California Agriculture Research Articles

Assessing foodborne pathogen survival in bird faeces to co‐manage farms for bird conservation, production, and food safety

Abstract Because birds can carry foodborne pathogens, widespread concern exists that birds impose food‐safety risks to farms. Growers are thus often encouraged to deter birds and forego harvesting crops near bird faeces (e.g., no‐harvest buffers). Developing a holistic understanding of the pathogen spillover process—from individual infection to pathogen persistence on crops—is essential to understand and manage food‐safety risks associated with birds. Here, we coupled field and greenhouse experiments to understand the relative risks associated with different bird species on California farms. We first compared E. coli survival in bird faeces on lettuce, soil, and plastic mulch to identify where pathogens are likely to persist. Next, we quantified pathogen survival in faeces from 10 bird species to identify higher‐risk species. Finally, we combined pathogen survival data with bird surveys and faecal transects to assess food‐safety risks across 29 California lettuce farms. E. coli abundance rapidly declined in bird faeces, but rates varied across substrates. E. coli survival was higher on lettuce compared to soil and plastic mulch, likely because of lettuce's cooler and wetter microclimate. E. coli persistence was also much higher in faeces from larger birds—which produce larger faeces—than small songbirds. Importantly, minimal differences in persistence among species were observed after all faeces were standardized to the same mass. Though bird faeces were common on farms, most birds entering farms, contacting crops, and defecating on crops were small songbirds that defecate small faeces. Coupled with our finding that ~90% of faeces were deposited on soil, these results suggest that most birds on farms present relatively low food‐safety risks. Synthesis and applications. Growers are often encouraged to deter all bird species and forego harvesting crops near all bird faeces, but our work suggests not all birds and faeces pose the same food‐safety risks. If growers ignored small bird faeces on soil, then we estimate that the area of California lettuce farms affected by no‐harvest buffers could decrease from ~10.3% to ~2.7%. More broadly, our results suggest farmers could promote small, insect‐eating birds by erecting nest boxes or preserving habitat without necessarily compromising food safety.

Evaluating environmental, weather, and management influences for sustainable beekeeping in California and Quebec: Enhancing beehive survival predictions.

Concerned about declining managed honeybee populations in North America, this study employed the random survival forest (RSF) model to assess beehive mortality, considering 18 diverse environmental, weather, and management practices. Our analysis focused on 15,906 and 6,690 beehives in California state, United States, and Quebec province, Canada for 2023, respectively. The accuracy of the RSF model was assessed through three accuracy metrics, namely concordance index (C-index), integrated Brier score (IBS), and time-dependent area under the curve (AUC). Besides, the variables' importance was assessed in both California and Quebec under two criteria configurations, incorporating beehive management criteria and excluding such criteria. Including beehive-management criteria improved accuracy: for the test dataset in California, C-index of 0.8845, IBS of 0.0177, and time-dependent AUC of 0.8819; in Quebec, C-index of 0.9618, IBS of 0.0121, and time-dependent AUC of 0.9687. Comparing feature importance across the regions revealed differences, with sugar-feeding frequency, precipitation, and Miticide-treatment frequency exerting more influence in California and DEM, precipitation, and sugar-feeding frequency playing more substantial roles in Quebec. Beekeeping suitability maps for both regions were provided, classifying land suitability for beekeeping into five categories from very low to very high. By aggregating the areas classified as highly and very highly suitable for beekeeping, the beekeeping suitability maps indicated that 64.712% of California and 66.423% of Quebec exhibit suitable conditions for beekeeping. This study could contribute to reducing honeybee colony losses and supporting the advancement of sustainable agriculture in California and Quebec through 1) pinpointing essential environmental, ecological, and meteorological factors, alongside beehive management practices affecting beehive mortality, and 2) providing maps illustrating land suitability for beekeeping.

