Effect of poultry litter soil amendment on antibiotic-resistant Escherichia coli.

Given the high cost and non-renewability of mineral-based fertilizers, there is increasing interest in the innovative use of manure-based materials, such as poultry litter (PL). However, manure-based fertilizers add both nutrients and microbes to the soil, including antibiotic-resistant Escherichia coli (AREc). PL soil amendment impact on AREc in corn fields was evaluated in a randomized field experiment (May-October 2017). Two winter cropping systems (fallow and cover crop) were assigned to whole plots, with three spring-applied fertilizer treatments (untreated control [UC], PL, and commercial fertilizer [CF]) assigned to subplots. Soil was collected from 0 to 15 cm on days 0, 7, 28, 70, 98, and 172 post-treatment applications. Samples were cultured for the enumeration and prevalence of generic, tetracycline-resistant (TETr), third-generation cephalosporin-resistant (3GCr) E. coli isolates, and extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae. PL soil amendment significantly (p < 0.05) increased the levels of generic E. coli, TETr E. coli, and 3GCr E. coli on days 7 and 28 compared to UC or CF. Beyond day 28, AREc did not significantly (p > 0.05) differ by fertilizer treatment and returned to baseline on day 70. ESBL-producing Enterobacteriaceae were detected from 16 samples, mostly on day 70. Cover crop significantly decreased TETr E. coli concentration on day 28, with no significant effects on the prevalence of 3GCr E. coli and ESBL-producing Enterobacteriaceae compared to no cover crop. All ESBL-producing Enterobacteriaceae and 79% of the 3GCr E. coli isolates were positive for blaCTX-M gene by polymerase chain reaction. Results show that PL soil amendment transiently increases the levels of AREc compared to mineral fertilizer.

Microbiome Diversity of Anaerobic Digesters Is Enhanced by Microaeration and Low Frequency Sound.

Biogas is produced by a consortium of bacteria and archaea. We studied how the microbiome of poultry litter digestate was affected by time and treatments that enhanced biogas production. The microbiome was analyzed at six, 23, and 42 weeks of incubation. Starting at week seven, the digesters underwent four treatments: control, microaeration with 6 mL air L-1 digestate per day, treatment with a 1000 Hz sine wave, or treatment with the sound wave and microaeration. Both microaeration and sound enhanced biogas production relative to the control, while their combination was not as effective as microaeration alone. At week six, over 80% of the microbiome of the four digesters was composed of the three phyla Actinobacteria, Proteobacteria, and Firmicutes, with less than 10% Euryarchaeota and Bacteroidetes. At week 23, the digester microbiomes were more diverse with the phyla Spirochaetes, Synergistetes, and Verrucomicrobia increasing in proportion and the abundance of Actinobacteria decreasing. At week 42, Firmicutes, Bacteroidetes, Euryarchaeota, and Actinobacteria were the most dominant phyla, comprising 27.8%, 21.4%, 17.6%, and 12.3% of the microbiome. Other than the relative proportions of Firmicutes being increased and proportions of Bacteroidetes being decreased by the treatments, no systematic shifts in the microbiomes were observed due to treatment. Rather, microbial diversity was enhanced relative to the control. Given that both air and sound treatment increased biogas production, it is likely that they improved poultry litter breakdown to promote microbial growth.

Reused poultry litter microbiome with competitive exclusion potential against Salmonella Heidelberg.

The success of poultry litter reuse in U.S. poultry production can be attributed to the efficient treatment methods used by producers during downtimes (the time lapse between consecutive flocks, during which the broiler house is empty). During this period, reused litter may be decaked, tilled/windrowed, or treated with acid-based amendments to reduce ammonia and bacteria levels. Competitive exclusion, pH, and temperature are proposed factors that influence the level of pathogens and the overall litter microbiome during downtimes. We previously reported on the bacterial genetic factors associated with the fitness of two strains of Salmonella enterica serovar Heidelberg (SH) incubated for 14 d in reused litter. Here, we investigated the physicochemical parameters and the microbiome of the litter correlating with SH abundance during this period. We used 16S ribosomal RNA gene sequencing to determine the litter microbiome and whole genome sequencing to characterize bacteria with competitive exclusion potential against SH. The ß diversity of the litter microbiome was significantly affected by the duration of incubation, microcosm, and microcosm plus Heidelberg strain combinations. In addition, ß diversity was significantly affected by litter parameters, including NH4 , pH, moisture, water activity, and aluminum. The major phyla observed in the reused litter throughout the 14-d incubation experiment were Firmicutes and Actinobacteria, although their abundance differed by microcosm and time. Amplicon-specific variants homologous to the members of the genera Nocardiopsis and Lentibacillus and the family Bacillaceae_2 were found to significantly correlate with the abundance of Salmonella. A consortium of Bacillus subtilis strains isolated from the litter microcosms reduced the growth of SH in vitro.

