Pramod K. Pandey

Contamination of water resources by pathogenic bacteria

Water-borne pathogen contamination in water resources and related diseases are a major water quality concern throughout the world. Increasing interest in controlling water-borne pathogens in water resources evidenced by a large number of recent publications clearly attests to the need for studies that synthesize knowledge from multiple fields covering comparative aspects of pathogen contamination, and unify them in a single place in order to present and address the problem as a whole. Providing a broader perceptive of pathogen contamination in freshwater (rivers, lakes, reservoirs, groundwater) and saline water (estuaries and coastal waters) resources, this review paper attempts to develop the first comprehensive single source of existing information on pathogen contamination in multiple types of water resources. In addition, a comprehensive discussion describes the challenges associated with using indicator organisms. Potential impacts of water resources development on pathogen contamination as well as challenges that lie ahead for addressing pathogen contamination are also discussed.

Impacts of Temperatures on Biogas Production in Dairy Manure Anaerobic Digestion

Batch anaerobic digestion of dairy manure was performed at low (25 o C), mesophilic (37 o C), and thermophilic (52.5 o C) temperatures to determine the influences of temperatures on biogas production. The experiment was run for 76, 40 and 29 days at 25, 37, and 52.5 o C, respectively. The biogas production was measured daily at each temperature. To estimate the solid reductions, we measured total solids (TS) and volatile solids (VS) over time. The biogas production at 52.5 o C and 37 o C were 49 and 17 times higher than that at 25 o C. Over incubation periods, the TS reduction at 25, 37, and 52.5 o C were 5.6, 57, 34%, respectively. The VS reductions were 127, 58.4, 42.5%, respectively. At 25 and 37 o C, pH was reduced, while at 52.5 o C pH was increased. The Oxidation Reduction Potential (ORP) values at 37 and 52.5 o C were negative over the incubation period. But at 25 o C, however, the ORP values were positive after Day 19. Findings from this study are useful for enhancing anaerobic digesters’ performance.

Sub-lethal effects of herbicides penoxsulam, imazamox, fluridone and glyphosate on Delta Smelt ( Hypomesus transpacificus )

Concerns regarding non-target toxicity of new herbicides used to control invasive aquatic weeds in the San Francisco Estuary led us to compare sub-lethal toxicity of four herbicides (penoxsulam, imazamox, fluridone, and glyphosate) on an endangered fish species Delta Smelt (Hypomesus transpacificus). We measured 17β-estradiol (E2) and glutathione (GSH) concentrations in liver, and acetylcholinesterase (AChE) activity in brain of female and male fish after 6 h of exposure to each of the four herbicides. Our results indicate that fluridone and glyphosate disrupted the E2 concentration and decreased glutathione concentration in liver, whereas penoxsulam, imazamox, and fluridone inhibited brain AChE activity. E2 concentrations were significantly increased in female and male fish exposed to 0.21 μM of fluridone and in male fish exposed to 0.46, 4.2, and 5300 μM of glyphosate. GSH concentrations decreased in males exposed to fluridone at 2.8 μM and higher, and glyphosate at 4.2 μM. AChE activity was significantly inhibited in both sexes exposed to penoxsulam, imazamox, and fluridone, and more pronounced inhibition was observed in females. The present study demonstrates the potential detrimental effects of these commonly used herbicides on Delta Smelt.

Assessing Salmonella typhimurium persistence in poultry carcasses under multiple thermal conditions consistent with composting and wet rendering

Mitigation of Salmonella associated with poultry carcasses is primarily accomplished by rendering or carcass composting. While rendering temperatures and pressures are well established for pathogen inactivation in poultry carcasses, parameters controlling composting processes are less defined in part because multiple conditions and procedures are utilized. Consequently, limited knowledge exists describing the impacts of composting with varying temperature and mixing protocols with respect to the inactivation of Salmonella in poultry carcasses. To improve the existing knowledge of Salmonella survival in poultry carcasses, inactivation of Salmonella enterica serovar Typhimurium (ST) LT2 was investigated. The impacts of various composting temperatures (55, 62.5°C) and low-rendering (i.e., pasteurization) temperatures (70, 78°C) on Salmonella inactivation were tested in a bench-top setting using a ground carcass slurry and whole birds under mixed and non-mixed conditions. Results showed that the ground carcass slurry and the whole carcass exposed to temperatures consistent with composting had no detectable Salmonella after 110 h with a level of detection of one CFU/mL of ground carcass slurry and one CFU/g of whole carcasses, respectively. In addition, grinding of carcasses as opposed to whole carcasses was more predictable with respect to Salmonella heat inactivation. Furthermore, results showed that constant mixing decreased the overall time required to eliminate Salmonella under composting and low-rendering temperatures.

Water and Sediment Microbial Quality of Mountain and Agricultural Streams

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 USEPAs existing water quality criteria for bacteria. However, the levels in the agricultural stream exceeded the USEPAs 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.

Effect of Dairy Manure Storage Conditions on the Survival of E. coli O157:H7 and Listeria

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.