Some Like It Hot: Differential Photosynthetic Performance and Recovery of English Walnut Accessions Under Emerging California Heat Waves

ABSTRACTHeat waves (HWs) pose a significant threat to California agriculture, with potential adverse effects on crop photosynthetic capacity, quality and yield, all of which contribute to significant economic loss. Lack of heat‐resilient cultivars puts perennial crop production under severe threat due to increasing HW frequency, duration and intensity. Currently, available walnut cultivars are highly sensitive to abiotic stress, and germplasm collections provide potential solutions via genotypes native to varied climates. We screened nine English walnut accessions (Juglans regia) for physiological heat stress resilience and recovery in the USDA‐ARS National Clonal Germplasm over 2‐years, and identified accessions with superior resilience to heat stress. Heat stress impacted photosynthetic capacity in most accessions, as evidenced by reductions in net (An) and maximum (Amax) assimilation rates, quantum efficiency of PSII, and changes in stomatal conductance (gs). However, two accessions exhibited either higher or complete recovery post‐irrigation. This aligns with the established practice of using irrigation to mitigate heat stress, as it improved recovery for several accessions, with A3 and A5 demonstrating the most resilience. One of these two superior accessions is native to one of the hottest and driest habitats of all studied accessions. These same accessions exhibited the highest An under non‐stressed conditions and at higher temperatures of 35° to 45°C. Higher performance for A3 and A5 under HWs was associated with greater carboxylation rates, electron transport rates, and Amax. All accessions suffered significant declines in photosynthetic performance at 45°C, which were the ambient leaf temperatures approached during record‐setting heat waves in California during September 2022.

For California perennial crops facing climate change, water use stays stable while planting density increases

With climate change, there has been increasing concern over allocations of scarce water supplies in California during times of drought. This study looks at how practices in perennial crops have changed over time, specifically related to application of irrigation water and to planting densities. We use University of California Sample Costs of Production Budgets from 1980 to 2021 for all major perennial crops in California to compile information on the commonly implemented irrigation and planting practices across various crops and regions. After controlling for regional variation in water applied due to agroclimatic factors, irrigation water use per acre has remained largely stable for most crops, while planting densities have increased for many crops, including olives, grapes, avocados, plums, and almonds. A notable exception is pistachios in the South San Joaquin Valley, which experienced an increase in water applied, with stable yields and planting densities. Our methods of calculating significant trends in water use, including yields and density of orchards, give further insight into the use of water in California agriculture.

Land use change and ecosystem service tradeoffs on California agricultural land

Abstract Introduction 
The need to transition to sustainable agricultural practices while maintaining high food yield and strengthening resilience to climate change cannot be overstated. California farmers have received incentive funding from federal and state agencies to use land management practices that are less impactful to the land and in line with California’s sustainability goals. However, there are no regional monitoring measures to determine whether farming is becoming more sustainable. 

Methods 
In this study, we used land cover change analysis and ecosystem services modeling to understand how farming practices influence environmental benefits on California farmland from 2010 to 2020. We analyzed the tradeoffs between soil erosion control, soil carbon storage, and production of California’s top agricultural commodities, and we compared these changes to changes in land cover in five agricultural regions statewide. 

Results and Conclusion 
We found that the trade-offs in ecosystem services and food production differ depending on the regional context, and that major expansion in almond production and land use changes have had different impacts throughout California. Statewide, soil organic carbon storage increased, soil erosion control increased slightly, and food production boomed for most commodities. Incentive programs that influence farming practices may need to operate at a regional level rather than a statewide level to achieve sustainable outcomes specific to each region.

