2.3 to 2.8 for the production of CO2 from endogenous detrital matter at close to in situ temperatures, when the soils were in natural state, immediately after sampling. The Q10 of methane oxidation, β-glucosidase, C2- and C4-esterases, exhibited values of 1.6 to 2.1 and the corresponding apparent activation energies were from 40 to 70 kJ mol-1. Detrital decomposition extrapolated to zero activity at -7 ± 1°C but the actual soil temperature under snow cover never dropped below -3°C. The degrading activities towards 0.2 to 2 ppm of phenanthrene and of 2,4,5-trichlorophenol showed Q10 values of 2.0 to 4.4 in the fine roots and the rhizosphere fraction of aspen forest soil but there was no activity in the bulk soil. Our results show that the detritus degrading microbial activities in forest soil were only moderately temperature dependent and significant activity continued over the winter.
Boreal Environment Research 01/2001; 6(1):19-28. · 1.14 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This thesis deals with the response of biodegradation of selected anthropogenic organic contaminants and natural autochthonous organic matter to low temperature in boreal surface soils. Furthermore, the thesis describes activity, diversity and population size of autotrophic ammonia-oxidizing bacteria (AOB) in a boreal soil used for landfarming of oil-refinery wastes, and presents a new approach, in which the particular AOB were enriched and cultivated in situ from the landfarming soil onto cation exchange membranes. This thesis demonstrates that rhizosphere fraction of natural forest humus soil and agricultural clay loam soil from Helsinki Metropolitan area were capable of degrading of low to moderate concentrations (0.2 50 µg cm-3) of PCP, phenanthrene and 2,4,5-TCP at temperatures realistic to boreal climate (-2.5 to +15 °C). At the low temperatures, the biodegradation of PCP, phenanthrene and 2,4,5-TCP was more effective (Q10-values from 1.6 to 7.6) in the rhizosphere fraction of the forest soil than in the agricultural soil. Q10-values of endogenous soil respiration (carbon dioxide evolution) and selected hydrolytic enzyme activities (acetate-esterase, butyrate-esterase and β-glucosidase) in acid coniferous forest soil were 1.6 to 2.8 at temperatures from -3 to +30 °C. The results indicated that the temperature dependence of decomposition of natural autochthonous soil organic matter in the studied coniferous forest was only moderate. The numbers of AOB in the landfarming (sandy clay loam) soil were determined with quantitative polymerase chain reaction (real-time PCR) and with Most Probable Number (MPN) methods, and potential ammonium oxidation activity was measured with the chlorate inhibition technique. The results indicated presence of large and active AOB populations in the heavily oil-contaminated and urea-fertilised landfarming soil. Assessment of the populations of AOB with denaturing gradient gel electrophoresis (DGGE) profiling and sequence analysis of PCR-amplified 16S rRNA genes showed that Nitrosospira-like AOB in clusters 2 and 3 were predominant in the oily landfarming soil. This observation was supported by fluorescence in situ hybridization (FISH) analysis of the AOB grown on the soil-incubated cation-exchange membranes. The results of this thesis expand the suggested importance of Nitrosospira-like AOB in terrestrial environments to include chronically oil-contaminated soils. Tämän väitöskirjan tavoitteena oli tutkia suomalaisen maaperän kykyä hajottaa orgaanisia ympäristömyrkkyjä ja maanperän omia luontaisia biopolymeerejä alhaisissa lämpötiloissa. Lisäksi tässä työssä tutkittiin ammoniakkia hapettavien bakteerien populaatiorakennetta ja aktiivisuuksia öljyhiilivetyjen voimakkaasti pilaamassa maaperässä. Orgaanisten ympäristömyrkkyjen biohajoamista tutkittiin Helsingin yliopiston Viikin koe- ja tutkimustilalla Helsingissä, ja metsämaan orgaanisen aineen hajotusaktiivisuuksia Helsingin yliopiston Hyytiälän metsäasemalla Juupajoella, Hämeessä. Väitöskirjassa osoitettiin, että viljellyn peltomaan ja luonnontilaisen lehtimetsän juuristovyöhykkeen mikrobit hajottivat polysyklisiä aromaattisia hiilivetyjä ja polykloorattuja fenoleja hiilidioksidiksi ja vedeksi pohjoisia oloja vastaavissa lämpötiloissa (-2.5º - +15 ºC). Tutkimustulokset viittaavat siihen, että maaperän mikrobien luontainen kyky hajottaa orgaanisia ympäristömyrkkyjä alhaisessa lämpötilassa oli tehokkaampaa pienissä (≤ 5.0 µg cm-3) kuin suurisssa (50 µg cm-3) haitta-ainepitoisuuksissa. Podsoloituneen havumetsämaan maahengitys- (hiilidioksidituotanto) ja hydrolyyttiset entsyymiaktiivisuudet olivat yhtäläisiä tai korkeampia lokakuussa kuin heinä-elokuussa. Tulokset osoittivat, että havumetsämaa oli biologisesti aktiivinen myös kylmänä vuosipuoliskona, ja että metsämaan mikrobiaktiivisuksia säätelivät myös muut tekijät kuin alhainen lämpötila. Tämä väitöskirjatutkimus osoitti lisäksi, että öljyisillä lietteillä voimakkaasti pilaantuneeseen ja urealannoitettuun peltomaahan oli kehittynyt ammoniakkia hapettava mikrobiyhteisö, joka sietää korkeita öljyhiilivetypitoisuuksia. Ammoniakkia hapettavat bakteerit olivat sopeutuneet kasvamaan öljyllä pilaantuneessa maassa, ja näin ollen ne voisivat toimia myös öljyisen maan puhdistajina. Nykyaikaisten, mikrobien DNA:ta hyödyntävien menetelmien ja maailmanlaajuisten tietokantojen avulla pystyttiin osoittamaan, että valtaosa öljyhiilivetyjen pilaaman peltomaan ammoniakkia hapettavista bakteereista oli läheisintä sukua Nitrosospira-sp. bakteereille. Öljyisen peltomaan luontaisesti ammoniakkia hapettavat bakteerit Nitrosospira-sp. onnistuttiin rikastamaan suoraan maahan sijoitettujen kationinvaihtokalvojen avulla. Tulokset osoittivat, että kationinvaihtokalvot soveltuvat hyvin ammoniakkia hapettavien bakteerien toteamiseen ja niiden ekologian tutkimiseen maaperässä.