Soil potential denitrification rates Denitrification rates were determined as described by Smith and Tiedje [33]. Fifty grams of soil were incubated in hermetically sealed glass (1.8 L) bottles, containing a nutrient solution with NO3 – (100 mg N l-1),

glucose (40 mg l-1) and chloramphenicol (10 mg l-1). The atmosphere in the bottle was replaced by pure N2 and approximately 10% of acetylene was added. Gas samples were removed after 0, 30, 60 and 90 min. Tests were conducted in triplicate. The N2O concentrations were quantified with a gas chromatograph (Shimadzu GC17A). Bacterial community structure and N cycle gene diversity Soil DNA was extracted in triplicate (only three soil samples randomly chosen from the five replicate Selleckchem LEE011 subplots) by using RAD001 mw the FastDNA® Spin Kit for Soil and a FastPrep® equipment (Bio 101, CA, USA), according to the manufacturer’s instructions. To analyze total bacterial community structure and diversity, we used a pair of universal primers for the domain Bacteria, which amplify the gene fragment coding for a fragment of the 16 S rRNA subunit (U968-GC and L1401) [34]. Specific primers for the functional genes amoA (AmoA1F-Clamp

and AmoA-2R-TC) [35] and nirK (F1aCu and R3CuGC) [26] were used to study the ammonia oxidizing and denitrifying bacteria, respectively. A CG-rich clamp was added to the end of one primer for each system [36]. Amplifications were carried out by PCR in 50 μL reactions containing approximately for 10 ng of DNA, Taq buffer 10X, MgCl2 (2.5 mM), dNTPs (0.2 mM), primers (0.2 μM), BSA (bovine serum albumin) (0.1 g l-1), formamide (1% v/v) and Taq DNA polymerase (Fermentas; 2.5 U). The bacterial PCR was run as follows: initial DNA denaturation step at 94°C for 4 min, followed by 35 cycles of 1 min

at 94°C, an annealing step of 1 min at 55°C, and amplification during 2 min at 72°C, with a final extension of 10 min at 72°C. The amoA gene-specific PCR was run with an initial denaturation at 94°C for 3 min, followed by 35 cycles of 30 s at 94°C, 1 min at 57°C, 1 min at 72°C, with a final extension of 10 min at 72°C. The denitrifying gene-specific PCR was run with an initial denaturation at 94°C for 3 min, followed by 5 cycles of 30 s at 94°C, 1 min at 60°C and 1 min at 72°C; 30 cycles of 30 s at 94°C, 1 min at 62°C, and 1 min at 72°C; with a final extension of 10 min at 72°C. The amplified fragments were analyzed via DGGE [37] on a Universal Dcode™ Mutation Detection System (Bio-Rad, Richmond, California, USA). We prepared the polyacrylamide gels (6%) using a selleck inhibitor mixture of 37.5:1 acrylamide/bisacrylamide (w:w) in a TAE 1X buffer (10 mM Tris-acetate, 0.5 mM EDTA pH 8.0), with denaturing gradients of: 45 to 65%, 45 to 65%, and 55 to 70%, for bacterial, ammonia oxidizing and denitrifying gene amplicons, respectively.