Unlocking the potential of electric and hybrid tractors via sensitivity and techno-economic analysis

The majority of agricultural vehicles in use today still rely on diesel-based propulsion, a major source of air pollution. Electrification is seen as a potential solution for decarbonizing these off-road vehicles but is hampered by higher upfront costs in energy storage and charging infrastructure. To better quantify these barriers, this paper proposes a techno-economic tool that can assist farmers in evaluating the total costs of ownership of electric and hybrid tractors. A pragmatic simulation model of the tractor is developed to predict the annual energy/fuel consumption and NOx emissions, while an economic model estimates the total acquisition, operation, and maintenance costs. For managing the energy in hybrid tractors, a new power split strategy based on model predictive control is developed, allowing the designer to balance energy efficiency and NOx emissions, while taking into account operational constraints of the electric powertrain. Additionally, we propose novel decision maps that allow farmers to quickly identify operating regions (in term of average load and yearly working time) where the deployment of electric/hybrid tractors is economically viable. To account for variability in the tractor’s operational conditions, we conduct both a deterministic sensitivity analysis with multi-parameter variation and a stochastic analysis of the total cost of ownership. The tool is validated with different mission profiles based on data from a California farm. The results show that, compared to diesel powertrains, electric tractors are more cost-effective for light-duty farming activities (engine loads less than 20%). On the other hand, hybrid powertrains are more economical for medium-duty tasks, where engine loads range from 20% to 60%.

Surfacing political clarity in farm and garden education

Farms and gardens are increasingly being recognized as dynamic educational settings through which learners can engage in a wide variety of activities and practices to connect with land, food, self, and community. Across these settings, teaching with political clarity represents a pathway for identifying, interrogating, and disrupting systems of oppression as they manifest in farm and garden education, as well as in land relations more broadly. Drawing on a series of interviews with farm and garden educators in California who identify as Black, Indigenous, and/or people of color, this study identifies key principles for sociopolitically conscious garden-based education by examining the ways in which study participants demonstrate political clarity with respect to their pedagogy. Findings center on educators’ work to build connections from learners’ cultural knowledge and practices, attend to intergenerational land-based traumas, take critical and holistic perspectives on health and well-being, engage land with intentionality and reverence, and flatten hierarchies and support collective decision-making. These pedagogical commitments offer an opportunity to more substantively attune the work of farm and garden education toward the goals of cultivating social and environmental justice.

Despotic dominion and union organizing: Law, property, and the historical geography of class struggle in California agribusiness

This paper examines the role of law, particularly law related to private property, in the historical geography of class struggle. At the center of the analysis is the ‘access rule’, written by the California Agricultural Labor Relations Board in 1975 and struck down by the United States Supreme Court in 2021. Responding to the specific geography of California agribusiness labor relations and the long history of violent repression of workers' organizing rights, the rule allowed union organizers onto growers' property under highly constrained conditions to speak with workers about the merits of unionization. The paper traces the ‘pre-history’ of the rule – the decades of law officers and growers' efforts to deny organizers access to California's rural working class – the working of the rule during its more than forty-five years of existence, and its demise at the hands of the current, conservative supreme court. In doing so, it shows how law not only shapes class composition in particular landscapes but is an essential tool, strategically deployed, by all sides in class struggles.

Evaluation of Organophosphate Pesticide Biomarker Levels in Central California Agricultural Communities

Evaluation of Organophosphate Pesticide Biomarker Levels in Central California Agricultural Communities

Cultivating climate resilience in California agriculture: Adaptations to an increasingly volatile water future

California agriculture will undergo significant transformations over the next few decades in response to climate extremes, environmental regulation and policy encouraging environmental justice, and economic pressures that have long driven agricultural changes. With several local climates suited to a variety of crops, periodically abundant nearby precipitation, and public investments that facilitated abundant low-priced irrigation water, California hosts one of the most diverse and productive agroecosystems in the world. California farms supply nearly half of the high-nutrient fruit, tree nut, and vegetable production in the United States. Climate change impacts on productivity and profitability of California agriculture are increasing and forebode problems for standard agricultural practices, especially water use norms. We highlight many challenges California agriculture confronts under climate change through the direct and indirect impacts on the biophysical conditions and ecosystem services that drive adaptations in farm practices and water accessibility and availability. In the face of clear conflicts among competing interests, we consider ongoing and potential sustainable and equitable solutions, with particular attention to how technology and policy can facilitate progress.

