Tracing nutrient pollution from industrialized animal production in a large coastal watershed

Local and Environmental Reservoirs of Salmonella enterica After Hurricane Florence Flooding

In many regions of the world, including the United States, human and animal fecal genetic markers have been found in flood waters. In this study, we use high-resolution whole genomic sequencing to examine the origin and distribution of Salmonella enterica after the 2018 Hurricane Florence flooding. We specifically asked whether S. enterica isolated from water samples collected near swine farms in North Carolina shortly after Hurricane Florence had evidence of swine origin. To investigate this, we isolated and fully sequenced 18 independent S. enterica strains from 10 locations (five flooded and five unflooded). We found that all strains have extremely similar chromosomes with only five single nucleotide polymorphisms (SNPs) and possessed two plasmids assigned bioinformatically to the incompatibility groups IncFIB and IncFII. The chromosomal core genome and the IncFIB plasmid are most closely related to environmental Salmonella strains isolated previously from the southeastern US. In contrast, the IncFII plasmid was found in environmental S. enterica strains whose genomes were more divergent, suggesting the IncFII plasmid is more promiscuous than the IncFIB type. We identified 65 antibiotic resistance genes (ARGs) in each of our 18 S. enterica isolates. All ARGs were located on the Salmonella chromosome, similar to other previously characterized environmental isolates. All isolates with different SNPs were resistant to a panel of commonly used antibiotics. These results highlight the importance of environmental sources of antibiotic-resistant S. enterica after extreme flood events.

Association of distance to swine concentrated animal feeding operations with immune-mediated diseases: An exploratory gene-environment study

BACKGROUND

Concentrated animal feeding operations (CAFOs) are a source of environmental pollution and have been associated with a variety of health outcomes. Immune-mediated diseases (IMD) are characterized by dysregulation of the normal immune response and, while they may be affected by gene and environmental factors, their association with living in proximity to a CAFO is unknown.

OBJECTIVES

We explored gene, environment, and gene-environment (GxE) relationships between IMD, CAFOs, and single nucleotide polymorphisms (SNPs) of prototypical xenobiotic response genes AHR, ARNT, and AHRR and prototypical immune response gene PTPN22.

METHODS

The exposure analysis cohort consisted of 6,464 participants who completed the Personalized Environment and Genes Study Health and Exposure Survey and a subset of 1,541 participants who were genotyped. We assessed the association between participants' residential proximity to a CAFO in gene, environment, and GxE models. We recombined individual associations in a transethnic model using METAL meta-analysis.

RESULTS

In White participants, ARNT SNP rs11204735 was associated with autoimmune diseases and rheumatoid arthritis (RA), and ARNT SNP rs1889740 was associated with RA. In a transethnic genetic analysis, ARNT SNPs rs11204735 and rs1889740 and PTPN22 SNP rs2476601 were associated with autoimmune diseases and RA. In participants living closer than one mile to a CAFO, the log-distance to a CAFO was associated with autoimmune diseases and RA. In a GxE interaction model, White participants with ARNT SNPs rs11204735 and rs1889740 living closer than eight miles to a CAFO had increased odds of RA and autoimmune diseases, respectively. The transethnic model revealed similar GxE interactions.

CONCLUSIONS

Our results suggest increased risk of autoimmune diseases and RA in those living in proximity to a CAFO and a potential role of the AHR-ARNT pathway in conferring risk. We also report the first association of ARNT SNPs rs11204735 and rs1889740 with RA. Our findings, if confirmed, could allow for novel genetically-targeted or other preventive approaches for certain IMD.

Using remote sensing to identify liquid manure applications in eastern North Carolina

Nutrient pollution from farm fertilizers and manure is a global concern. Excess nitrogen and phosphorous has been linked to algal blooms and a host of other water quality issues. In the U.S., most animal production occurs in concentrated animal feeding operations (CAFOs) housing a significant number of animals in a confined space. CAFOs tend to cluster in space and thus generate large quantities of manures within a small area. Liquid manure from CAFOs is often stored in open-air lagoons and then applied via irrigation to crops on nearby 'sprayfields'. The full scope and extent of CAFO impacts remain unclear because of the paucity of public information regarding animal numbers, barn and lagoon locations, and manure management practices. Where and when manure is applied on the landscape is key missing data that is needed to better understand and mitigate consequences of CAFO management practices. The aim of this study was to detect land applications of liquid manure using a remote sensing approach. We used random forest models incorporating C-Band synthetic-aperture radar, multispectral imagery, and other predictors to examine soil moisture conditions indicating probable liquid manure applications across known sprayfields in eastern North Carolina. Our models successfully distinguished saturated and unsaturated soils within corn, soybean, grassland, and 'other' crops, with 93-98% accuracy against validation for clear weather periods during the dormant, early, and late growing seasons. A Kruskal-Wallis test revealed that the mean soil saturation frequency was significantly higher on sprayfields than non-sprayfields of the same crop type (p < 2.2e-16). We also found that manure applications were concentrated within ∼1 km from the point of generation. This is the first application of satellite-based radar for identifying the location and timing of manure applications over broad areas. Future work can build on these methods to further understand manure management at CAFOs, as well as to improve pollution source tracking and modeling.

