Åsa Jarvis

Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE

We re-evaluated PCR primers targeting nirS, nirK and nosZ genes for denaturing gradient gel electrophoresis as a tool to survey denitrifying community composition in environmental samples. New primers for both nirS and nosZ were combined with existing primers, while for nirK the previously published F1aCu:R3Cu set was chosen for denaturing electrophoresis. All three sets yielded amplicons smaller than 500 bp and amplified the correct fragment in all environmental samples. The denaturing gradient gel electrophoresis worked satisfactorily for nirK and nosZ, but not for nirS. This was probably due to the multiple melting domains in this particular nirS fragment. From the excised and sequenced bands, only sequences related to the target genes were detected and tree analysis showed that the selected primers acted as broad range primers for each of the three genes. By use of the new nirS primers it was demonstrated that agricultural soil harbours a substantial diversity of nirS denitrifiers.

Improvement of a grass-clover silage-fed biogas process by the addition of cobalt

Abstract Batch assays were performed with samples from a silage-fed mesophilic biogas process accumulating acetate to examine if the addition of single trace elements (iron, nickel, cobalt and molybdenum) or a mixture of trace elements could improve the process. The results from the batch assays led to the addition of cobalt to reach a concentration of 0.2 mg L −1 . This made it possible to increase the organic loading rate (OLR) above that in a parallel process not receiving any extra cobalt. Problems with low gas production and decreasing pH were overcome by the daily supply of this single element in small amounts. Acetate conversion to methane was improved, which was confirmed by increased specific methanogenic activity (SMA) with acetate as a substrate. As a consequence, an OLR of 7.0 g VS L −1 day −1 was achieved at a hydraulic retention time (HRT) of 20 days with an equivalent increase in methane production. Without cobalt addition, an OLR of 5.0 g VS L −1 day −1 with an HRT of 20 days was reached after 70 weeks operation.

Comparison of signature lipid methods to determine microbial community structure in compost

The microbial community structure changes substantially during the composting process and simple methods to follow these changes can potentially be used to estimate compost maturity. In this study, two such methods, the microbial identification (MIDI) method and the ester-linked (EL) procedure to determine the composition of long-chain fatty acids, were applied to compost samples of different age. The ability of the two methods to describe the microbial succession was evaluated by comparison with phospholipid fatty acid (PLFA) analysis on the same samples.Samples were taken from a 200-l laboratory compost reactor, treating source-separated organic household waste. During the initial stages of the process, the total concentration of fatty acids in compost samples treated with the EL and MIDI methods was many times higher than with the PLFA method. This was probably due to the presence of fatty acids from the organic material in the original waste. However, this substantial difference between PLFA and the other two methods was not found later in composting. Although the PLFA method gave the most detailed information about the growth and overall succession of the microbial community, the much simpler MIDI and EL methods also successfully described the shift from the initially dominating straight chain fatty acids to iso- and anteiso branched, 10 Me branched and cyclopropane fatty acids in the later stages of the process. Thus, the MIDI and EL extraction methods appear to be suitable for analysis of microbial FAME profiles in compost, particularly in the later stages of the process.

Community survey of ammonia-oxidizing bacteria in full-scale activated sludge processes with different solids retention time

Aims:  To study the effects of different solids retention time (SRT) on the nitrification activity and community composition of ammonia‐oxidizing bacteria (AOB) in two full‐scale activated sludge processes during a 5‐month period.

Development of compost maturity and Actinobacteria populations during full-scale composting of organic household waste

Aims:  This study investigates changes in microbiological and physicochemical parameters during large‐scale, thermophilic composting of a single batch of municipal organic waste. The inter‐relationships between the microbial biomass and community structure as well as several physicochemical parameters and estimates of maturation were evaluated.

Activity and composition of ammonia oxidizing bacterial communities and emission dynamics of NH3 and N2O in a compost reactor treating organic household waste

Aims:  To monitor emissions of NH3 and N2O during composting and link these to ammonia oxidation rates and the community structure of ammonia oxidizing bacteria (AOB).

Ammonia-oxidizing communities in agricultural soil incubated with organic waste residues

The impact of organic compounds present in different kinds of organic fertilizers, i.e., anaerobically digested household waste, composted organic household waste, swine manure, and cow manure, on microbial communities in arable soil was investigated using microcosms. Soil was amended with dried residues or organic extracts of the residues and incubated for 12 weeks at 25°C. The microbial community composition was investigated by phospholipid fatty acid (PLFA) analysis, and the community of ammonia-oxidizing bacteria (AOB) was assessed by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA fragments, followed by sequencing. All dried residues increased the AOB activity, determined as potential ammonia oxidation, whereas the organic extracts from the thermophilically digested waste and the swine manure caused a decreased potential activity. However, no differences in the DGGE banding patterns were detected, and the same AOB sequences were present in all samples treated with the residue extracts. Moreover, the PLFA composition showed that none of the residue additions affected the overall microbial community structure in the soil. We conclude that the AOB community composition was not affected by the organic compounds in the fertilizers, although the activity in some cases was.

Stimulation of conversion rates and bacterial activity in a silage-fed two-phase biogas process by initiating liquid recirculation.

The effects of liquid recirculation on a liquefaction-acidogenic reactor in an anaerobic two-phase digesting system operating with grass-clover silage was studied during 40 days after initiating recirculation of effluent from the methanogenic reactor to the liquefaction-acidogenic reactor. An increase in alkalinity and, thus, an increase in pH from 5.2 to 6.0 occurred in the liquefaction-acidogenic reactor. During the same period, a 10-fold increase (from 0.2 to 1.9 g·l−1·h−1) in the degradation rate of mannitol and an almost 9-fold increase in the activity of hydrogenotrophic methanogens was observed. The estimated number of these bacteria increased by one order of magnitude. The average degradation rate of lactate increased 3-fold, probably as a consequence of the more efficient hydrogen consumption by the hydrogenotrophic methanogens. An observed increase in net mineralization of organic nitrogen compounds was probably the main reason for an enhanced net production of organic acids (from 0.2 to 0.9 g·l−1·d−1). The liquefaction of cellulose and hemicellulose was low from the start of recirculation (3% and 20% reduction, respectively) and did not seem to be affected by the liquid recirculation. This was in accordance with the low number of cellulose degraders (4.0·102 counts·ml−1) observed. The results from this investigation show that the initiation of liquid recirculation in silage-fed two-phase biogas processes will stimulate the activity of hydrogenotrophic methanogens in the liquefaction-acidogenic reactor. This will lead to more thermodynamically favourable conditions for acidification reactions which are dependent upon interspecies transfer of reducing equivalents.

Nitrous oxide and methane emissions from food waste composting at different temperatures.

Emissions of methane (CH₄) and nitrous oxide (N₂O) from composting of source-sorted food waste were studied at set temperatures of 40, 55 and 67°C in 10 trials performed in a controlled environment 200L compost reactor. CH₄ and N₂O concentrations were generally low. In trials with 16% O₂, the mean total CH₄ emission at all temperatures was 0.007% of the mineralized carbon (C), while at 67°C this fraction was 0.001%. Total CH₄ production was higher in the 40°C trial and the limited oxygen (1% O₂) trial, with emissions of 0.029 and 0.132% of the mineralized C respectively. An early increase in N₂O production was observed in trials with higher initial nitrate contents. Increased CH₄ and N₂O production in trials at 40 and 55°C after 50% of the initial C was mineralized resulted in higher total greenhouse gas emissions. Overall, the global warming potentials in CO₂-equivalents from CH₄ emissions were higher than from N₂O, except for composts run at 67°C.