Climate smart agriculture: assessing needs and perceptions of California's farmers

California is the largest agricultural economy in the United States; however, its current and projected climate risks pose significant challenges. Farmers will need to adapt to climate change in their farming practices. The goal of this needs assessment was to understand farmers' perceptions and experiences with climate change exposures; the risk management practices they currently use; and what tools and resources would assist them in making strategic decisions. A statewide survey was conducted through Qualtrics with farmers (n = 341). Results showed that 67% of the farmers agree (agree + strongly agree) that climate change is happening, and 53.1% agreed that actions are required. Moreover, historically underrepresented farmers were very concerned about climate change-related impacts related to water, temperatures, and natural disasters. Farmers are currently implementing adaptation practices related to water management, soil health, and renewable energy and are also seeking insurance and government assistance programs to increase agricultural resilience. They also expressed interest and a high need for information on those adaptation practices to acquire skills and knowledge to manage various challenges of farming in variable climates. Also, the assessment established that farmers (47.5%) use decision-support tools, mostly weather stations (22.4%); and 51.9% indicated their interest in using online tools designed to translate climate information into forms that support production decision-making. Farmers (60.8%) responded that they would or may attend workshops to learn about adaptation practices. The findings of this needs assessment will inform the development of extension education programs on climate-smart agriculture for farmers in California and elsewhere.

First Report of Calosphaeria pulchella causing Canker and Twig Dieback of Peach (Prunus persica) in California, U.S.A.

California leads the United States in peach (Prunus persica L.) production, with approximately 505,000 tons produced in 2021 and valued at $378.3 million (California Agriculture Statistics Review, 2021-2022). During the spring and summer of 2023, twig and branch dieback were observed in three peach orchards (cvs. Late Ross and Starn) in San Joaquin County, California. Wood cankers and discoloration also occurred in branches, generally initiating at pruning wounds. Approximately 8 symptomatic twigs or branches per orchard were collected to proceed with the isolation of necrotic tissues on acidified potato dextrose agar (APDA). Isolations consistently yielded colonies of the fungal pathogen Calosphaeria pulchella (Pers. : Fr.) J. Schröt. (Réblová et al. 2004; Trouillas et al. 2012). Pure cultures were obtained by transferring single hyphal tips onto new APDA Petri plates. Colonies on APDA grew dark pink to red or purple in their center, with a white margin. Conidiogenesis was phialidic, producing round conidial masses at the tip of phialides. Conidia were produced abundantly on APDA, and were hyaline, allantoid to oblong-ellipsoidal, 4 to 5.5 (7) × 1.2 to 2.3 μm (n = 60). Two representative isolates (SJC-62 and SJC-64) were selected for genomic DNA extraction and sequencing of the internal transcribed spacer region (ITS) using ITS5/ITS4 universal primers and the beta-tubulin (TUB2) gene region using primers Bt2a and Bt2b. Consensus sequences of the two genes for the two isolates (ITS: PP063990, PP063991; TUB2: PP068303, PP068304) were compared to reference sequences (Réblová et al. 2015; Trouillas et al. 2012) using BLAST analysis. The ITS sequences of SJC-62 and SJC-64 were 99.8 and 99.5% identical to that of C. pulchella ex-type strain CBS 115999 (NR145357) and reference strain SS07 (HM237297); the TUB2 sequences were at least 98.5% identical to that of C. pulchella CBS 115999 (KT716476). Pathogenicity tests were conducted in 2- to 3-year-old healthy branches on 7-year-old peach trees, cvs. Loadel, Late Ross and Starn using the two fungal isolates and a control treatment (1 branch per treatment and 3 branches per tree) on each of 8-tree replicates. Branches were inoculated in June 2023 following wounding with a 5 mm cork borer to remove the bark and placing an agar plug from the margin of 10-day-old colonies on APDA directly into the fresh wound. Sterile agar plugs were used as controls. Inoculation sites were covered with petroleum jelly and wrapped with Parafilm to retain moisture. The experiment was completed twice. After four months, cankers and vascular discolorations developed around the inoculation sites. Length of vascular discoloration in inoculated branches averaged 72, 75, and 79 mm, for the Loadel, Starn, and Late Ross cvs., respectively. Calosphaeria pulchella was re-isolated from inoculated branches at 80 to 100% recovery rate, thus fulfilling Koch's postulates. The average length of vascular discoloration in the control was 13.5 mm and no fungi were recovered from control branches. Calosphaeria canker caused by C. pulchella is a global disease of sweet cherry. Recently, it was reported to cause cankers in peach trees in Chile (Grinbergs et al. 2023). To our knowledge, this is the first report of C. pulchella causing cankers and twig dieback of peach trees in the United States. These findings improve our knowledge of the etiology of canker diseases affecting peach trees and is critical for the development of effective disease management strategies.

