Widespread contamination of groundwater by MTBE has triggered the exploration of different technologies for in situ removal of the pollutant. After laboratory studies revealed that bacterial strain PMl is capable of rapid and complete MTBE biodegradation, the organism was tested in an in-situ bioaugmentation field study at Port Hueneme Naval Base, Oxnard, CA. Two small pilot test plots (A and B) located down gradient from an MTBE source were injected with pure oxygen at two depths. One plot (B) was also inoculated with Strain PMl. MTBE concentrations upstream from plots A and B initially varied temporally from 1.5 to 6 mg per L. By six months after treatment began, MTBE concentrations wells downstream from the injection bed substantially decreased in the shallow zone of the groundwater in both plots, even in the absence of Strain PM 1. In the deeper zone, downstream MTBE concentrations also decreased substantially in Plot A and to lesser extent in Plot B. Difficulties in delivery of oxygen to the deep zone of Plot B, evidenced by low dissolved oxygen concentrations, are likely responsible for low rates of MTBE removal at that location. We measured the survival and movement of PMl in groundwater using three different methods for detection of PMl rDNA sequences: TaqMan quantitative peR, Denaturing Gradient Gel Electrophoresis (DGGE), and Intergenic Spacer Region (ITS) analysis. A naturally occurring organism with >99% rDNA sequence similarity to Strain PMl was detected in groundwater collected outside the test plots. Changes in the groundwater microbial community were also monitored over time using ITS, a PCR-based DNA fingerprinting method. The largest differences in the microbial community profiles were observed between the shallow and deep groundwater samples, regardless of whether they were from plot A or B.

This dissertation investigates how management with different combinations of practices, namely mineral N fertilizer, cover cropping, compost amendment, furrow irrigation and subsurface drip irrigation have impacted soil carbon, nutrients, and microbial communities in a 25-year long term experiment. First, I investigated how subsoil carbon stocks have increased under a combination of compost and cover crops after 25 years. I found that a potential synergistic effect between soluble C, soluble N and soil pores created by cover crop roots that allowed for greater C and N transport to subsoils. This transport of soluble C and N was associated with reduced microbial stress levels, and potentially longer C residence times. Secondly, I looked at how soil microbial community structure and microbial functional potential changed after 20 years of management practices intended to improve soil health. I found significant changes in functional potential for C breakdown and N transformation, but no significant changes in microbial community structure. These changes in functional potential were associated with changes in soil health measurements and may indicate the potential impact of practices intended to improve soil health. Finally, I examined how soils under a combination of compost and cover crops changed carbon and nutrient distribution under 5 years of subsurface drip irrigation (SDI) and furrow irrigation. I found that soils under SDI and furrow irrigation only differed in carbon and nutrient distribution in the top 30 cm, and that furrow irrigation was associated with a loss of surface organic matter after 5 years while SDI was not. The differences in spatial distribution and amount of water under SDI vs furrow irrigation may not significantly reduce the amount of carbon and nutrients stored in subsoils but may have an impact on surface organic matter content. In conclusion, the impacts of management practices on soils with similar climate and mineralogy may be difficult to measure over the course of a single season, but these impacts may accumulate over multiple years to result in significant shifts in soil edaphic and microbial properties.

Soils contain diverse and dynamic communities of microbes that interact with, and influence, microbiota in and on plants, animals, and humans. These exchanges, such as between soil and human microbiota, are part of a vast, integrated microbial ecosystem that underpins much of terrestrial life on Earth. This dissertation addresses relationships between soil microbiota and human microbiota, and their connections with human health. I approached these investigations by collecting and compiling a range of data spanning soil microbiota, child gut microbiota, health and disease factors, household characteristics, and biophysical landscape characteristics among 144 households across three rural counties in western Kenya. Using these data I first investigated the variation in gut microbial communities between children living in different rural environments, including agriculture, rural settlements, and uncultivated forest and shrubland landscapes. Although we did not find differences in child gut microbial diversity between children from these different landscapes, we found (1) significant differences in abundances of specific gut microbial taxa that are associated with health and disease, and (2) landscape-level differences in the taxa that discriminate children with a recent diarrheal episode from those without. These findings are initial evidence of a potential landscape association with the child gut microbiota, with implications for understanding childhood diarrheal disease burden. Next I investigated the relationship between the child gut microbial community and the soil microbiota in children’s households using a microbial source tracking approach. I found that the proportion of the gut microbiota attributed to soils (S2F proportion) varied among households, and in some was greater than a third, indicating a significant relationship between soil and gut microbiota at the household level. Furthermore I observed that S2F proportions were notably higher in households where I collected data later in the region’s seasonal rainy-dry cycle. Using three complementary regression modeling approaches, I examined potential correlates of S2F proportion from among the household and landscape biophysical data. I found stronger associations among soil and climate characteristics than among household and social factors, and soil pH and seasonal precipitation had the greatest association with S2F proportion. These results demonstrate the potential involvement of seasonal climate and soil properties in the relationship between the child gut microbiota and soil microbiota. Finally, I evaluated the capability of the soil and fecal microbiota to predict child and household characteristics using a series of machine-learning based classifier models. Utilizing only the fecal microbial data, the classifier successfully identified household-level landscape classes. With soil microbial data, the model successfully classified households by their landscape classes, soil classes, drinking water source, and season of sampling. A relatively small number of soil taxa were more important in the model’s performance, including taxa commonly found in the human gut. These findings indicate that a seasonal change in soil microbiota may influence the composition of the child gut microbiota in rural households. Altogether, this research presents novel evidence that household- and landscape-level exposures, including to soil microbiota, are strongly associated with the human gut microbial community, and that these associations hold potential implications for health and disease.