Persistence of antibiotic resistance genes in beef cattle backgrounding environment over two years after cessation of operation.

Confined animal feeding operations can facilitate the spread of genes associated with antibiotic resistance. It is not known how cattle removal from beef cattle backgrounding operation affects the persistence of antibiotic resistance genes (ARGs) in the environment. We investigated the effect of cessation of beef cattle backgrounding operation on the persistence and distribution of ARGs in the beef cattle backgrounding environment. The study was conducted at a pasture-feedlot type beef cattle backgrounding operation which consisted of feeding and grazing areas that were separated by a fence with an access gate. Backgrounding occurred for seven years before cattle were removed from the facility. Soil samples (n = 78) from 26 georeferenced locations were collected at the baseline before cattle were removed, and then one year and two years after cattle were removed. Metagenomic DNA was extracted from the soil samples and total bacterial population (16S rRNA), total Enterococcus species and class 1 integrons (intI1), and erythromycin (ermB and ermF), sulfonamide (sul1 and sul2) and tetracycline (tetO, tetW and tetQ) resistance genes were quantified. Concentrations of total bacteria, Enterococcus spp., class 1 integrons, and ARGs were higher in the feeding area and its immediate vicinity (around the fence and the gate) followed by a gradient decline along the grazing area. Although the concentrations of total bacteria, Enterococcus spp., class 1 integrons and ARGs in the feeding area significantly decreased two years after cattle removal, their concentrations were still higher than that observed in the grazing area. Higher concentrations over two years in the feeding area when compared to the grazing area suggest a lasting effect of confined beef cattle production system on the persistence of bacteria and ARGs in the soil.

Field-scale fluorescence fingerprinting of biochar-borne dissolved organic carbon.

Biochar continues to receive worldwide enthusiasm as means of augmenting recalcitrant organic carbon in agricultural soils. Realistic biochar amendment rate (typically less than 1 wt%) in the field scale, and subsequent loss by sizing, rain, and other transport events demand reliable methods to quantify the remaining portions of amended biochar. This study employed fluorescence excitation-emission (EEM) spectrophotometry and parallel factor analysis (PARAFAC) to specifically target pyrogenic dissolved organic carbon (DOC) released by amended biochar during the course of a field trial at Bowling Green, KY experimental site. Toluene/methanol (1:6 v/v) extracts of surface (0-15 cm) soils amended with 21.28 t ha(-1) fast pyrolysis biochar afforded PARAFAC fingerprints representing different degrees of aromaticity. Compared to the control without treatments, biochar treatment (with and without poultry manure or chemical fertilizer) increased the relative contribution of PARAFAC fingerprint attributable to labile polyaromatic DOC structures. Poultry manure or chemical fertilizer alone (without biochar) did not influence the amounts of polyaromatic DOC structures. Existence of biochar could be further validated by the changes in %DOC (relative to the total carbon), fixed C content, and UV absorbance (360 nm), whereas FTIR, %O, and sorption of model agrochemical (deisopropylatrazine) did not reflect the presence of biochar in the soil samples. Developed toluene/methanol-based EEM-PARAFAC technique will provide a sensitive, rapid, and cost-competitive method to validate the long-term carbon sequestration by the biochar soil amendment.

Mercury emission and plant uptake of trace elements during early stage of soil amendment using flue gas desulfurization materials.

A pilot-scale field study was carried out to investigate the distribution of Hg and other selected elements (i.e., As, B, and Se), i.e., emission to ambient air, uptake by surface vegetation, and/or rainfall infiltration, after flue gas desulfurization (FGD) material is applied to soil. Three FGD materials collected from two power plants were used. Our results show Hg released into the air and uptake in grass from all FGD material-treated soils were all higher (P < 0.1) than the amounts observed from untreated soil. Hg in the soil amended with the FGD material collected from a natural oxidation wet scrubber (i.e., SNO) was more readily released to air compared to the other two FGD materials collected from the synthetic gypsum dewatering vacuum belt (i.e., AFO-gypsum) and the waste water treatment plant (i.e., AFO-CPS) of a forced oxidation FGD system. No Hg was detected in the leachates collected during the only 3-hour, 1-inch rainfall event that occurred throughout the 4-week testing period. For every kilogram of FGD material applied to soil, AFO-CPS released the highest amount of Hg, B, and Se, followed by SNO, and AFO gypsum. Based on the same energy production rate, the land application of SNO FGD material from Plant S released higher amounts of Hg and B into ambient air and/or grass than the amounts released when AFO-gypsum from Plant A was used. Using FGD material with lower concentration levels of Hg and other elements of concern does not necessary post a lower environmental risk. In addition, this study demonstrates that considering only the amounts of trace elements uptake in surface vegetation may under estimate the overall release of the trace elements from FGD material-amended soils. It also shows, under the same soil amendment conditions, the mobility of trace elements varies when FGD materials produced from different processes are used.