Identification and Pathogenicity of Fungal Species Associated with Branch Canker and Shoot Blight on Persimmons (Diospyros kaki) in California.

Persimmon is a relatively new crop to California agriculture. Asian persimmons (Diospyros kaki) are the dominant species commercially cultivated in the United States, primarily grown in California, covering approximately 1,153 ha of bearing trees. In the growing seasons of 2020 and 2021, unusual shoot blight and branch cankers were observed in several persimmon orchards in San Joaquin and Solano counties in California. The most prevalent symptoms were well-defined black discoloration in the cambium and streaking in the vascular tissues of green shoots. On woody branches and old pruning wounds, symptoms manifested as black wedge-shaped cankers. Isolations from affected tissues revealed the occurrence of Diaporthe species, including D. chamaeropis, D. foeniculina, and an undescribed Diaporthe sp. as the most frequent isolated pathogens, followed by Eutypella citricola and Phaeoacremonium iranianum. The isolates were identified through multilocus phylogenetic analyses using nucleotide sequences of the rDNA internal transcribed spacer, β-tubulin, and translation elongation factor 1-alpha genes. To fulfill Koch's postulates, mycelium plugs of the various fungal species identified were inserted in 2-year-old branches of mature persimmon trees after making wounds using a corkborer in field conditions. Results showed that Diaporthe spp., E. citricola, and P. iranianum are the main causal agents of branch canker and shoot dieback of persimmon trees in California, with Diaporthe spp. being the most frequently isolated pathogen.

Spatial planning offshore wind energy farms in California for mediating fisheries and wildlife conservation impacts

Achieving a blue economy will require reconciling the value of emerging ocean uses with their impacts on the seascape and sectors with historical access to marine resources and areas. To meet this challenge, we developed an analytical framework for conducting marine spatial planning through tradeoff analysis, and applied it to prospective offshore wind energy development in the ∼974 km2 Morro Bay, California, USA Wind Energy Area (WEA). We generated spatial data layers estimating MW power production and impacts on fisheries value and marine wildlife conservation (seabird and cetacean populations) from wind farm development. We then quantified each sector's response to plans of development across the WEA and inside three leases recently acquired by the energy industry for prospective development. Finally, we integrated the sector response data into an analytical framework for mitigating sector tradeoffs with novel spatial planning solutions (maps of wind farm size, location, and configuration) that optimally maximize value to the emergent energy sector (MW power) while minimizing impacts to historical (fisheries and wildlife) sectors. We found that western sites in the WEA had the highest potential power production concurrent with the lowest impact on the historical sectors, revealing the eastern lease to be less efficient at optimally balancing the sector's objectives relative to the development of the central or western leases or the optimal spatial plans identified in the tradeoff analysis. Within a lease, tradeoff analysis found spatial planning able to generate out-sized savings in fisheries value with only modest losses in MW power – for example, by avoiding development in just 5% of the eastern lease to preserve nearly half its fisheries value and still generate 95% its total power potential. Small-scale development opportunities (e.g., a pilot project) with significant power potential and no fisheries impact were also identified, in this case by placing turbines in an area in the western lease with no fisheries value and high power production potential. These plans would also have a relatively low impact on the wildlife conservation sectors, due to decreases in vulnerability levels of both seabird and cetacean populations to turbines going from east to west across the WEA. Our results can inform site evaluation and permitting processes for wind energy development in the Morro Bay WEA. We also expect the tradeoff analysis framework we developed to provide a simple and actionable analytical tool for supporting marine spatial planning of offshore wind energy and other emerging blue economy activities from a balanced perspective that values emerging uses of marine resources alongside existing socio-economic and conservation interests.

