Avian influenza has greatly impacted the commercial poultry industry worldwide. Limited knowledge exists on the interactions between avian influenza viruses (AIV) and the environmental factors associated with poultry farms. To improve our existing understanding of AIV survival in various environmental conditions, experiments were conducted to investigate the persistence of AIV in reused poultry litter. Additionally, we investigated the effects of a litter acidifier, based on sodium bisulfate, as well as different composting temperatures on the survivability of this virus. The highly pathogenic AIV was found to persist much longer than low pathogenic AIV (LPAIV) in litter material, regardless of the number of cycles the litter was used. No clear association was detected between litter cycle use and viral persistence. In terms of litter acidification, the acidifier amendment immediately inactivated LPAIV when directly mixed with the virus and in the presence of broiler litter. Differing results were obtained in turkey litter where the virus persisted less than 48 h. Finally, when testing composting temperatures, LPAIV was inactivated in litter after 30 min of viral contamination but before the target temperatures were reached. In carcass material with and without litter, LPAIV survived for less than 30 min, before reaching 50 degrees C or 60 degrees C, showing a detrimental effect on LPAIV survivability. These studies provide information that helps improve the understanding of interactions between environmental factors and AIV.

The disposal of by-products, such as poultry litter, and carcasses is a serious issue because of risks associated with microbial pathogens, and controlling the pathogen risks requires identifying improved pre-treatment methods capable of inactivating pathogens. As poultry litter and carcasses are known to be major reservoirs of pathogenic microorganisms such as Salmonella and Escherichia coli (E. coli), improvement in existing understanding of the inactivation of these pathogens in poultry litter and carcasses is needed to determine the effective treatment time and temperature. Here we conducted a study to assess the thermal inactivation of 2 common bacteria in poultry productive systems: Escherichia coli (E. coli) and Salmonella enterica (Salmonella). The inactivation study was conducted at 50°C and 60°C using 3 different feedstocks: (1) poultry carcasses, (2) poultry litter, and (3) mixture of poultry litter and carcasses. Each feedstock was inoculated with known concentrations of E. coli and Salmonella prior to thermophilic digestion experiments at 50°C and 60°C. Regardless of feedstock types, E. coli survival was extended beyond 3 d at 50°C. In contrast, Salmonella was no longer detectable within 3 d at 50°C. At 60°C, both E. coli and Salmonella were undetected within an hour. There was no significant difference (at P < 0.05) in pathogen survival among 3 feedstocks.

The occurrence of Escherichia coli O157 and Salmonella spp. in solid bovine manure was investigated through a multi-county survey in California. Solid bovine manure samples (n = 91) were collected from 13 dairy farms located in multiple counties in California between June 2016 and August 2017. To quantify pathogens, DNA was extracted from bacteria in manure samples. Afterwards, the prevalence and levels of E. coli O157 and Salmonella spp. in solid bovine manure were determined by real-time quantitative PCR (qPCR). The prevalence of E. coli O157 and Salmonella spp. in solid bovine manure was 15 center dot 4 and 6 center dot 6% respectively. Escherichia coli O157 and Salmonella spp. levels in positive samples ranged from 3 center dot 1 to 5 center dot 3 log CFU per g and from positive (the population was <3 log CFU per g) to 5 center dot 2 log CFU per g respectively. Surface samples of manure piles had higher prevalence and levels of E. coli O157 and Salmonella spp. than subsurface samples, while no seasonal effects on pathogen occurrence were observed. Our results indicated that solid bovine manure is a source of E. coli O157 and Salmonella spp. and the application of untreated manure as biological soil amendments may pose potential risks to public health. Significance and Impact of the Study Our findings suggested that the presence of Escherichia coli O157 and Salmonella spp. in solid bovine manure may pose potential risks if untreated manure is applied as biological soil amendments. Considering the large-scale sampling used in this study, the observations provide a holistic assessment in terms of pathogen prevalence in solid bovine manure.

