Previous studies emphasized that microbiota change depending on whether it is associated with solid particles or liquid fractions. As a consequence, the mode of manure application will likely to influence the microbial load in the cropland receiving manure as fertilizer. Both liquid and solid manure are applied as fertilizer in developing as well as developed countries; however, a detailed research in terms of microbial communities of compost manure and irrigation manure is rare—if not unavailable. Increasing public concern with regards to the microbial load in manure fertilizers and associated health risks necessitates the scope of such studies. Moreover, the trend in dairy industry shows that larger dairies, which confine the relatively large animal population in limited acreages, are more efficient than smaller dairies, and their number is increasing consistently. This means that the manure production in future dairy farms will increase as a result of higher animal density in a relatively limited area. Eventually, the increased manure production will be applied in cropland with or without treatment. There are many treatment options for manure, including anaerobic digestion, composting, lagoon,and drying, and the impacts of these methods on microbial population are relatively unknown at a large scale. In addition to manure treatment methods, both environmental and dairy farm specific factors influence the microbial communities in manure. Previous studies, rolling grow tables which have explored the microbial community in anaerobic digestion treatment of various waste including sludge, dairy manure, and slaughterhouse waste, indicated the presence of microbial communities of Bacteroidetes, Proteobacteria, Firmicutes, Chloroflexi, Spirochetes, Clostridia, and Synergistia.
Other studies reporting the microbial population of cow gut indicated the presence of various microbial communities including Spirochaetes, Flavobacteria, Sphingobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Proteobacteria species. Of these, all studies dealing with animal waste-borne microbial pathogens indicated that animal waste may act as a reservoir of human pathogens, and it has a potential to contaminate ambient water resources and pose risk to public and animal health.The risk of microbial pollution caused by the application of manure fertilizer can be minimized by improving the existing understanding of microbial population in manure, and the effects of available treatment methods, which are in general used or recommended. This reconnaissance research based on our hypothesis proved that a relatively large microbial population persists in manure even after treatment. Regardless of composting, drying, solid-liquid separation, and lagoon, a diverse microbial population that includes pathogenic bacteria resides in manure, and the elimination of these microbial pathogens in manure requires further research. The ranking of top 15 species in FP and CP is shown in Table 1. In general, the abundance of bacteria for FP and CP was different than the abundance in FM, PL, and SL . As an example, the top right corner showed the high abundance of microbial communities mostly in CP and FP, and these microbial communities were less abundant in top left corner of heat map mostly showing FM, PL, and SL . Similarly, species such as Desulfobulbus, Bacteroidetes, Clostridiales, Clostridium, and Ruminococcaceae were more abundant in FM, PL, and SL than in CP and FP . A heat map displaying the bacterial community in liquid samples and solid samples and corresponding PCA plots are shown in supplementary figures . Considering that manure is abundantly used as fertilizer, we hypothesized that the methods of manure handling may have different impacts on microbial population in liquid manure.
We examined the top 15 microbial communities in liquid manure samples obtained from lagoons. Table 2 indicates the rankings of top 15 microbial communities in FM, PL, and SL samples. In PL, Bacteroidetes, Ruminococcaceae, and Cloacibacillus accounted 10.6%, 6.7%, and 4.5%, respectively. The unclassified bacteria in PL accounted 12.4%. Compared to PL, the three most abundant species in FM were Ruminococcaceae, Clostridium, and Flavobacteriaceae accounting for 8.9%, 5.1%, and 2.8%, respectively. The unaccounted bacteria in FM were 18.1%. The abundance of the top three species in SL samples was 9.8%, 7.6% and 2.6%, respectively. Moreover, the pathogenic bacteria of genus Clostridium persist in all three types of liquid samples . Compared to liquid manure samples, this population was not as dominant in solid manure samples. Solid manure, which was collected in this study, had been passed through either a compost or piling system. One plausible reason could be ascribed to the elevated temperature of manure piles. In general, the temperature profile of compost piles reaches to 55–60˚C, while the temperature of lagoon manure remains low . Considering our sampling strategy, which involves collecting samples from multiple dairies, certain differences in microbiota among solid and liquid samples are expected, and results are tabulated in Tables 1 and 2. The ranking of top 15 species in overall solid and liquid samples was developed, and results are shown in Table 3. The common species in solid and liquid samples include Flavobacteriaceae, Ruminococcaceae, and Pseudomonas. As asserted in our hypothesis, the level of microbial population in manure fertilizer changes with the mode of samples , which indicates that the treatment methods such as composting may have different impacts on manure in terms of microbial population compared to lagoon system. The results listed in Table 3 and Fig 5 prove our hypothesis to be true. Overall results showed that manure pile samples cluster together, while the flushed manure and lagoon samples cluster together.
