Anders Priemé

Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments

ABSTRACT Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kgNha(-1)year(-1)) and cattle manure (75 and 150 kgNha(-1)year(-1)) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different. Also, these sites significantly differed from the control plot (no fertilizer treatment), whereas the patterns for low and high N-additions were barely separable from each other. Sequencing and phylogenetic analysis of 54 nirK clones revealed that the major part of the nirK-containing bacteria investigated belonged to a yet uncultivated cluster of denitrifying bacteria.

Slow increase in rate of methane oxidation in soils with time, following land use change from arable agriculture to woodland

In a successional range of sites on former arable land in Denmark and Scotland, CH4 oxidation rates took more than 100 y to reach pre-cultivation level. During the first 2–5 y following abandonment of agriculture, CH4 oxidation decreased slightly, eventually followed by an increase from 5–15 μg CH4 m−2 h−1 to a substantially higher rate of 100–150 μg CH4 m−2 h−1 in the oldest (200 y) woodlands.

Seasonal and spatial variation of methane oxidation in a Danish spruce forest

Abstract Methane oxidation in a Danish spruce forest was measured monthly from September 1993 to June 1995 using 30 closed chambers (78 cm2) in permanent positions along a 58 m transect. Average daily CH4 oxidation rates ranged from 27.1 to 57.7 μg CH4 m−2 h−1 and were positively correlated with soil temperature (P 10 cm) layer of humus or humus-enriched soil. In addition, we measured CH4 in soil air and found a positive correlation along the transect between the steepness of the CH4 concentration gradient and CH4 flux at the soil surface (P 1.2 μmol N g dry wt−1) reduced CH4 oxidation in incubated soil. It is possible that CH4 oxidizing microbes are dismissed from the upper soil layer by high ammonium and nitrate concentrations, but other possibilities could not be excluded. Overall, CH4 flux at the soil surface was controlled by the dynamics of the CH4-oxidizing microbes and to some extent limitation of CH4 diffusion into the soil. In this loamy sand, diffusion limitation is probably operating mainly at high soil water content or at conditions resulting in high CH4-oxidizing activity, e.g. at high temperatures and in areas of high CH4-oxidizing potential.

Effect of land use on the rate of methane uptake by surface soils in Northern Europe

The effect of historical land use change on methane uptake by aerobic soils has been studied by measurements on paired sites (forest/woodland and agricultural land) in Scotland, Denmark and Poland. Rates were observed in the range 0.01–3.3 mg CH4 m−2 d−1. The mean reduction in uptake rates resulting from conversion to agriculture was 60%; this change is greater than that reported for the effect of nitrogen inputs through fertilisation or atmospheric deposition. The total current methane sink in forest soils in Europe is estimated at about 0.6 Tg CH4 yr−1, and the corresponding sink in agricultural land at 0.23 Tg CH4 yr−1.

The influence of soil gas transport properties on methane oxidation in a selection of northern European soils

The oxidation of atmospheric methane in soils was measured in situ at a selection of sites in northern Europe, mainly under forest but also under moorland and agricultural arable land and grassland. Our objective was to examine how land use, soil type, and location affected methane oxidation through their impact on gas diffusivity and air permeability. Gas diffusivity at the soil surface and, in some cases, after removal of any surface organic layer was measured in situ using Freon-22 tracer in a portable probe. For about half of the sites, gas diffusivity was also measured in intact topsoil core samples in the laboratory using krypton 85. Air permeability and porosity were also measured on these cores. Although the method of measurement of CH4 oxidation varied between sites, the same techniques were used to measure soil physical properties at all sites. CH4 oxidation rates ranged from 0 to 2.5 mg m−2 d−1. Diffusivity also covered a very wide range, being lowest in loam cores from wet grassland in Norway and highest in relatively dry, sandy soils in Denmark and Scotland. CH4 oxidation tended to increase with gas diffusivity measured in situ at the soil surface, though the relationship was poor at high diffusivities, presumably because CH4 oxidation was not limited by diffusion. Removal of the surface organic layer reduced in situ diffusivity at the surface and improved its relationship with CH4 oxidation rate. Sites where soils had well-developed structure and a loose and permeable organic layer at the surface tended to have the highest CH4 oxidation rates. Core measurements, particularly of air permeability, could not be obtained at some sites owing to the inability to take suitable samples. Diffusivity measured in cores generally decreased with increasing depth of sampling in the topsoil, with the 50-to 100-mm depth giving the best correlation with CH4 uptake; cores from within this layer also gave the highest CH4 oxidation during laboratory incubation. Effective comparisons between sites were hampered by the differing responses of CH4 oxidation and diffusivity to soil properties. However, multivariate cluster analysis that included the above transport variables plus others relevant to CH4 oxidation (namely, soil texture; bulk density; airfilled porosity; pH; carbon, nitrogen, and water contents; presence and depth of organic layers; and N deposition) confirmed the importance of soil water content, structure and texture in distinguishing different soil and site conditions.

