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Methods linking environmental function and microbial community composition are limited by phylogenetic resolution and throughput time. Denaturing gradient gel electrophoresis (DGGE) allows for resolution of ammonia-oxidizing bacteria strains separated by as little as one base pair (bp) in 16S rRNA gene sequence but is low throughput. In contrast, microarrays are high throughput. We have designed a microarray platform to identify the majority of environmental strains of betaproteobacterial ammonia oxidizers using signature oligonucleotide sequences. Seventy-seven target sequences or single-nucleotide polymorphisms (SNP) were derived from 183 betaproteobacterial ammonia oxidizer 16S rRNA gene sequences representing the genera Nitrosospira and Nitrosomonas of the β sub-class of Proteobacteria and the cluster groups of strains within each genera identified using DNA homology values. These sequences were obtained from the National Center for Biotechnology Information database. Templates isolated from pure cultures of betaproteobacterial ammonia oxidizers and soil samples incubated with and without dairy slurry were amplified using primers CTO189f and CTO654r. Amplicons were analyzed via DGGE and microarray hybridization. Mixtures of pure culture strains of betaproteobacterial ammonia oxidizers were used to simulate environmental samples containing a known number of sequences and template concentrations. Our DNA oligonucleotide microarray demonstrated highly specific detection of individual betaproteobacterial ammonia oxidizer strains amplified from pure cultures, model communities, and soil samples and provided resolution of community composition comparable to that of DGGE. High-throughput analyses of betaproteobacterial ammonia oxidizer communities will further our knowledge of their ecology and link process level functions to management practices such as dairy slurry applications and specific strains of betaproteobacterial ammonia-oxidizing bacteria.

Humic acid (HA) is an important soil component that can improve nutrient availability and impact other important chemical, biological, and physical properties of soils. We investigated the lability of phosphorus (P) in the mobile HA and calcium humate fractions of four rice soils as measured by orthophosphate-releasing enzymatic hydrolysis and UV irradiation. Enzymatic hydrolysis releases hydrolyzable organic P, and UV irradiation abiotically releases P by breaking down phosphate-HA complexes. Less than 25% of the P in these fractions was detected in the soluble orthophosphate form (detectable soluble Pi). Enzymatic incubation increased detectable soluble Pi to 60% of total P. Treatment by UV irradiation alone released an additional 5% to 20% of humic-bound P compared with the untreated fractions. However, treatment by both UV irradiation and enzymatic hydrolysis released 0% to 14% of humic-bound P more than the amount of organic P that was enzymatically released from nonirradiated samples. The smaller amounts of P that were released from some humic fractions by both UV irradiation and enzymatic hydrolysis than by UV irradiation alone indicated some overlap between UV-degradable organic P and enzymatically labile organic P. Generally, about one half to two thirds of humic P in these rice soils was labile. These data demonstrated that either assumption that no P in humic fractions was labile P or all P in humic fractions was labile is not true. The lability of humic-bound P should be experimentally evaluated as reported in this work.

Management practices that influence the quantity of C inputs returned to the soil from cropping systems and compost applications alter subsequent biotic activity broadly, contribute to seasonal fluctuations in nutrient dynamics, and may increase C sequestration. The effects of crop rotations and compost applications on soil-C sequestration and decompostion, and the turnover time of C 4 -derived corn C were assessed via changes in the C content and 13 C values of particulate organic matter (POM) and total soil organic C (SOC). The majority of organic inputs entered the POM fraction, defined as the sand-sized soil separates remaining on a 53-μm sieve after removal of residues (>2 mm), dispersion in 5% sodium polyphosphate, and 12 h of shaking. Before the application of compost to soil, 85% of the C in the compost material was classified as POM. Measurements of POM-C in the soil were 45% higher and SOC was 16% greater where compost was applied in place of N fertilizer. Addition of compost to POM-C diminished the value of POM as an indicator of short-term changes in nutrient dynamics. However, POM-C remaining from compost applications made during the period 1993 to 1997 may be an indicator of enhanced macroaggregate stability: improved soil tilth and the retention of soil C and N. The turnover time of C 4 -derived C in the POM fraction was 11 years compared with 22 years in SOC. The presence of compost C did not affect the turnover time of corn-derived C. High cropping intensity and chisel plow management increased C sequestration relative to the preceding alfalfa management.