Additionally, fresh solid samples cluster with the flush manure samples, indicating a certain degree of microbial commonality in untreated fresh liquid and solid samples. The distinct microbial communities in solid and liquid samples might be attributed to the varying effects of the anaerobic process in lagoon environment and composting process in the pile system. Interestingly, fresh piles and old piles did not show considerable differences in microbial communities, which suggest a need for further investigation to understand the effect of manure drying and composting on the change in microbial communities. In general, primary lagoon samples showed relatively high clustering. Secondary lagoon samples were less varied, which suggest that over time, microbial communities in lagoon environment develop similar profiles. Future studies focused on understanding the effect of manure retention time in lagoon microbial community and functional profile can provide additional insights needed for evaluating the microbiota of manure fertilizers. The results of this study suggest that the microbial diversity can potentially change during manure handling, and adapting suitable methods may influence cropland soil microbiota positively.Excessive application of dairy manure as fertilizer is considered to be a cause microbial pollution in ambient water. To understand the potential impact of dairy manure application as fertilizer in terms of microbial pollution and diversity, here we studied the microbiome of dairy manure under various treatment conditions. Analysis was performed on the flushed manure, solid manure, and manure of lagoon systems. The 16S rRNA-based microbial analysis demonstrated that a large, diverse bacterial population inhabits the manure and changes with manure treatments. Results showed a considerable difference in population among microbiomes of liquid and solid manure. The microbiomes of primary and secondary lagoon manure were comparable. The microbial populations of fresh manure piles and old manure piles were similar, which might be attributable to a lesser impact of composting and drying under the studied conditions. The considerable differences among microbiomes of liquid and solid samples indicate that the application of solid manure as fertilizer may have different impacts on cropland in terms of microbial population compared to when liquid manure is applied as fertilizer.This thesis deals with two important trends in the U.S. dairy industry: 1) increases in farm size, and 2) the increases in prevalence of female dairy farm operators. This research explores detailed data on farm size changes in major U.S. dairy states and document consolidation and other trends in the patterns of dairy farm size distributions. The dairy industry is of interest, not only because it is an important industry measured by production value, flood drain table but also because of its environmental and social importance. Declines in the number of dairies have raised concerns based on their impact on rural communities, particularly movement of dairies out of local regions and, the potential fall in local employment opportunities. New data on farm operator characteristics allow us to better analyze the trends of gender demographics and the influence of operators’ ages relative to farm size. There has been very little economic research related to the increasing role of female operators in the dairy industry. Trends toward more women operators and fewer dairy farms suggests correlations between the role of women in the dairy industry and herd size per farm and other farm characteristics. Looking overall at U.S. trend in operations with milk cows, Figure 1.1 shows that since 1982, the number of operations with milk cows has decreased rapidly and the average number of milk cows per farm has increased. This graph describes a trend of consolidation in the dairy industry, as defined as operations with milk cows. Despite the slight decrease in number of milk cows there has been an increase in the U.S. milk production . These changes characterize the consolidation within the dairy industry.These national trends mask large differences by state. Some states, such as California, has seen growth of herd sizes into the range of 2,000 or more milk cows per farm. Other states, such as Wisconsin have experienced equally rapid increases in herd size per farm in percentage terms, but herd sizes of larger farms in Wisconsin are in the range of 500 cows per farm. Consolidation is common in other farm industries. An important contribution of this thesis is to document and characterizes this trend over time for an important industry, which is of significance to agricultural economic research.
Consolidation may have allowed dairies to capture improved productivity and efficiency on the farm. How dairy farm size changes in response to these and other factors are important in considering future trends in farm size and their impact on milk production in the United States. My research seeks to help explain recent patterns of farm size change in the dairy industry, considering trends in operator characteristics and management, while accounting for regional differences. The share of women dairy farmers has increased. Historically, farming has been a stereotypically male occupation. Despite contributing to farm production and farm management, surveys, and censuses, have been limited in their collection of data on the contributions of women as farm operators. I hypothesize that some of growth in female contribution to farm operation is due to changes in social and gender norms in reporting. One contribution of my research is to attempt to separate, to the extent possible, changes in management and operations on dairy farms from how such activities are reported. Demographic trends in farm operation and management are important because they help researchers and policy makers get a better sense of who runs the operations in an industry by age, gender, and other characteristics. The dairy industry remains predominately male. However, since 2002, there has been a substantial increase in the share of women dairy farm operators and an increase in the absolute number of dairy farms with at least one female operator in many places. The share of commercial dairies with at least one female core operator has increased across all states, except New Mexico. New York saw the largest increase in the share of commercial dairies with at least one female core operator from 36% to 55%. California saw a 40% increase in the share of commercial dairies with at least one female core operator. This trend, which has occurred while dairy farm consolidation has proceeded at a similar pace suggests that the participation of female dairy farm operators may positively affect dairy farm herd size and economic viability.As noted in the previous chapter, for the statistical estimation in the thesis I will utilize data for the USDA COA. Under “Census of Agriculture Act of 1997”, The COA is a federally mandated Census of all U.S. farms and ranches every five years, and it captures individual farm-level data on production costs, operators’ characteristics, land use, number of milk cows, revenue, etc. The data and statistics resulting from this Census are reported at the county or state level and research using the individual level data is restricted to USDA research or special request for non-USDA entities. I was given special permission to have access to individual farm-level data for census years of 2002, 2007, 2012, and 2017 from the following specified states: California, Idaho, New Mexico, New York, Texas, and Wisconsin.