Spatiotemporal land use change and environmental degradation surrounding CAFOs in Michigan and North Carolina

Concentrated Animal Feeding Operations (CAFOs) have arisen and expanded in the U.S. and globally to address efficiencies in livestock production. CAFOs tend to cluster in space for logistical purposes. Efficient distribution of concentrated manures produced by these operations is often not economically feasible, which may lead to accumulation on land near CAFOs, potentially resulting in local environmental changes. Moreover, as CAFOs are established or expand, they may need more lands to apply their manures, likely driving land use changes even after their establishment. Studies have yet to investigate these spatiotemporal impacts of CAFOs. We investigated whether the presence of regulated liquid waste CAFOs is associated with land use change over time and space as well as degraded environmental conditions surrounding those facilities. We used MODIS (Moderate Resolution Imaging Spectrometer) images from 2000 to 2018 to examine these questions in Michigan and North Carolina- states with varied CAFO establishment histories. We found that cropland extent increased while savanna and forest decreased near CAFOs. Similar observations did not occur outside of areas influenced by CAFOs. We also found evidence of environmental degradation, including decreased evapotranspiration and increased day and nighttime land surface temperatures in North Carolina. This study advances our understanding of environmental impacts surrounding CAFOs. Our findings can support policy changes and highlight the need to better understand these globally increasing entities.

Beef cattle feedlot surface water containing multi-class agrochemicals elicits physiological and behavioral responses among Daphnia pulex

Despite increasing public concern about air and water pollution risks posed by concentrated animal feeding operation areas (CAFOs), there is little information about bioavailability and ecosystem impacts of agrochemicals used to increase productivity. In this study, we investigated the toxicity of wastewaters originating from beef cattle feeding operation on Daphnia pulex. Specifically, we assessed lethal and chronic sublethal exposure effects using various endpoints including survival, oxygen consumption, morphology, reproduction, and swimming behavior. Exposure assessments (acute and chronic) were performed with ten (10) surface water samples collected from on-site retention ponds designated as A, B, C, D, E, F, G, H, I, and R (reference site). Surface water samples were diluted to yield five concentrations (stock, 1 × , 2 × , 3 × , and 4 ×) as treatments and deionized water was used as control. Results showed site-specific and concentration-related effects on toxicity endpoints. Among treatments, significant (p < 0.05) increase in mortality rate (for A, E, F, and H) and decreasing total body length and width (for B, C, D, and G) of D. pulex were observed with increasing wastewater concentration. However, treatments did not have significant effect on swimming behavior (average speed) after exposure to the wastewater samples from all sites except for site E. Evidence from this study suggested that surface waters near beef cattle feed yards affected physiological responses in D. pulex and therefore may similarly affect organisms in the surrounding aquatic ecosystems.

Sustainable Swine Manure Management: A Tale of Two Agreements

Intensification and concentration of swine farming has provided economic benefit to rural communities but also negative environmental and human health impacts, particularly from the use of the lagoon-sprayfield system for manure management. Although cost effective, this system is susceptible to poor management, unpleasant odor and other emissions, and inundation during extreme weather events. Competition for manure-spreading acres with other livestock or encroaching development can also pose a problem. This study examines two agreements between industry and government designed to develop and implement improved manure management technologies for swine farms: a voluntary agreement between the attorney general of North Carolina and Smithfield Foods and a consent judgment between the State of Missouri and Premium Standard Farms. Individuals involved in executing these agreements were interviewed to gain insight from their perspective on those processes and lessons they learned from their experience. Common themes among participant responses to support transition processes included the need to involve multiple stakeholder groups, clearly define goals, understand the system, allow time for incremental change, and provide adequate “protected space” for technology development and implementation. Viewing these themes through the lens of multi-level perspective theory identifies leverage points throughout the system to support transitioning farms to a more sustainable path of manure management.