Colostrum immunoglobulin G concentration of multiparous Jersey cows at first and second milking is associated with parity, colostrum yield, and time of first milking, and can be estimated with Brix refractometry

The objective of this study was to evaluate colostrum IgG concentration harvested at first and second milking from multiparous Jersey cows, the dams lactation number, colostrum yield, and time of first milking. In addition, we validated the use of a Brix refractometer to estimate IgG concentration in colostrum from multiparous Jersey cows using radial immunodiffusion as the reference method. Colostrum samples and total weight of colostrum harvested at first (n = 134) and second (n = 68) milking were collected from 134 multiparous Jersey cows housed in a California herd. Fresh colostrum samples were analyzed for IgG concentration with Brix refractometry and frozen samples by radial immunodiffusion. A total of 90.4 and 42.7% of the samples from first and second milking met industry standards of quality for IgG concentration (>50 g/L). Second and third lactation cows had similar colostrum IgG concentration but lower than cows on their fourth and greater lactation. At second milking, 56.4% of cows on their fourth or greater lactation had colostrum IgG concentrations >50 g/L. When colostrum yield increased from low (<3 kg), medium (3 to 6 kg), to high (>6 kg), IgG concentration decreased. Higher IgG concentration was observed on colostrum harvested at <6 h (short) versus 6 to 11 h (medium) after calving. However, IgG concentration in colostrum harvested after 11 h (long) was similar to that harvested at short and medium time. Readings of %Brix were highly correlated with IgG at first (r = 0.81) and second (r = 0.77) milking. The best Brix threshold to identify colostrum from first milking with >50 IgG g/L was 20.9% based on logit equations with Youdens index criterion and 18.0% based on accuracy criterion. For colostrum harvested at second milking, similar Brix thresholds were obtained, 19.2 and 19.0%, regardless of whether Youdens index or accuracy was used as the selection criterion. Our results indicate that the dams lactation number, colostrum yield, and time of first milking relative to calving are associated with IgG concentration in colostrum from multiparous Jersey cows. Second milking colostrum from mature Jersey cows should be evaluated to extend colostrum supply on dairies especially during times of shortage. Readings of %Brix can be used to rapidly estimate IgG concentration in Jersey colostrum harvested at first and second milking.

Modelling animal waste pathogen transport from agricultural land to streams

The transport of animal waste pathogens from crop land to streams can potentially elevate pathogen levels in stream water. Applying animal manure into crop land as fertilizers is a common practice in developing as well as in developed countries. Manure application into the crop land, however, can cause potential human health. To control pathogen levels in ambient water bodies such as streams, improving our understanding of pathogen transport at farm scale as well as at watershed scale is required. To understand the impacts of crop land receiving animal waste as fertilizers on streams pathogen levels, here we investigate pathogen indicator transport at watershed scale. We exploited watershed scale hydrological model to estimate the transport of pathogens from the crop land to streams. Pathogen indicator levels (i.e., E. coli levels) in the stream water were predicted. With certain assumptions, model results are reasonable. This study can be used as guidelines for developing the models for calculating the impacts of crop lands animal manure on stream water.

Effect of the macroalgae Asparagopsis taxiformis on methane production and the rumen microbiome assemblage

Background Recent studies using batch-fermentation suggest that the red macroalgae Asparagopsis taxiformis might reduce methane (CH4) emission from beef cattle by up to ~99% when added to rhodes grass hay, a common feed in the Australian beef industry. These experiments have shown significant reductions in methane without compromising other fermentation parameters (i.e. volatile fatty acid production) with A. taxiformis organic matter (OM) inclusion rates of up to 5%. In the study presented here, A. taxiformis was evaluated for its ability to reduce methane production from dairy cattle fed a mixed ration widely utilized in California; the largest milk producer in the US. Results Fermentation in a semi-continuous in-vitro rumen system suggests that A. taxiformis can reduce methane production from enteric fermentation in dairy cattle by 95% when added at a 5% OM inclusion rate without any obvious negative impacts on volatile fatty acid production. High-throughput 16S ribosomal RNA (rRNA) gene amplicon sequencing showed that seaweed amendment effects rumen microbiome communities consistent with the Anna Karenina hypothesis, with increased beta-diversity, over time scales of approximately three days. The relative abundance of methanogens in the fermentation vessels amended with A. taxiformis decreased significantly compared to control vessels, but this reduction in methanogen abundance was only significant when averaged over the course of the experiment. Alternatively, significant reductions of methane in the A. taxiformis amended vessels was measured in the early stages of the experiment. This suggests that A. taxiformis has an immediate effect on the metabolic functionality of rumen methanogens whereas its impact on microbiome assemblage, specifically methanogen abundance, is delayed. Conclusions The methane reducing effect of A. taxiformis during rumen fermentation makes this macroalgae a promising candidate as a biotic methane mitigation strategy in the largest milk producing state in the US. But its effect in-vivo (i.e. in dairy cattle) remains to be investigated in animal trials. Furthermore, to obtain a holistic understanding of the biochemistry responsible for the significant reduction of methane, gene expression profiles of the rumen microbiome and the host animal are warranted.

16S rRNA analysis of diversity of manure microbial community in dairy farm environment.

Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers.