Effects of organic fertilization on soil bacterial community structure in incubated microcosms

Addressing the growing demand for food from a burgeoning population requires agricultural methods that sustainably support increases in crop production while maintaining environmental health. Agricultural practices that include the use of compost, in lieu of mineral fertilizers, have been shown to reduce environmental impacts and improve soil health. Producers seeking to improve sustainability through compost use are challenged by the chemical form and availability of nutrients in organic amendments, limiting their ability to predict when nutrients will be available to crops. To better understand nutrient dynamics in soils amended with organic fertilizers, we compared the soil microbial community response to amendments with differing carbon and nitrogen content. Composted horse manure was chosen to represent an organic high carbon amendment, and alfalfa hay was chosen to represent a high nitrogen amendment. Amended soils were incubated for 97 days and destructively sampled on seven progressively longer incubation intervals. DNA was extracted for microbial community characterization, and measurements of nitrogen, carbon, and biomass were also compared for all samples. Our results showed significant shifts in soil microbial communities due to both time and amendment. Nutrient release was highly associated with amendment composition, with alfalfa showing the greatest release of plant available nutrients. We observed complex interactions between soils and amendments, with specific bacteria associated with nitrogen and carbon metabolism. These bacteria are targets for further characterization and better knowledge of their role in decomposition may contribute to the increased use of high organic matter fertilizer by producers and lead to a better understanding of sustainable crop production techniques

Evaluation of Organic Soybean Varieties

According to the USDA National Organic Program, certified organic farmers must source organic seed (seed from organically raised crops). The organic seed industry is currently growing in Iowa and the Midwest. With this growth, organic growers are looking for university-based recommendations on organic varieties to use in Iowa. The Organic Agriculture Program at Iowa State University has been using organic seed at the Southeast Research Farm for 11 years with excellent results

Understanding soil bacterial communities for sustainable agriculture

Nutrient loss from synthetic fertilizer use contributes to poor water quality, conversion of native landscapes to agricultural production reduces biodiversity, and antibiotic use in animal production contributes to antibiotic resistance. Therefore, agriculture can have adverse effects on local and global environments. Soil bacteria mediate processes that can influence the impact of agriculture on the environment. Characterizing soil bacterial communities in response to changes in agricultural management may inform scientific understanding of how management decisions can alter soil bacteria. Several management practices aim to reduce the impact of agriculture on the environment and improve its sustainability. Offsetting synthetic fertilizer use with organic amendments can reduce nitrate losses and improve water quality. However, the microbially mediated and hard to predict the release of plant-available nutrients from organic amendments can limit their adoption and use. Installation of prairie strips as a conservation practice can reduce sediment loss and provide habitat for native animals, improving diversity. However, the impact of prairie strips on the soil bacterial community remains under characterized. Grasses can filter antibiotics and antibiotic resistance genes in runoff water from manure treated fields, though the ability of prairie strips to reduce antibiotic resistance in runoff water is not understood. The experiments described in this dissertation contribute to a scientific understanding of soil bacteria\u27s response to organic amendment and prairie strip installation, as well as the impact of prairie strips on attenuating the transport of manure associated bacteria and antibiotic resistance genes. Soil bacterial communities\u27 response to organic amendments of varying quality was compared against soil receiving no amendment during an incubated microcosm study. Soil bacterial communities exhibited community similarity in two temporal groupings in all amended and un-amended soils. In response to organic several bacterial taxa became significantly more abundant in amended soils and were associated with amendment quality. Alpha and beta diversity of soil bacteria were compared between agricultural soil and prairie strip soil at two sites. Prairie strips examined were less than five years old and did not significantly differ from agricultural soils at the two sites. Bacterial richness, Shannon\u27s diversity, and Simpson\u27s diversity were significantly greater in prairie soils than agricultural soils at one site and only in response to rainfall. The abundance of manure-associated bacteria in runoff water was compared between plots receiving manure without prairie strips and plots receiving manure. Prairie strip appended plots had lower abundances of manure associated taxa and lower detection of antibiotic resistance genes than plots without prairie strips. Conservation practices designed to reduce nutrient loss, such as the use of composts or the installation of prairie strips, are essential practices that can improve agricultural sustainability, yet have impacts on bacterial dynamics that are not well understood. Characterizing bacterial communities in soils under various conservation practices will inform our understanding of how these practices impact the soil bacterial community

RefSoil: A reference database of soil microbial genomes

A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 922 genomes of soil-associated organisms (888 bacteria and 34 archaea). Using this database, we evaluated phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cell genomics in a pilot experiment to sequence 14 genomes. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps

Spatial Structuring of Cellulase Gene Abundance and Activity in Soil

Microbial mechanisms controlling cellulose degradation in soil habitats remains a critical knowledge gap in understanding and modeling terrestrial carbon-cycling. We investigated land management and soil micro-habitat influences on soil bacterial communities and distribution of cellulose-degrading enzyme genes in three bioenergy cropping systems (corn, prairie, and fertilized prairie). Within the soil, aggregates have been examined as potential micro- habitats with specific characteristics influencing resource partitioning and regulation, thus we also investigated genes associated with cellulose degradation within soil aggregate fractions from the fertilized prairie system. Soil bacterial communities and carbon-cycling gene presence varied across land management and soil microhabitats. Examination of genes specifically involved in cellulose-degradation pathways showed high levels of redundancy across the bioenergy cropping systems, but medium macroaggregates (1,000–2,000 μm) supported greater cellulose-degrading enzyme gene abundance than other aggregate fractions and whole soil. In medium aggregates, the enriched cellulose-degrading genes were most similar to genes previously observed in Actinobacteria. These findings represent gentic potential only, and our previous work on the same samples found elevated cellulase exo-enzyme activity in microaggregates. These contrasting results emphasize the importance of measuring community, functional genes, and metabolic potentials in a coordinated manner. Together, these data indicate that location within the soil matrix matters. Overall, our results indicate that soil aggregate environments are hot-spots that select for organisms with functional attributes like cellulose degradation, and future work should further explore micro-environmental factors that affect realized C-cycling processes

Strategies to improve reference databases for soil microbiomes

Microbial populations in the soil are critical in our lives. The soil microbiome helps to grow our food, nourishing and protecting plants, while also providing important ecological services such as erosion protection, water filtration and climate regulation. We are increasingly aware of the tremendous microbial diversity that has a role in soil heath; yet, despite significant efforts to isolate microbes from the soil, we have accessed only a small fraction of its biodiversity. Even with novel cell isolation techniques

Effects of organic fertilization on soil bacterial community structure in incubated microcosms

Addressing the growing demand for food from a burgeoning population requires agricultural methods that sustainably support increases in crop production while maintaining environmental health. Agricultural practices that include the use of compost, in lieu of mineral fertilizers, have been shown to reduce environmental impacts and improve soil health. Producers seeking to improve sustainability through compost use are challenged by the chemical form and availability of nutrients in organic amendments, limiting their ability to predict when nutrients will be available to crops. To better understand nutrient dynamics in soils amended with organic fertilizers, we compared the soil microbial community response to amendments with differing carbon and nitrogen content. Composted horse manure was chosen to represent an organic high carbon amendment, and alfalfa hay was chosen to represent a high nitrogen amendment. Amended soils were incubated for 97 days and destructively sampled on seven progressively longer incubation intervals. DNA was extracted for microbial community characterization, and measurements of nitrogen, carbon, and biomass were also compared for all samples. Our results showed significant shifts in soil microbial communities due to both time and amendment. Nutrient release was highly associated with amendment composition, with alfalfa showing the greatest release of plant available nutrients. We observed complex interactions between soils and amendments, with specific bacteria associated with nitrogen and carbon metabolism. These bacteria are targets for further characterization and better knowledge of their role in decomposition may contribute to the increased use of high organic matter fertilizer by producers and lead to a better understanding of sustainable crop production techniques.</p