Fluridone is widely used as a herbicide for controlling invasive aquatic plants such as hydrilla in surface water bodies. When applied on surface waters fluridone can attach to bed sediment, requiring rigorous extraction methods prior to analysis. Currently, very limited information exists in terms of fluridone residue detection in delta sediment. In this study, we researched fluridone detection in both water and sediment. To extract fluridone from sediment, here we have tested two extraction methods: (1) a rotavapor method (RM); and (2) a quick, easy, cheap, effective, rugged and safe (QuEChERS) method (QM). The extraction results of RM were compared with those of QM. To quantify fluridone concentrations in extracts, a high-performance liquid chromatography (HPLC)-UV detector was used. HPLC separation was achieved using an Allure C18 5 µm 150 × 4.6 mm column with a mobile phase composed of acetonitrile and water (60:40, v/v). The UV detector was operated at 237 nm. The method was tested and validated using a series of water and sediment samples taken from Sacramento–San Joaquin Delta in California. The average recovery of fluridone was 73% and 78% using RM and QM respectively. The proposed method can be used for testing fluridone in water and sediment samples.

Pathogen contamination in stream water is a serious concern, which can pose risks to public and animal health, and reducing the risks of pathogens requires enhanced knowledge of pathogen sources and pathogen survival under various environmental and controlled conditions. One of the major factors, which affect pathogen survival, is temperature. To improve existing understanding of pathogen inactivation in stream water and sediment at various temperature conditions, we executed a series of microcosm studies in batch mode for assessing pathogen survival. Water and sediment samples from stream water column and bed sediment of Merced River Watershed, California were collected, and stored at 4°C prior to experiments. Subsequently, heat shock experiments were conducted under temperature controlled conditions. Initial pathogen levels in water and sediment samples were controlled by mixing the inoculum of E. coli, Salmonella, and Listeria, which are water and foodborne pathogens, known for causing illnesses in humans. We studied pathogen survival at 30°C, and 50°C. Results showed that the temperature of heat shock and incubation time under heat shock played crucial role in reducing pathogen levels. Low temperature (30°C) heat shocks and limited time heat shocks with relatively higher temperature (50°C) may not have considerable impacts in reducing pathogen levels.

This study was conducted to assess the temperature profile and corresponding pathogen inactivation in lab-scale compost piles. The variation in temperature at different locations of piles and E. coli concentrations was evaluated. The experiment design included plastic containers of different height filled with organic feedstock. Cotton balls soaked with pathogens (E. coli and E. coli O157:H7) were placed inside the feedstocks at various depths. Subsequently, change in pathogen concentrations, feedstock characteristics, and temperature was monitored over time. Observations showed fluctuation in temperature of piles. The peak temperature (> 50 °C) was reached after two weeks of expertiment. The concentrations of E.coli and E. coli O157: H7 at different depths varied among piles during the 35 days of experiments. The reductions in E. coli concentrations ranged 1- 4 orders of magnitude. In certain piles, reduction in E. coli concentrations was followed by increased in E. coli levels indicating the possibility of perturbation of bacteria in the feedstock potentially at low temperature. We anticipate these preliminary results will provide additional insights on pathogen inactivation in compost system. The approach used here can be implemented at field-scale compost piles for assessing pathogen inactivation during compost process under field conditions.

Increased public health risk caused by pathogen contamination in streams is a serious issue, and mitigating the risk requires improvement in existing microbial monitoring of streams. To improve understanding of microbial contamination in streams, we monitored in stream water columns and streambed sediment. Two distinct streams and their subwatersheds were studied: (i) a mountain stream (Merced River, California), which represents pristine and wild conditions, and (ii) an agricultural stream (Squaw Creek, Iowa), which represents an agricultural setting (i.e., crop, manure application, cattle access). Stream water column and sediment samples were collected in multiple locations in the Merced River and Squaw Creek watersheds. Compared with the mountain stream, water column concentrations in the agricultural stream were considerably higher. In both mountain and agricultural streams, concentrations in bed sediment were higher than the water column, and principal component analysis indicates that land use affected water column levels significantly ( < 0.05). The cluster analysis showed grouping of subwatersheds for each basin, indicating unique land use features of each watershed. In general, water column levels in the mountain stream were lower than the USEPA's existing water quality criteria for bacteria. However, the levels in the agricultural stream exceeded the USEPA's microbial water quality criteria by several fold, which substantiated that increased agricultural activities, use of animal waste as fertilizers, and combined effect of rainfall and temperature may act as potential determining factors behind the elevated levels in agriculture streams.

