Ivan Mahne

Influence of temperature and soil water content on bacterial, archaeal and denitrifying microbial communities in drained fen grassland soil microcosms

In this study, microcosms were used to investigate the influence of temperature (4 and 28 degrees C) and water content (45% and 90% WHC) on microbial communities and activities in carbon-rich fen soil. Bacterial, archaeal and denitrifier community composition was assessed during incubation of microcosms for 12 weeks using terminal restriction fragment length polymorphism (T-RFLP) profiling of 16S rRNA and nitrous oxide reductase (nosZ) genes. In addition, microbial and denitrifier abundance, potential denitrification activity and production of greenhouse gases were measured. No detectable changes were observed in prokaryote or denitrifier abundance. In general, cumulatively after 12 weeks more carbon was respired at the higher temperature (3.7 mg CO(2) g(-1) soil), irrespective of the water content, whereas nitrous oxide production was greater under wet conditions (98-336 microg N(2)O g(-1) soil). After an initial lag phase, methane emissions (963 microg CH(4) g(-1) soil) were observed only under warm and wet conditions. T-RFLP analyses of bacterial 16S rRNA and nosZ genes revealed small or undetectable community changes in response to temperature and water content, suggesting that bacterial and denitrifying microbial communities are stable and do not respond significantly to seasonal changes in soil conditions. In contrast, archaeal microbial community structure was more dynamic and was strongly influenced by temperature.

Nitrous Oxide Reductase (nosZ) Gene Fragments Differ between Native and Cultivated Michigan Soils

ABSTRACT The effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosZ) fragments from denitrifying prokaryotes in native and cultivated soil was explored. Thirty-six soil cores were composited from each of the two soil management conditions. nosZ gene fragments were amplified from triplicate samples, and PCR products were cloned and screened by restriction fragment length polymorphism (RFLP). The total nosZ RFLP profiles increased in similarity with soil sample size until triplicate 3-g samples produced visually identical RFLP profiles for each treatment. Large differences in total nosZ profiles were observed between the native and cultivated soils. The fragments representing major groups of clones encountered at least twice and four randomly selected clones with unique RFLP patterns were sequenced to verify nosZ identity. The sequence diversity of nosZ clones from the cultivated field was higher, and only eight patterns were found in clone libraries from both soils among the 182 distinct nosZ RFLP patterns identified from the two soils. A group of clones that comprised 32% of all clones dominated the gene library of native soil, whereas many minor groups were observed in the gene library of cultivated soil. The 95% confidence intervals of the Chao1 nonparametric richness estimator for nosZ RFLP data did not overlap, indicating that the levels of species richness are significantly different in the two soils, the cultivated soil having higher diversity. Phylogenetic analysis of deduced amino acid sequences grouped the majority of nosZ clones into an interleaved Michigan soil cluster whose cultured members are α-Proteobacteria. Only four nosZ sequences from cultivated soil and one from the native soil were related to sequences found in γ-Proteobacteria. Sequences from the native field formed a distinct, closely related cluster (Dmean = 0.16) containing 91.6% of the native clones. Clones from the cultivated field were more distantly related to each other (Dmean = 0.26), and 65% were found outside of the cluster from the native soil, further indicating a difference in the two communities. Overall, there appears to be a relationship between use and richness, diversity, and the phylogenetic position of nosZ sequences, indicating that agricultural use of soil caused a shift to a more diverse denitrifying community.

Nitrification/denitrification in nitrogen high-strength liquid wastes

Abstract To evaluate the possibility of nitrogen removal from nitrogen high-strength wastewaters, nitrification rates, denitrification and related energy problems, emerging in nondiluted wastewater from a pig production plant, are studied on a laboratory level. Excess nitrogen can be removed by utilising a nitrification process first and a denitrification process afterwards, and so reduce the content of residual mineral nitrogen to less than 100 mg l −1 . Oxidation of ammonium, the most critical phase, is carried out with an inoculum of nitrifying bacteria adapted to the wastewater type under adequate aeration, and carefully controlled pH. The dilution of wastewater is not needed, nor external organic carbon to reduce nitrate.

Nitrogen mineralization in marsh meadows in relation to soil organic matter content and watertable level