Comparison of two methods for collecting antimicrobial usage in large dairy farms in Ohio and California

Quantification of on-farm antimicrobial use (AMU) is critical to correlate with patterns of antimicrobial resistance, surveil­lance programs and formulate interventions to optimize its use. Prior studies have used the empty drug container (EDC) method to quantify AMU; however, the method is labor-intensive and time-consuming. Therefore, this study aimed to compare it against farm treatment records (FTR) as a reliable method to collect on-farm AMU. We hypothesized a low level of agreement in on-farm treatment incidence (TI) obtained between these 2 different collection methods.

Technical, economic, and environmental feasibility of rice hull ash from electricity generation as a mineral additive to concrete

A circular economy based on symbiotic relationships among sectors, where the waste from one is resource to another, holds promise for cost-effective and sustainable production. This research explores such a model for the agriculture, energy, and construction sectors in California. Here, we develop new an understanding for the synergistic utilization mechanisms for rice hull, a byproduct from rice production, as a feedstock for electricity generation and rice hull ash (RHA) used as a supplementary cementitious material in concrete. A suite of methods including experimental analysis, techno-economic analysis (TEA), and life-cycle assessment (LCA) were applied to estimate the cost and environmental performance of the system. TEA results showed that the electricity price required for break even on expenses without selling RHA is $0.07/kWh, lower than the market price. As such, RHA may be available at little to no cost to concrete producers. Our experimental results showed the viability of RHA to be used as a supplementary cementitious material, meaning it can replace a portion of the cement used in concrete. LCA results showed that replacing 15% of cement with RHA in concrete can reduce carbon dioxide equivalent (CO2e) emissions by 15% while still meeting material performance targets. While the substitution rate of RHA for cement may be modest, RHA generated from California alone could mitigate 0.2% of total CO2e from the entire cement production sector in the United States and 1% in California.

Equine neuroaxonal dystrophy/degenerative myeloencephalopathy in Gypsy Vanner horses.

Equine neuroaxonal dystrophy/degenerative myeloencephalopathy (eNAD/EDM) is a neurodegenerative disease that primarily affects young, genetically predisposed horses that are deficient in vitamin E. Equine NAD/EDM has not previously been documented in Gypsy Vanner horses (GVs). To evaluate: (1) the clinical phenotype, blood vitamin E concentrations before and after supplementation and pedigree in a cohort of GV horses with a high prevalence of neurologic disease suspicious for eNAD/EDM and (2) to confirm eNAD/EDM in GVs through postmortem evaluation. Twenty-six GVs from 1 farm in California and 2 cases from the Midwestern U.S. Prospective observational study on Californian horses; all 26 GVs underwent neurologic examination. Pre-supplementation blood vitamin E concentration was assessed in 17- GVs. Twenty-three were supplemented orally with 10 IU/kg of liquid RRR-alpha-tocopherol once daily for 28 days. Vitamin E concentration was measured in 23 GVs after supplementation, of which 15 (65%) had pre-supplementation measurements. Two clinically affected GVs from California and the 2 Midwestern cases had necropsy confirmation of eNAD/EDM. Pre-supplementation blood vitamin E concentration was ≤2.0 μg/mL in 16/17 (94%) of GVs from California. Post-supplementation concentration varied, with a median of 3.39 μg/mL (range, 1.23-13.87 μg/mL), but only 12/23 (52%) were normal (≥3.0 μg/mL). Normalization of vitamin E was significantly associated with increasing age (P = .02). Euthanized horses (n = 4) had eNAD/EDM confirmed at necropsy. GVs could have a genetic predisposition to eNAD/EDM. Vitamin E supplementation should be considered and monitored in young GVs.