Escherichia coli persistence kinetics in dairy manure at moderate, mesophilic, and thermophilic temperatures.

Dairy manure is regularly applied to crop fields as a solid or liquid to improve the soil nutrient status. However, pathogens may survive during manure storage and enter the environment during application. In this study, three storage practices were evaluated to understand the survival patterns of O157:H7 and spp. in dairy manure using a culture-based approach. To replicate common farm manure storage techniques, solid manure was stacked as piles with periodic turning or as static piles without turning, whereas liquid manure (feces, urine, and water) was stored as a slurry in small tanks to simulate lagoon conditions. The and levels in the manure samples were determined for 29 wk. Results showed that there was an initial reduction in bacteria levels in the first month; however, both and managed to survive in the solid manure piles for the full study period. In slurry samples, was not detected after 14 wk, but survived until the end of the experiment at relatively lower levels than in the solid manure piles. Ambient weather and pile size were identified as the main reasons for bacteria survival during the course of the experiment. The outcome of this study is important in terms of understanding pathogen survival in manure piles and slurries prior to their application to crop fields.

Runoff generated from livestock manure amended row crop fields is, one of the major pathways of hormone transport to the aquatic environment. The study determined the effects of manure handling, tillage methods, and rainfall timing on the occurrence and transport of steroid hormones in runoff from the row crop field. Stockpiled and composted manure from hormone treated and untreated animals were applied to test plots and subjected to two rainfall simulation events 30 days apart During the two rainfall simulation events, detection of any steroid hormone or metabolites was identified in 8-86% of runoff samples from any tillage and manure treatment The most commonly detected hormones were 17 beta-estradiol, estrone, estriol, testosterone, and alpha-zearalenol at concentrations ranging up to 100-200 ng L-1. Considering the maximum detected concentrations in runoff, no more than 10% of the applied hormone can be transported through the dissolved phase of runoff. Results from the study indicate that hormones can persist in soils receiving livestock manure over an extended period of time and the dissolved phase of hormone in runoff is not the preferred pathway of transport from the manure applied, fields irrespective of tillage treatments and timing of rainfall. (C) 2016 Elsevier B.V. All rights reserved.

To provide additional insights on pathogen survival, we evaluated the relative efficacy of acidification (pH 2.7), thermophilic treatment (55 °C), and low temperature pasteurization (68 °C) on the inactivation of E. coli O157:H7 , Salmonella, and Listeria monocytogenes in ground beef. A series of experiment was conducted under biosafety level 3 environments for assessing the impacts of heat and low pH on pathogen survival. Results showed that 5-log reductions of E. coli O157:H7 could take more than 2640 min at 55 °C, 134 min at 68 °C and 120 min under pH 2.7. Compared to E. coli O157:H7, the 5-log reduction of Salmonella was obtained in 4836, 126, 86 min at 55 °C, 68 °C, and pH 2.7, respectively. The 5-log reduction of Listeria was achieved in 4704, 200, and 115 min under 55 °C, 68 °C, and pH 2.7, respectively. The results of this study will provide additional insights for developing improved methods for controlling pathogens in ground beef.

