Effect of Sulfadiazine-Contaminated Pig Manure on the Abundances of Genes and Transcripts Involved in Nitrogen Transformation in the Root-Rhizosphere Complexes of Maize and Clover▿ †

The antibiotic sulfadiazine (SDZ) can enter the environment by application of manure from antibiotic-treated animals to arable soil. Because antibiotics are explicitly designed to target microorganisms, they likely affect microbes in the soil ecosystem, compromising important soil functions and disturbing processes in nutrient cycles. In a greenhouse experiment, we investigated the impact of sulfadiazine-contaminated pig manure on functional microbial communities involved in key processes of the nitrogen cycle in the root-rhizosphere complexes (RRCs) of maize (Zea mays) and clover (Trifolium alexandrinum). At both the gene and transcript level, we performed real-time PCR using nifH, amoA (in both ammonia-oxidizing bacteria and archaea), nirK, nirS, and nosZ as molecular markers for nitrogen fixation, nitrification, and denitrification. Sampling was performed 10, 20, and 30 days after the application. SDZ affected the abundance pattern of all investigated genes in the RRCs of both plant species (with stronger effects in the RRC of clover) 20 and 30 days after the addition. Surprisingly, effects on the transcript level were less pronounced, which might indicate that parts of the investigated functional groups were tolerant or resistant against SDZ or, as in the case of nifH and clover, have been protected by the nodules

Accumulation of Sulfonamide Resistance Genes in Arable Soils Due to Repeated Application of Manure Containing Sulfadiazine ▿

Two soils were amended three times with pig manure. The abundance of sulfonamide resistance genes was determined by quantitative PCR 2 months after each application. In both soils treated with sulfadiazine-containing manure, the numbers of copies of sul1 and sul2 significantly increased compared to numbers after treatments with antibiotic-free manure or a control and accumulated with repeated applications

Comparison of lipid biomarker and gene abundance characterizing the archaeal ammonia-oxidizing community in flooded soils

In the last years, archaea have been identified as key players in global N cycling, especially in nitrification. Ammonia-oxidizing archaea (AOA) are postulated to belong to the new phylum Thaumarchaeota for which the lipid crenarchaeol should be specific. The ratios between two independent markers for AOA, the ammonia monooxygenase gene and crenarchaeol have been studied in different aerated soils, but so far not in flooded soils. This study investigated ammonia-oxidizing archaea in four paddy soils and a tidal wetland. Ratios were significantly higher in the paddy soils compared to the tidal wetland and in general higher as in upland soils, leading to the assumption that archaeal ammonia oxidizers different from crenarchaeol-containing Thaumarchaeota may play an important role in paddy soils. © 2011 Springer-Verlag

Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield

Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions