Doctor of Philosophy / Department of Plant Pathology / Ari Jumpponen / Megan Kennelly / Soil microbial communities play fundamental and complex roles in the productivity of agriculture. However, we still have a limited understanding of the response of microbial communities to different farming systems, such as organic and conventional fertility management regimens. We applied high-throughput sequencing to develop a better understanding of how soil microbial communities (bacteria and fungi) in vegetable production respond to organic or conventional soil fertility management. Specifically, my three studies examined the following questions: 1. How do soil microbial communities from cDNA and DNA samples compare in organic and conventional fertility treatments? 2. How do soil microbial communities in a tomato cropping season respond to long-term organic vs. conventional soil fertility treatments? 3. How do soil bacterial and fungal communities respond to high tunnels, plastic mulch and organic amendments across a tomato cropping season? The first two questions were addressed at the Kansas State University Horticulture and Extension Center in Olathe, KS, using organic and conventional field plots with three levels of fertilizer. We sampled the plots during the development of a tomato crop. The third question was addressed at a commercial farm in Lawrence, KS, during its transition to organic vegetable production, during a tomato crop. The Lawrence experiment included as treatments field plots versus high tunnels, and three organic nutrient amendments. We used 454-pyrosequencing of bacterial and fungal ribosomal markers to compare total resident (DNA) and active microbial communities (cDNA, which is DNA synthesized from a single stranded RNA template) for our first question. We used Illumina MiSeq metabarcoding of bacterial and fungal ribosomal markers for our second and third questions. In all three studies we evaluated bacterial and fungal community responses using Simpson´s diversity index, Simpson´s evenness and richness for each experiment. For the first question, when we compared DNA and cDNA, bacterial diversity was higher in cDNA samples from organic compared to conventional management. In addition, fungal diversity from cDNA samples was higher than from DNA samples. In contrast, in the second question, bacterial and fungal diversity indices did not differ in the tomato crop under organic and conventional management systems. For our third question, high tunnels did not affect bacterial or fungal diversity. Use of plastic mulch for a tomato crop in open field plots did not affect bacterial richness, but decreased fungal richness compared to open field plots without plastic mulch. High-throughput sequencing provides a new perspective on the structure and dynamics of these communities. Information from this approach will ultimately improve our ability to manage soil for sustainable productivity by promoting beneficial microorganisms and suppressing pathogenic ones.

Typescript (photocopy). / Digitized by Kansas Correctional Industries

In Lombok (Indonesia), annual cropping patterns in irrigated areas are divided into three cropping cycles of four months each. In better irrigation schemes, there are normally two irrigated flooded-rice crops, i.e. wet season and dry season lowland rice crops in sequence, followed by one non-rice crop cycle during the driest months (this is referred to as the twice-rice system). In less developed irrigation schemes, one lowland rice crop is normally grown during the rainy season, followed during the driest months by two cycles of non-rice crops, or a non-rice crop and a fallow (this is referred to as the once-rice system). In rainfed areas, especially in the vertisol soil areas, there are upland rice systems in the highland or hillsides, and “Gora” (dry seeded-flooded) rice systems in the lowland. In this area, rice is grown only once a year during the rainy season of the monsoon. Farmers in Lombok do not normally fertilise the non-rice crops such as soybean and mungbean grown following rice, and application rates of fertiliser to rice have fallen since the economic crisis in 1998. Therefore phosphorus (P) deficiency may be expected, which may explain the very low yields of soybean and mungbean achieved by farmers in Lombok. With low P, arbuscular mycorrhizas (AM) might be expected to play an important role in plant nutrition, but inoculation with arbuscular mycorrhizal fungi (AMF) increased root colonisation and yield of these crops in a recent field experiment in Lombok. There had been no survey of AMF populations in rice-based systems in Lombok prior to the work reported here, and little such work anywhere internationally. Therefore, an extensive survey was conducted in Lombok on the two main soil types with rice-based systems. Another field survey was conducted in the Riverina rice-growing area (Australia), as a comparative study to the Lombok survey. In Lombok, rice systems with longer total annual flooding duration had lower populations compared with upland or Gora rice systems. It was therefore suggested that the lower colonisation level in flooded rice was due to the flooded conditions, as well as soil chemical properties associated with flooded conditions, rather than the rice plant itself. There are options for improving AMF population for better growth of non-rice rotation crops, or even for rice crop in Lombok as fertilisers become less affordable and their use on flooded rice is declining. The easiest option is to inoculate AM fungi in the nursery or to make nursery beds in a paddock previously cropped with AMF-stimulating species, such as soybean, to start infection on rice seedlings, which should be better with a dry nursery. The second option is to modify the technique of growing rice, such as applying the SRI (System of Rice Intensification) principles, in which rice is grown without flooded conditions but intermittent short flooded and upland conditions. This will keep the soil in an aerobic condition much of the time and should facilitate the development of beneficial microbial populations and activities in the soil, such as AMF and nitrogen fixers. The SRI method has been reported to increase rice yield dramatically, even in soil with low fertility levels. / Doctor of Philosophy (PhD)

This thesis develops two related themes.The first is that participatory approaches to agricultural research and extension can provide a sound process for all stakeholders to learn how to develop more sustainable agriculture. The second is that appropriate levels of participation can be used to link knowledge from three important sources: local knowledge, scientific knowledge and experiential knowledge.The thesis develops these two related themes by examining the inconsistencies between esposed theories of participatory approaches (i.e.intended behaviour) and theories in action (i.e. what is actually practised).The study was based upon the work of a major research, development and extension (R, D and E)project known as the Western Farming Systems Project (WSFP),which was concerned with the development of sustainable rotations and cropping practices in south western Queensland and north western N.S.W. between 1994-1999. The study was conducted in the Balonne Shire, centred on the town of St. George, Queensland, Australia. / Master of Science (Hons)

The major objective of this study was to determine whether or not food production per unit space can be increased by intercropping summer squash (Cucurbita pepo L.) with mung bean (Phaseolus aureus Roxb.) or pinto bean (Phaseolus vulgaris L.), and to identify the factors associated with growth and yield of summer squash, mung bean and pinto bean under intercropping regimes. A series of experiments were conducted during the period: Summer, 1977 to February, 1980, at both the University of Arizona, Experiment Station, Marana, and in a greenhouse at the University of Arizona, Campbell Avenue Farm. Intercropping mung beans or pinto beans with summer squash in either adjacent rows or within the row did not significantly influence the bean seed yield, although adjacent row intercropping tended to outyield the within row intercropping. Summer squash yield was more significantly reduced by within row intercropping than adjacent row intercropping. Root and shoot dry weights of container grown mung beans or pinto beans were significantly reduced by intercropping with summer squash, but summer squash root and shoot dry weights were not significantly affected. Intercropping summer squash with either mung beans or pinto beans was more beneficial at low nitrogen and phosphorus fertility levels than at higher levels. Summer squash fruit and shoot dry weights per unit space increased with increase in plant population, but they were not significantly influenced by intercropping with either mung beans or pinto beans. Intercropping high population summer squash with low population mung beans or pinto beans reduced both seed and biomass yields of the beans. However, increasing the bean plant populations had no influence on their seed and biomass yields. Harvest index of mung beans or pinto beans was neither influenced by intercropping with summer squash nor by increasing the bean plant population. Leaf area per unit space increased with increase in plant population, but intercropping had no significant influence in all cases. Specific leaf weight, leaf area-to-leaf weight ratio, and leaf weight ratio were neither influenced by intercropping nor by varying the plant populations. Mung bean seed yield was significantly to highly significantly correlated with harvest index and biomass, but highly negatively correlated with leaf area index, while pinto bean seed yield was very highly correlated with biomass and harvest index. Summer squash fruit yield was significantly to highly significantly correlated with shoot dry weight, leaf area, leaf area index and specific leaf weight. Accumulations of nitrate nitrogen and/or phosphorus in the leaf petioles of mung beans, pinto beans or summer squash were neither influenced by intercropping nor by increasing the nitrogen or phosphorus fertility levels. The economic yields of field grown mung beans, pinto beans or summer squash were not significantly correlated with petiole accumulations of nitrate nitrogen and phosphorus. While summer squash exhibited autotoxicity, mung bean root leachates tended to promote growth of pinto beans and summer squash. Food production per unit space was increased by as much as 76% by intercropping summer squash with pinto beans, while intercropping summer squash with mung beans increased food production by 63%. Under certain plant combinations, dry matter yield per unit space was increased by as much as 185% by intercropping summer squash with mung beans, while intercropping summer squash with pinto beans increased the dry weight yield by as much as 81%.

This item was digitized as part of the Million Books Project led by Carnegie Mellon University and supported by grants from the National Science Foundation (NSF). Cornell University coordinated the participation of land-grant and agricultural libraries in providing historical agricultural information for the digitization project; the University of Arizona Libraries, the College of Agriculture and Life Sciences, and the Office of Arid Lands Studies collaborated in the selection and provision of material for the digitization project.

In consideration of the chronic poverty of farmers in Rwanda as well as in other developing countries where self-sufficient agriculture is practiced, this study examines what the well studied theory of specialization and trade, if implemented, could bring to Rwandan farmers in terms of production and profits. / To attain this objective, a spatial optimization model with linear programming was built and used to maximize the potential production and net returns which were compared to those from the traditional system. The model was built in a way that it also shows the pattern of trade and quantities traded. / The results show that a regional specialization system would allow, on the national level, more production, higher net returns, and more trade than the traditional system (self-sufficient agriculture) as expected according to the theory of specialization and trade. Nevertheless, the net return in some regions decreases in the new system, which necessitates a compensation plan for those regions. / However, it has to be noted that despite these gains, the adoption of the new plans requires a consideration of many other factors that are not covered in this study. Of those factors, the most obvious are the need to improve the transportation and marketing infrastructure, changing farmers' attitudes and objectives towards commercial agriculture, and securing equity, security, and sustainability in the system.

This thesis examined the effect of continuous row-cropping on soil structure measured by bulk density and compaction ratings. Undisturbed core samples were collected from the selected sample sites to determine the bulk density. Compaction ratings were obtained by using a Proctor Penetrometer. A total of 192 soil samples were collected for this investigation. Comparisons of mean bulk densities, mean compaction ratings, and mean moisture percentages of the surface and Bt horizons of Blount and Pewamo soils in Delaware County, Indiana under three different field conditions: woods (untilled), field cultivated fields (continuous row-cropped), and plowed fields (continuous row-cropped) were made. This was done by calculating F-ratios and Bayesian Least Significant Difference ratios. Pearson's Product Moment Correlation' Coefficients were also calculated between selected parameters of the data. Conclusions drawn from these statistical analysis were discussed.

Thesis (Ph.D.)--Industrial and Systems Engineering, Georgia Institute of Technology, 2007. / Committee Co-Chair: Griffin, Paul; Committee Co-Chair: Serban, Nicoleta; Committee Member: Liang, Steven; Committee Member: Sharp, Gunter; Committee Member: Tsui, Kwok-Leung

Thesis (Ph.D.)--University of Missouri-Columbia, 2004. / Typescript. Vita. Includes bibliographical references. Also available on the Internet.