Field-scale crop water consumption estimates reveal potential water savings in California agriculture

Efficiently managing agricultural irrigation is vital for food security today and into the future under climate change. Yet, evaluating agriculture’s hydrological impacts and strategies to reduce them remains challenging due to a lack of field-scale data on crop water consumption. Here, we develop a method to fill this gap using remote sensing and machine learning, and leverage it to assess water saving strategies in California’s Central Valley. We find that switching to lower water intensity crops can reduce consumption by up to 93%, but this requires adopting uncommon crop types. Northern counties have substantially lower irrigation efficiencies than southern counties, suggesting another potential source of water savings. Other practices that do not alter land cover can save up to 11% of water consumption. These results reveal diverse approaches for achieving sustainable water use, emphasizing the potential of sub-field scale crop water consumption maps to guide water management in California and beyond.

Native blue elderberry in hedgerows bridges revenue and conservation goals

Field edge hedgerows have long been promoted by UC Cooperative Extension and other organizations as a way to bring needed biodiversity to California farms. However, adoption of hedgerow planting still falls far short of available edge capacity. Our study explores a new multifunctional model of hedgerows that combines production with environmental conservation goals by considering the revenue potential of harvesting blue elderberry. Blue elderberry is a drought-tolerant native species well adapted to multiple microclimates in California and the western United States. The growth of elderberry herbal products and specialty foods markets is currently skyrocketing nationally and globally, and blue elderberry may offer a promising entry into these markets. Blue elderberry is also sought out by Indigenous people as one important component in efforts to restore cultural and food sovereignty. A field demonstration trial in the southern Sacramento Valley found that elderberry yields from 1,000-foot-long multi-species hedgerows could potentially provide from $2,000 to $3,000 in net annual revenue within 3 to 5 years, with much more possible as the hedgerows mature.

Microbial diversity in dairy manure environment under liquid-solid separation systems

ABSTRACT In dairy manure, a wide array of microorganisms, including many pathogens, survive and grow under suitable conditions. This microbial community offers a tremendous opportunity for studying animal health, the transport of microbes into the soil, air, and water, and consequential impacts on public health. The aim of this study was to assess the impacts of manure management practices on the microbial community of manure. The key novelty of this work is to identify the impacts of various stages of manure management on microbes living in dairy manure. In general, the majority of dairy farms in California use a flush system to manage dairy manure, which involves liquid-solid separations. To separate liquid and solid in manure, Multi-stage Alternate Dairy Effluent Management Systems (ADEMS) that use mechanical separation systems (MSS) or weeping wall separation systems (WWSS) are used. Thus, this study was conducted to understand how these manure management systems affect the microbial community. We studied the microbial communities in the WWSS and MSS separation systems, as well as in the four stages of the ADEMS. The 16S rRNA gene from the extracted genomic DNA of dairy manure was amplified using the NovoSeq Illumina next-generation sequencing platform. The sequencing data were used to perform the analysis of similarity (ANOSIM) and multi-response permutation procedure (MRRP) statistical tests, and the results showed that microbial communities among WWSS and MSS were significantly different (p < 0.05). These findings have significant practical implications for the design and implementation of manure management practices in dairy farms.