Production and emission of methane in a brackish and a freshwater wetland

There is no clear consensus on how environmental and biotic factors control microbiallymediated methane production in wetlands, as well as emission of this important ‘greenhouse gas’ from wetlands into the atmosphere. To provide insight, I studied rates of methane production and emission into the atmosphere, as well as factors controlling those rates, along a toposequence from non-flooded to seasonally flooded in a coastal meadow and in a fen in Denmark. Methane production was estimated from anaerobic soil slurries while emission was estimated from static flux chambers. Methane emission into the atmosphere averaged 0.04 μg C-CH4 dm−2 h-−1 in the coastal meadow and 1.9 μg C-CH4 dm−2 h−1 in the fen. A comparison of potential CH4 production and CH4 emission into the atmosphere showed that in the coastal meadow, but not in the fen, emission increased when production increased during summer. Relationships between potential CN4 production and soil water content as well as soil temperature are discussed. Arrhenius plots indicated strikingly similar temperature responses of CH4 production in the two wetlands. Also, both wetlands showed different temperature responses in saturated soils (Q10 = 3.1 and 3.6; Eh=79 and 84 kJ mol−1) compared to unsaturated soils (Q10 = 8.1 and 8.7; eh = 138 and 142 kJ mol−1). My results suggest that different types of methanogens inhabit saturated and unsaturated soils in both a coastal meadow and a fen. Overall, the study indicates that CH4 production in wetlands and CH4 emission into the atmosphere from wetlands are controlled by a complex set of environmental and biotic factors which differ between wetlands.

Bacterial diversity in permanently cold and alkaline ikaite columns from Greenland.

Bacterial diversity in alkaline (pH 10.4) and permanently cold (4°C) ikaite tufa columns from the Ikka Fjord, SW Greenland, was investigated using growth characterization of cultured bacterial isolates with Terminal-restriction fragment length polymorphism (T-RFLP) and sequence analysis of bacterial 16S rRNA gene fragments. More than 200 bacterial isolates were characterized with respect to pH and temperature tolerance, and it was shown that the majority were cold-active alkaliphiles. T-RFLP analysis revealed distinct bacterial communities in different fractions of three ikaite columns, and, along with sequence analysis, it showed the presence of rich and diverse bacterial communities. Rarefaction analysis showed that the 109 sequenced clones in the 16S rRNA gene library represented between 25 and 65% of the predicted species richness in the three ikaite columns investigated. Phylogenetic analysis of the 16S rRNA gene sequences revealed many sequences with similarity to alkaliphilic or psychrophilic bacteria, and showed that 33% of the cloned sequences and 33% of the cultured bacteria showed less than 97% sequence identity to known sequences in databases, and may therefore represent yet unknown species.

Methane uptake by a selection of soils in Ghana with different land use

We measured the oxidation of atmospheric methane in tropical soils in Ghana covering a moisture gradient from the moist forest zone to the savanna zone at the onset of the rainy season. Land use at the sites covered undisturbed (forest and savanna) and cultivated soil, including burning. Generally, the methane oxidation rates in the tropical forest and savanna soils were low (range from 9 to 26 μg CH4 m−2 h−1) compared to, for example temperate forest soils. In the savanna soil, annual fire had decreased soil methane oxidation rates to 5 μg CH4 m−2 h−1 compared to 9 μg CH4 m−2 h−1 at a site not subjected to fire for 6 years. In paired sites of moist forest and arable soils, methane oxidation rates were lower by >60% in the arable soils. Methane oxidation rates in three arable soils in the savanna zone soils ranged from 7 to 11 μg CH4 m−2 h−1 before the first rain but increased to 23–28 μg CH4 m−2 h−1 after the rain. These rates are comparable to other reports from arable soils in tropical and temperate regions. Thus arable agriculture and, to a lesser extent, biomass burning decreased methane oxidation rates by the investigated soils.

SPATIAL VARIABILITY OF CH4 UPTAKE IN A DANISH FOREST SOIL AND ITS RELATION TO DIFFERENT MEASUREMENT TECHNIQUES

Abstract We measured CH 4 uptake in a Danish beech forest soil using traditional closed chambers (0.0078 m 2 ) with gas chromatographic analysis of headspace CH 4 and a megachamber (64 m 2 ) with Fourier transform infrared (FTIR) spectroscopy for CH 4 analysis. The two techniques gave uptake rates of 22.5 and 21.8 μg CH 4 m 2 h −1 , respectively. CH 4 uptake rates from 122 small chambers were normally distributed. Geostatistical analysis of uptake rates indicated that a megachamber covering 10–12 m will encompass most of the spatial variability. Thus, the 29 × 2.2 m megachamber would cover most of the variability, and this explains the similar uptake rates obtained by this technique and the 0.0078 m2 chambers. In a parallel study, 0.0078 and 0.49 m 2 closed chambers showed similar CH 4 uptake rates indicating that both chamber sizes are adequate for estimating CH 4 uptake.

Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure

Copper has been intensively used in industry and agriculture since mid-18(th) century and is currently accumulating in soils. We investigated the diversity of potential active bacteria by 16S rRNA gene transcript amplicon sequencing in a temperate grassland soil subjected to century-long exposure to normal (∼15 mg kg(-1)), high (∼450 mg kg(-1)) or extremely high (∼4500 mg kg(-1)) copper levels. Results showed that bioavailable copper had pronounced impacts on the structure of the transcriptionally active bacterial community, overruling other environmental factors (e.g. season and pH). As copper concentration increased, bacterial richness and evenness were negatively impacted, while distinct communities with an enhanced relative abundance of Nitrospira and Acidobacteria members and a lower representation of Verrucomicrobia, Proteobacteria and Actinobacteria were selected. Our analysis showed the presence of six functional response groups (FRGs), each consisting of bacterial taxa with similar tolerance response to copper. Furthermore, the use of FRGs revealed that specific taxa like the genus Nitrospira and several Acidobacteria groups could accurately predict the copper legacy burden in our system, suggesting a potential promising role as bioindicators of copper contamination in soils.