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Soddy-podzolic soils are widely distributed in European Russia, but their role as a sink for atmospheric methane is poorly documented and there is no information on the methanotroph diversity. We analysed the potential CH 4 -oxidation rates in soil samples and showed that the rate was significantly higher in forest soil than in arable soil, 1.21 and 0.40 ng CH 4 g soil −1 day −1 , respectively. PCR-DGGE and clone library analysis indicated the distinct methanotrophic communities in these soils. The pmoA sequences associated with uncultured soil methanotrophs, referred to as NUSC, dominated forest soil, while in agricultural soil, type I ( Methylobacter, Methylocaldum ) and type II ( Methylocystis, Methylosinus ) methanotrophs were dominant. A newly developed primer set was applied in qPCR analysis and revealed that the copy number of pmoA genes of NUSC methanotrophs in forest soil was (9.2 ± 0.87) × 10 4 g soil −1 , whereas the transcript number was (1.33 ± 0.31) × 10 6 g soil −1 . We concluded that differences between the CH 4 oxidation rates between forest and agriculture soils were driven by the structure of the methane-oxidizing community and that a novel group of methanotrophs may be an active participant in this process. [ABSTRACT FROM AUTHOR]

The integrated effects of environmental factors on soil nitrification are largely unknown. Here, we performed a microcosm experiment to investigate the interactive effects of pH and NH 4 + on nitrification activity in two acidic soils with different land use patterns (Anhui soil, a forest soil; Jiangxi soil, a brush land soil). Both soils were incubated under native pH and CaCO 3 -manipulated pH in the presence or absence of added ammonium for 60 days. The addition of CaCO 3 alone did not change the nitrification activity of either soil. Ammonium addition stimulated nitrification in Anhui soil, but not in Jiangxi soil, and this stimulation was more pronounced with increased CaCO 3 . The ammonia monooxygenase ( amoA ) gene copy number of both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was much higher in Anhui soil than in Jiangxi soil. The amoA gene copy number of AOB in Anhui soil was more highly upregulated under CaCO 3 + NH 4 + than NH 4 + during incubation. In Anhui soil, changes in the denaturing gradient gel electrophoresis (DGGE) fingerprint patterns of bacterial amoA genes were parallel to changes in the amoA gene copy number of AOB. In Jiangxi soil, DGGE could not be performed because the PCR for bacterial DGGE did not yield any products, while quantitative PCR revealed that the amoA gene copy number of AOB changed during incubation. These results suggest that AOB plays an important role in CaCO 3 -enhanced nitrification of Anhui soil with ammonium addition. The low nitrification rates of Jiangxi soil regardless of CaCO 3 with or without NH 4 + supply may be ascribed to the lower activity of both AOB and AOA, especially AOA. [ABSTRACT FROM AUTHOR]

Highlights: [•] We investigated CH4 oxidation in an afforested chronosequence in Denmark. [•] We linked CH4 oxidation with the abundance of methane oxidizing bacteria (MOB). [•] CH4 oxidation increased with time since afforestation. [•] The abundance of MOB also increased following afforestation. [•] Changes in soil organic carbon and bulk density were the main drivers. [ABSTRACT FROM AUTHOR]

Highlights: [•] Increasing nutrient loads and soil pH selected distinct groups of AOA and AOB. [•] AOB was the most abundant and diverse group in highly impacted areas. [•] Changes on AOB community structure were mainly driven by ammonium concentrations. [•] AOA was dominant in less impacted areas and reacted to changes on pH and nitrogen. [ABSTRACT FROM AUTHOR]

Abstract: In a greenhouse study we investigated the potential of wood ash amended composts to ameliorate acid tropical soils. Three composts (produced with 0%, 8% and 16% wood ash admixture, respectively), and two acid tropical soils, an Oxisol and an Ultisol from Cameroon were used for that purpose. In this paper we report the effects on the soil microbiota at the end of the cropping cycle (100 days soybean plus 100 days fallow). Principal coordinate analysis of denaturing gradient gel electrophoresis patterns of ammonium oxidizing bacteria (AOB) indicated that they were stimulated by addition of compost. AOB communities of the compost treated soils differed from the control ones, and no significant differences among the different composts were found in both soils. Soil type clearly influenced the AOB community. Ester-linked phospholipid fatty acids increased in compost treated soils, up to an ash amendment of 8%. The ratio of cyclopropyl-to-monoenoic precursor (cy19:0 to 18:1ω7), which has been proposed as an indicator of stress conditions, decreased upon compost addition and did not differ among the treated soils. Community level physiological profiling indicated an increase in activities after addition of compost, the effect was most distinct for the compost with 16% ash. Based on these results, compost with moderate dose of wood ash is considered beneficial to the soil microbiota and could thus be used for ameliorating tropical acid soils. [Copyright &y& Elsevier]

Abstract: Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) co-exist in soil, but their relative distribution may vary depending on the environmental conditions. Effects of changes in soil organic matter and nutrient content on the AOB and AOA are poorly understood. Our aim was to compare effects of long-term soil organic matter depletion and amendments with labile (straw) and more recalcitrant (peat) organic matter, with and without easily plant-available nitrogen, on the activities, abundances and community structures of AOB and AOA. Soil was sampled from a long-term field site in Sweden that was established in 1956. The potential ammonia oxidation rates, the AOB and AOA amoA gene abundances and the community structures of both groups based on T-RFLP of amoA genes were determined. Straw amendment during 50 years had not altered any of the measured soil parameters, while the addition of peat resulted in a significant increase of soil organic carbon as well as a decrease in pH. Nitrogen fertilization alone resulted in a small decrease in soil pH, organic carbon and total nitrogen, but an increase in primary production. Type and amount of organic matter had an impact on the AOB and AOA community structures and the AOA abundance. Our findings confirmed that AOA are abundant in soil, but showed that under certain conditions the AOB dominate, suggesting niche differentiation between the two groups at the field site. The large differences in potential rates between treatments correlated to the AOA community size, indicating that they were functionally more important in the nitrification process than the AOB. The AOA abundance was positively related to addition of labile organic carbon, which supports the idea that AOA could have alternative growth strategies using organic carbon. The AOB community size varied little in contrast to that of the AOA. This indicates that the bacterial ammonia oxidizers as a group have a greater ecophysiological diversity and potentially cover a broader range of habitats. [Copyright &y& Elsevier]