The shedding of Escherichia coli O157:H7 and Listeria monocytogenes in the feces of ruminants and the consequential risk to the public and environmental health is well reported. However, the influence of dietary manipulation on the shedding of fecal bacteria is not well understood. This study was conducted to improve understanding of the relationship between dietary feed composition and shedding of E. coli O157:H7 and Listeria spp. in dairy feces. Twelve cows were randomly assigned to four treatment diets of two dietary forage levels: low forage (37.4% dry matter, DM) vs. high forage (53.3% of DM) and two dietary crude protein (CP) levels: low protein (15.2% of DM) vs. high protein (18.5% of DM) in a 4×4 replicated Latin square design with four periods each including a 14 d adaptation and 3 d sample collection periods. Generic E. coli was detected in some of the feed ingredients, such as cotton seed, alfalfa hay, almond, and CaCO3, while Listeria was detected in the alfalfa hay and mineral mix. A significant interaction effect was observed between dietary forage and CP on the presence of fecal E. coli O157:H7 (P=0.01) but not with Listeria. On average, the greatest E. coli O157:H7 level (6.6log10 CFU/g of feces) was observed from the high forage and high protein diet and the lowest level was 6.1log10 CFU/g from the low forage and high protein diet. The average Listeria shedding rate was within the range of 1.7–2.3log10 CFU/g among the dietary forage and CP treatments. For the CP treatments, significantly low levels of Listeria were observed from cows fed the high protein (0.9−1.6log10 CFU/g) compared to the low protein (1.3–2.1log10 CFU/g) diet. Considering temporal fluctuations, no significant diurnal pattern was observed for either E.coli O157:H7 or Listeria. In addition, no time of sampling over day by dietary forage or CP content interaction on fecal E.coli O157:H7 or Listeria level was observed. This study showed that diets can influence the shedding of potentially pathogenic bacteria in dairy cow excreta.

Vermicomposting (VC) has proven to be a promising method for treating garden, household, and municipal wastes. Although the VC has been used extensively for converting wastes into fertilizers, pathogens such as Escherichia coli (E. coli) survival during this process is not well documented. In this study, both lab and field scale experiments were conducted assessing the impacts of earthworms in reducing E. coli concentration during VC of food waste. In addition, other pertinent parameters such as temperature, carbon and nitrogen content, moisture content, pH, volatile solids, micronutrients (P, K, Ca, Mg, and S), and heavy metals (Zn, Mn, Fe, and Cu) were monitored during the study. The lab and field scale experiments were conducted for 107 and 103 days, respectively. The carbon to nitrogen ratio (C/N) decreased by 54 % in the lab scale study and by 36 % in the field study. Results showed that VC was not significantly effective in reducing E. coli levels in food waste under both lab and field scale settings. The carbon to nitrogen ratio (C/N) decreased by 54 % in the lab scale study and by 36 % in the field study.

Increasing emphasis on controlling the uses of chemical fertilizers requires identifying safe Organic Soil Amendments (USA) to use as alternatives. Converting organic waste, such as foodwaste into an USA can be an option. Such approaches are also an attempt to make beneficial use of the enormous amount of foodwaste generated globally. In this study we conducted a pathogen challenge to determine the inactivation of three foodborne pathogens in an USA derived from a complex foodwaste stream. Further, the physiochemical characteristics of the USA were assessed at pilot-scale experiments. The inactivation of three most common foodborne pathogens (Escherichia coli O157:H7, Salmonella enterica subspecies enterica sv Typhimurium LT2, and Listeria monocytogenes) was determined using bench-scale tests, simulating the process adopted at a pilot-scale facility. The pilot-scale facility uses three processes (enzyme digestion (55-57 degrees C), pasteurization (75-77 degrees C), and acidification treatments) for producing the USA In addition, the yields and nutrient characteristics of the USA were analyzed using 16 pilot-scale batch tests. The results showed that the process adopted in this study for converting foodwaste to the USA produced a soil amendment with non-detectable levels of E. coli O157:H7, Salmonella LT2, and L. monocytogenes. The yield of the USA was 84-96% of the initial foodwaste inputs, and organic matter and C: N ratio of the USA were 20-25% and 12:1, respectively. We anticipate that the results presented here will help in enhancing agricultural sustainability. (C) 2015 Elsevier Ltd. All rights reserved.

Elevated levels of Salmonella in dairy farm generated wastewater can contaminate food and water. Controlling the risk of Salmonella infection requires improving the existing understanding of Salmonella decay in impaired dairy wastewater. Enhanced understanding of Salmonella inactivation in dairy wastewater can help in deriving improved animal waste management practices capable of mitigating the risk of pathogen contamination to cropland as well as water resources. Considering the importance of the animal waste borne pathogen issue, the primary objective of the study was set to determine the degradation pattern of Salmonella in a mesophilic environment (37 degrees C). To do so, the impact of sampling timing (morning vs evening) on the changes in Salmonella counts were assessed. Further, a heat stress study was conducted to identify the critical die-off time at thermophilic temperatures (48 degrees C and 58 degrees C). Results from the study showed that there was a 5.2 log(10) reduction in Salmonella count observed over the 14 d study period. There was no significant difference in Salmonella count during the sampling of morning or evening. Heat stress study showed that the first 30 min was the major die-off time. Regrowth of Salmonella was observed at a thermophilic temperature after 2 d further incubation. The outcome of the study will help to understand pathogen inactivation in dairy waste-water, and to derive improved animal waste treatment methods.