Agricultural stakeholders are becoming increasingly aware of the need for sustainable food systems. In a shift from an agricultural paradigm that prioritizes yield, there is now growing interest in multifunctional food systems that simultaneously promote environmental integrity while also providing adequate yield and nutrition. An investigation into how current and proposed alternatives to annual grain systems address the multifaceted objectives of food system sustainability is necessary given that annual grains currently comprise nearly 70% of earth’s cultivated land and provide majority of the world’s food. Furthermore, it is crucial to conduct research on these grain systems in highly productive and economically valuable agroecological regions, such as California (CA). As the largest and most diverse agricultural state in the U.S., CA provides market opportunities while also heralding what current and future food systems must overcome to maintain food supply amid projected water and weather extremes. Thus, we investigated the multifunctionality of a tilled annual wheat system and two proposed alternatives, no-till annual wheat production and novel perennial grain production, in the Mediterranean climate of California. We measured plant and soil parameters for three years in intermediate wheatgrass or IWG, no-till annual wheat, and tilled annual wheat at four nitrogen rates. IWG had significant fluctuations in aboveground biomass (AGB) and had the highest soil carbon (C) mineralization at each soil depth. No-till wheat had stable AGB and the highest soil C stabilization and microbial biomass in the topsoil, which suggests plant productivity and a lack of soil disturbance over time are key factors underpinning enhanced soil C stabilization and gains in microbial biomass in the topsoil. Yield stability, soil carbon storage and nitrogen use efficiency (NUE) were then compared among the three systems using a multifunctionality framework. IWG had large interannual fluctuations in grain yield and NUE, while annual wheat (till and no-till) had stable grain yields and higher NUE than IWG. Soil carbon gains in IWG and no-till wheat relative to the tilled wheat were contingent upon N fertilization and constrained to the topsoil, while tilled wheat stored carbon at depth and across the whole soil profile. Finally, soil microbial community composition and soil carbon were compared in tilled annual wheat and IWG during the final year of the experiment. Bacterial community composition was more sensitive to soil depth than crop type, whereas fungal community composition was influenced largely by crop type. While the fungi : bacteria ratio was higher in IWG at deep soil depths, tilled annual wheat had a higher abundance of fungal taxa known to positively correlate with soil carbon and higher soil carbon mass than IWG at the 60-90 cm soil depth. The two major takeaways from this three-year field experiment were: 1) sampling the subsoil (> 30 cm) is crucial when comparing system-level soil carbon storage potential of annual and perennial grain systems; and 2) plant productivity underpins numerous components of agricultural multifunctionality and thus plant adaption is of utmost importance when designing and implementing future food systems.

Methyl bromide is highly effective in reducing soil pathogens. Although its use was to be phased out completely in the United States by Jan. 1, 2005, due to environmental concerns, a 1-year critical-use exemption will allow tree fruit growers to use the fumigant through the end of the year. To explore possible replacements for methyl bromide, we compared the effects of pre- and postplant treatments and amendments on soil microbial communities and tree vigor in a replanted peach orchard. Both soil sterilization treatments and organic carbon amendments changed the composition of microbial communities in the soil. High microbial biomass is generally considered beneficial to agricultural soils; we found that it was usually highest in soils that received the organic carbon amendment and lowest in those with soil sterilization. However, tree vigor was highest with the sterilization treatments. The effects of a microbial inoculants/organic carbon combination on microbial communities and plant vigor were no different from simply adding organic carbon.