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Soil chemical properties during the transition from conventional to organic and low‐input farming practices were studied over 8 yr in California's Sacramento Valley to document changes in soil fertility status and nutrient storage. Four farming systems differing in crop rotation and external inputs were established on land previously managed conventionally. Fertility in the organic system depended on animal manure applications and winter cover crops; the two conventional systems received synthetic fertilizer inputs; the low‐input system used cover crops and animal manure during the first 3 yr and cover crops and synthetic fertilizer for the remaining 5 yr. At 4 and 8 yr after establishment, most changes in soil chemical properties were consistent with predictions based on nutrient budgets. Inputs of C, P, K, Ca, and Mg were higher in the organic and low‐input systems as a result of manure applications and cover crop incorporations. After 4 yr, soils in the organic and low‐input systems had higher soil organic C, soluble P, exchangeable K, and pH. Ceasing manure applications in the low‐input system in Year 4 resulted in declining levels of organic C, soluble P, and exchangeable K. Crop rotation (the presence or absence of corn) also had a significant effect on organic C levels. Differences in total N appeared to be related in part to inputs, but perhaps also to differing efficiency of the farming systems at storing excess N inputs: the low‐input system appeared to be most efficient, and the conventional systems were least efficient. Electrical conductivity (EC), soluble Ca, and soluble Mg levels were tightly linked but not consistently different among treatments. Relatively stable EC levels in the organic system indicate that animal manures did not increase salinity. Overall, our findings indicate that organic and lowinput farming in the Sacramento Valley result in small but important increases in soil organic C and larger pools of stored nutrients, which are critical for long‐term fertility maintenance.

Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (-C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.