The North American rendering industry processes approximately 24 million metric tons (Mt) of raw materials and produces more than 8 million Mt of rendered products. More than 85 % of rendered products produced annually in the USA are used for producing animal feed. Pathogen contamination in rendered products is an important and topical issue. Although elevated temperatures (115–140 °C) for 40–90 min during the standard rendering processes are mathematically sufficient to completely destroy commonly found pathogens, the presence of pathogens in rendered products has nevertheless been reported. Increased concern over the risk of microbial contamination in rendered products may require additional safeguards for producing pathogen-free rendered products. This study provides an overview of rendered products, existing microbial pathogen quality criteria of rendered products (MPQCR), limitations, and the scope of improving the MPQCR.

Excessive amount of foodwaste in global food supply chain is a serious issue, and additional controlling measures are needed to prevent wastages of food. In our approach to tackle this global problem, we developed an improved composting system, which can be used as a small decentralized unit for treating food and green wastes in urban environment. A new closed loop heating system was developed to enhance the temperature of compost piles, and accelerate the inactivation of pathogens during the process. The system involved a heated bath circulator, an air injector, and a system of copper piping used as heat exchangers in bins. The system was tested under aerated, static, and plowed composting conditions. To test the pathogen inactivation in the composting, the concentrations of Salmonella and Escherichia coli in compost were measured. In addition, the changes in C:N ratio, pH, and moisture content were observed to understand the quality of the compost in terms of nutrient concentrations. Results showed that the Salmonella levels reached to non-detectable limit in 34, 5, and 34 days of composting in aerated, static, and plowed composting system, respectively. The E. coli levels were detectable till day 70 indicating longer survival of E. coli cells compared to Salmonella under composting environment. In the current system, feedstock C:N ratio was reduced by 71, 70, and 62% in static, plowed, and aerated composting, respectively. We anticipate that the proposed system will yield a new composting design with less dependency on environmental conditions. The proposed design can be used for developing an in-door composting system to convert food and green wastes into pathogen free soil amendment. (C) 2016 Published by Elsevier Ltd.

To derive new methods for converting food and green wastes into soil amendment, this study researched on a in-vessel composting system. The performance of an in-vessel composting system was evaluated during food and green wastes digestion. A series of experiments was conducted using both pilot-scale and bench-scale in-vessel systems. During the digestion process, external heat and continuous mixing were provided for achieving the typical composting temperature of 60 degrees C. The feedstock included food waste, horse manure, palm-tree waste, and green waste. The digestate was tested for understanding the inactivation of pathogens (Escherichia coli (E. coli) and Salmonella enterica serovar Typhimurium LT2 (Salmonella)). Subsequently, pathogen inactivation models were developed to determine the quantitative time-dependent relationships between digestion time and potential pathogen cells in digestate. The digestate was also analyzed for evaluating the changes in pH, moisture level, variations in carbon content, and carbon to nitrogen ratio during the digestion process. Further, the effects of additives on the digestion process and digestate were evaluated by comparing the digestate quality under additive and without additives conditions. Results showed that the proposed method produced a pathogen-free soil amendment from the food and green wastes. The pH and moisture content of the digestate of pilot-scale experiment varied from 3.8 to 4 and 60.6-67.9%, respectively. The observations showed that E. coli survived greater than 10 h, while Salmonella counts were not detectable beyond 40 min of digestion. The results of predictive models showed that Salmonella could survive till 80 min during in-vessel corn posting at 60 degrees C, while the elimination of E. coli may take 16-25 h. The authors anticipate that the in vessel digestion system, which is proposed here, will help in accelerating the conversion of organic waste into pathogen-free soil amendment, thereby, enhancing sustainable agriculture. (C) 2016 Elsevier Ltd. All rights reserved.