Understanding soil bacterial communities for sustainable agriculture

Nutrient loss from synthetic fertilizer use contributes to poor water quality, conversion of native landscapes to agricultural production reduces biodiversity, and antibiotic use in animal production contributes to antibiotic resistance. Therefore, agriculture can have adverse effects on local and global environments. Soil bacteria mediate processes that can influence the impact of agriculture on the environment. Characterizing soil bacterial communities in response to changes in agricultural management may inform scientific understanding of how management decisions can alter soil bacteria. Several management practices aim to reduce the impact of agriculture on the environment and improve its sustainability. Offsetting synthetic fertilizer use with organic amendments can reduce nitrate losses and improve water quality. However, the microbially mediated and hard to predict the release of plant-available nutrients from organic amendments can limit their adoption and use. Installation of prairie strips as a conservation practice can reduce sediment loss and provide habitat for native animals, improving diversity. However, the impact of prairie strips on the soil bacterial community remains under characterized. Grasses can filter antibiotics and antibiotic resistance genes in runoff water from manure treated fields, though the ability of prairie strips to reduce antibiotic resistance in runoff water is not understood. The experiments described in this dissertation contribute to a scientific understanding of soil bacteria's response to organic amendment and prairie strip installation, as well as the impact of prairie strips on attenuating the transport of manure associated bacteria and antibiotic resistance genes. Soil bacterial communities' response to organic amendments of varying quality was compared against soil receiving no amendment during an incubated microcosm study. Soil bacterial communities exhibited community similarity in two temporal groupings in all amended and un-amended soils. In response to organic several bacterial taxa became significantly more abundant in amended soils and were associated with amendment quality. Alpha and beta diversity of soil bacteria were compared between agricultural soil and prairie strip soil at two sites. Prairie strips examined were less than five years old and did not significantly differ from agricultural soils at the two sites. Bacterial richness, Shannon's diversity, and Simpson's diversity were significantly greater in prairie soils than agricultural soils at one site and only in response to rainfall. The abundance of manure-associated bacteria in runoff water was compared between plots receiving manure without prairie strips and plots receiving manure. Prairie strip appended plots had lower abundances of manure associated taxa and lower detection of antibiotic resistance genes than plots without prairie strips. Conservation practices designed to reduce nutrient loss, such as the use of composts or the installation of prairie strips, are essential practices that can improve agricultural sustainability, yet have impacts on bacterial dynamics that are not well understood. Characterizing bacterial communities in soils under various conservation practices will inform our understanding of how these practices impact the soil bacterial community.</p

Understanding soil bacterial communities for sustainable agriculture

Nutrient loss from synthetic fertilizer use contributes to poor water quality, conversion of native landscapes to agricultural production reduces biodiversity, and antibiotic use in animal production contributes to antibiotic resistance. Therefore, agriculture can have adverse effects on local and global environments. Soil bacteria mediate processes that can influence the impact of agriculture on the environment. Characterizing soil bacterial communities in response to changes in agricultural management may inform scientific understanding of how management decisions can alter soil bacteria. Several management practices aim to reduce the impact of agriculture on the environment and improve its sustainability. Offsetting synthetic fertilizer use with organic amendments can reduce nitrate losses and improve water quality. However, the microbially mediated and hard to predict the release of plant-available nutrients from organic amendments can limit their adoption and use. Installation of prairie strips as a conservation practice can reduce sediment loss and provide habitat for native animals, improving diversity. However, the impact of prairie strips on the soil bacterial community remains under characterized. Grasses can filter antibiotics and antibiotic resistance genes in runoff water from manure treated fields, though the ability of prairie strips to reduce antibiotic resistance in runoff water is not understood. The experiments described in this dissertation contribute to a scientific understanding of soil bacteria's response to organic amendment and prairie strip installation, as well as the impact of prairie strips on attenuating the transport of manure associated bacteria and antibiotic resistance genes. Soil bacterial communities' response to organic amendments of varying quality was compared against soil receiving no amendment during an incubated microcosm study. Soil bacterial communities exhibited community similarity in two temporal groupings in all amended and un-amended soils. In response to organic several bacterial taxa became significantly more abundant in amended soils and were associated with amendment quality. Alpha and beta diversity of soil bacteria were compared between agricultural soil and prairie strip soil at two sites. Prairie strips examined were less than five years old and did not significantly differ from agricultural soils at the two sites. Bacterial richness, Shannon's diversity, and Simpson's diversity were significantly greater in prairie soils than agricultural soils at one site and only in response to rainfall. The abundance of manure-associated bacteria in runoff water was compared between plots receiving manure without prairie strips and plots receiving manure. Prairie strip appended plots had lower abundances of manure associated taxa and lower detection of antibiotic resistance genes than plots without prairie strips. Conservation practices designed to reduce nutrient loss, such as the use of composts or the installation of prairie strips, are essential practices that can improve agricultural sustainability, yet have impacts on bacterial dynamics that are not well understood. Characterizing bacterial communities in soils under various conservation practices will inform our understanding of how these practices impact the soil bacterial community

Comparison of Organic and Conventional Crops at the Neely-Kinyon Long-term Agroecological Research (LTAR) Site

The Neely-Kinyon LTAR site was established in 1998 to study the long-term effects of organic production in Iowa. Treatments at the LTAR site, replicated four times in a completely randomized design, include the following rotations: conventional Corn-Soybean (C-S), organic Corn-Soybean-Oats/Alfalfa (C-S-O/A), organic Corn-Soybean-Oats/Alfalfa-Alfalfa (CS-O/A-A). A new rotation of Corn-SoybeanCorn-Oats/Alfalfa (C-SB-C-O/A) replaced the old S-W/RC rotation.</p