The objective of the present study was to asses the effect of watertable level on N mineralization in a Histosol and a Humic Gleysol profile under natural meadows in Ljubljana marsh, Slovenia. The two soils differ significantly in organic matter content (27—40 % in Histosol and 14—20 % in Humic Gleysol) but not in C : N ratio (13—20) and pH (6.5—7.0). For each soil, the watertable was maintained at two levels (above or below 50 cm from the soil surface) for approximately one year. The four main plots, according to soil carbon content and watertable level were divided into 4 subplots, according to 4 fertilization treatments (unfertilized control, PK, PK + 50 kg N ha—1, PK + 3 × 50 kg N ha—1). Net N mineralization in unfertilized subplots was estimated from indices of N mineralization obtained by incubation of soil samples in the laboratory and by seasonal dynamics of mineral N content in the field. Annual uptake of N in herbage under the 4 fertilization treatments was also measured. Total mineral N content in topsoil was 20—80 % higher in Histosol than in Humic Gleysol. Similarly, aerobic N mineralization potentials along the entire soil profile (0—90 cm) were 20—130 % higher in Histosol than in Humic Gleysol. By contrast, anaerobic N mineralization potentials in subsoil were 10—60 % lower in Histosol than in Humic Gleysol. Both, aerobic and anaerobic N mineralization potentials strongly depended on watertable levels at sampling time. Seasonal dynamics of soil mineral N content as well as N mineralization potentials indicated that the N mineralization in the Histosol could be 10—40 % higher at low than at high watertable level. In the Humic Gleysol the N mineralization could be 10—100 % higher at high watertable level. Higher N availability in Histosol at low watertable and in Humic Gleysol at high watertable was also reflected in higher N uptake in herbage. These results indicate that N mineralization in Histosol and Humic Gleysol, was proportional to soil organic matter content, whereas in both soils, higher N mineralization rates can be expected at watertable levels between 40 and 60 cm below the soil surface, than at higher/lower watertable levels. Einfluss des Humusgehaltes und des Grundwasserspiegels auf die Stickstoffmineralisation in Boden aus Feuchtgebieten Ziel dieser Untersuchung war es, den Einfluss der Hohe des Grundwasserspiegels auf die N-Mineralisation in einem Histosol und einem Humic Gleysol unter Naturwiesen des Ljubljanaer Moors, Slowenien, festzustellen. Die zwei untersuchten Bodentypen unterscheiden sich signifikant im Gehalt der organischen Substanzen (27—40 % in Histosol und 14—20 % in Humic Gleysol), aber nicht im C : N-Verhaltnis und pH-Wert (6.5—7.0). In jedem Bodentyp wurden fur die Dauer von 1 Jahr kunstlich jeweils ein hoher und ein niedriger Grundwasserspiegel eingestellt. Jede der 4 daraus resultierenden Haupt-Versuchsparzellen wurde weiter geteilt in 4 Dungungs-Teilstucke: Ungedungt, PK, PK + 50 kg N ha—1 und PK + 3 × 50 kg N ha—1. Die Netto-N-Mineralisation auf ungedungten Teilstucken der Haupt-Versuchparzellen (2 Bodentypen, 2 Grundwasserspiegel) wurde bestimmt durch die N-Mineralisationspotenziale bei anaerober und aerober Inkubation der Bodenproben im Labor sowie durch die saisonale Dynamik des N-Gehaltes im Boden sowie durch den N-Entzug der Vegetation in 4 Dungungsvarianten. Wahrend der Messperiode lag der Gehalt am gesamten mineralischen Stickstoff in der oberen Bodenschicht des Histosol um 20 bis 80 % hoher als im Humic Gleysol. Ahnlich waren die aeroben N-Mineralisationspotenziale im Bodenprofil des Histosols um 20 bis 130 % hoher als im Humic Gleysol. Die anaeroben N-Mineralisationspotenziale waren dagegen in tieferen Bodenschichten des Histosol um 10 bis 60 % niedriger als im Humic Gleysol. Die Anderungen der Mineralisationspotenziale in aerob und anaerob inkubierten Bodenproben waren zugleich vom Grundwasserspiegel zur Zeit der Beprobung abhangig. Sowohl die zeitliche Dynamik des Gehaltes an mineralischem N in der Zeit als auch die aeroben und anaeroben N-Mineralisationspotenziale zeigen aber einheitlich, dass die N-Mineralisation im Histosol bei niedrigem Grundwasserspiegel um 10 bis 40 % groser sein kann, wahrend im Humic Gleysol die N-Mineralisation bei hohem Grundwasserspiegel um 10 bis 100 % groser sein kann. Hohere N-Verfugbarkeit im Boden widerspiegelt sich auch im hoheren N-Entzug durch die Vegetation. Die Ergebnisse dieser relativ kurzen Untersuchung zeigen, dass die N-Mineralisation in Histosol und in Humic Gleysol proportional dem Humusgehalt verlauft; in beiden Bodentypen kann bei Grundwasserspiegeln von 40—60 cm eine starkere N-Mineralisation erwartet werden als bei daruber oder darunter liegendem Wasserspiegel.

Organisms of the Nitrogen Cycle Under Extreme Conditions: Low Temperature, Salinity, pH Value and Water Stress

Publisher Summary This chapter provides a general understanding of the importance of the denitrification and other reactions of the N-cycle in these environments to global ecology, the principles governing their activities and ongoing adaptations that enable the microbes to thrive in such environments. To survive at low T, microbes can reduce their cell size and their capsular polysaccharide coat thickness; they can also change their fatty acid and phospholipid composition. The unfrozen microsites, surrounded by ice, have limited gas exchange, which leads to the development of O2 deficiency thereby, favoring denitrification. Most of the studies exploring gas emissions from soil at low T have focused on the periods of soil thaw, when peaking emission rates can be observed. Finally, the T responses of N2O production and reduction rates might significantly differ among different soil types depending upon the composition of the microbial communities. The term “halophile” includes organisms that require NaCl or another salt for growth (“salt-resistant organisms”) and those which thrive in both non-saline and saline habitats. The chapter gives a description of halophilic environment. The aerobic halophilic Archaea of the family Halobacteriaceae are the halophiles par excellence. Extreme halophilic and non-salt-tolerant bacteria are found site-by-site at all salt concentrations in the soil. The chapter lists the most representative prokaryotic denitrifiers described from halophilic environments and covers the relationship between soil pH and denitrification.