| Urban areas are increasing worldwide, but little is known about the effects of urbanization on soil microbial communities and the biogeochemical cycles they mediate. Urban soils surrounding residences and commercial structures are commonly landscaped by removing native vegetation and covering the soil with mulch. The most widespread mulching materials are bark and gravel, used to exclude undesired vegetation and promote landscaped plant growth. Mulching involves a high degree of soil disturbance and has strong potential for altering soil nitrogen (N) transformations. Nitrification, the microbially mediated oxidation of exchangeable ammonium to mobile nitrate, is arguably the most critical N transformation process occurring in soils because it has such a significant effect on N species mobility. Soil microorganisms responsible for nitrification are also expected to be affected by mulching. The ammonia oxidizers are an especially important group of nitrifiers because they carry out the first and rate-limiting step of nitrification. Two distinctive groups of ammonia-oxidizing prokaryotes (AOP) co-exist in soils: ammonia-oxidizing archaea (AOA) and bacteria (AOB). For this dissertation, three studies were conducted to investigate the effects of mulches on AOP abundance and diversity: (1) an observational study in which AOA diversity and AOP abundance were determined in soils from mulched and unmown experimental plots; (2) a controlled greenhouse study in which the abundance of AOP, potential nitrification and other soil variables were measured over time in mulched, grass-sown, and fallow soils at two temperatures; and (3) a microcosm study of whole soils and clay/silt fractions comparing abundances of AOB, AOA, and a rare lineage of AOA in the presence and absence of added ammonium. Diversity of AOA was determined after generating clone libraries of genes encoding ammonia monooxygenase subunit A (amoA), while abundance of AOP was determined using quantitative PCR. In the first study, AOA community structure in gravel-mulched soils was significantly different from that in the unmowed "parent" soil, and AOA abundance was lower under bark mulch than under all other treatments. The abundance of AOB was similar in all treatments. In the second study, soil cover and temperature significantly affected the abundance of AOP over time. At both temperatures (18 and 28°C) AOA abundance was greater than AOB in all treatments. Whereas AOA abundance declined in all soils, AOB increased in mulched soils at 18°C while remaining similar in fallow and grass-sown soils. Due to overall lower abundance of AOB relative to AOA, transcriptional activity of AOB was not detectable, compared to AOA transcript levels, which were higher at 18°C than at 28°C. Further, a correlation was found between AOA abundance and potential nitrification at 18°C. In study 3, incubation of whole soils and silt/clay fractions resulted in the enrichment of a lineage of AOA sequences that had not been detected in previous clone libraries. Abundance of these sequences, which were more closely related to 1.1a crenarchaea than to the commonly recovered 1.1b and 1.3 sequences representative of soils, increased during incubation as pH decreased. These studies demonstrate different responses by AOA and AOB to mulching in urban environments and increase our knowledge of the environmental factors influencing their abundance and activity. |