Links among nitrification, nitrifier communities, and edaphic properties in contrasting soils receiving dairy slurry.

Soil biotic and abiotic factors strongly influence nitrogen (N) availability and increases in nitrification rates associated with the application of manure. In this study, we examine the effects of edaphic properties and a dairy (Bos taurus) slurry amendment on N availability, nitrification rates and nitrifier communities. Soils of variable texture and clay mineralogy were collected from six USDA-ARS research sites and incubated for 28 d with and without dairy slurry applied at a rate of ~300 kg N ha(-1). Periodically, subsamples were removed for analyses of 2 M KCl extractable N and nitrification potential, as well as gene copy numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Spearman coefficients for nitrification potentials and AOB copy number were positively correlated with total soil C, total soil N, cation exchange capacity, and clay mineralogy in treatments with and without slurry application. Our data show that the quantity and type of clay minerals present in a soil affect nitrifier populations, nitrification rates, and the release of inorganic N. Nitrogen mineralization, nitrification potentials, and edaphic properties were positively correlated with AOB gene copy numbers. On average, AOA gene copy numbers were an order of magnitude lower than those of AOB across the six soils and did not increase with slurry application. Our research suggests that the two nitrifier communities overlap but have different optimum environmental conditions for growth and activity that are partly determined by the interaction of manure-derived ammonium with soil properties.

Evaluation of nitrogen retention and microbial populations in poultry litter treated with chemical, biological or adsorbent amendments.

Poultry litter is a valuable nutrient source for crop production. Successful management to reduce ammonia and its harmful side-effects on poultry and the environment can be aided by the use of litter amendments. In this study, three acidifiers, two biological treatments, one chemical urease inhibitor and two adsorber amendments were added to poultry litter. Chemical, physical and microbiological properties of the litters were assessed at the beginning and the end of the experiment. Application of litter amendments consistently reduced organic N loss (0-15%) as compared to unamended litter (20%). Acidifiers reduced nitrogen loss through both chemical and microbiological processes. Adsorbent amendments (water treatment residuals and chitosan) reduced nitrogen loss and concentrations of ammonia-producing bacteria and fungi. The use of efficient, cost-effective litter amendments to maximum agronomic, environmental and financial benefits is essential for the future of sustainable poultry production.

Microbial mineralization of organic nitrogen forms in poultry litters.

Ammonia volatilization from the mineralization of uric acid and urea has a major impact on the poultry industry and the environment. Dry acids are commonly used to reduce ammonia emissions from poultry houses; however, little is known about how acidification affects the litter biologically. The goal of this laboratory incubation was to compare the microbiological and physiochemical effects of dry acid amendments (Al+Clear, Poultry Litter Treatment, Poultry Guard) on poultry litter to an untreated control litter and to specifically correlate uric acid and urea contents of these litters to the microbes responsible for their mineralization. Although all three acidifiers eventually produced similar effects within the litter, there was at least a 2-wk delay in the microbiological responses using Poultry Litter Treatment. Acidification of the poultry litter resulted in >3 log increases in total fungal concentrations, with both uricolytic (uric acid degrading) and ureolytic (urea degrading) fungi increasing by >2 logs within the first 2 to 4 wk of the incubation. Conversely, total, uricolytic, and ureolytic bacterial populations all significantly declined during this same time period. While uric acid and urea mineralization occurred within the first 2 wk in the untreated control litter, acidification resulted in delayed mineralization events for both uric acid and urea (2 and 4 wk delay, respectively) once fungal cell concentrations exceeded a threshold level. Therefore, fungi, and especially uricolytic fungi, appear to have a vital role in the mineralization of organic N in low-pH, high-N environments, and the activity of these fungi should be considered in best management practices to reduce ammonia volatilization from acidified poultry litter.

Determination of ammonia and greenhouse gas emissions from land application of swine slurry: a comparison of three application methods.

In this study, the comparison and monitoring of the initial greenhouse gas (GHG) emissions using a flux chamber and gas analyzer from three different liquid manure application methods at a swine farm in Kentucky were carried out. Swine slurry was applied to farmland by row injection, surface spray, and Aerway injection. Ammonia and GHG concentrations were monitored immediately after application, 72 and 216h after application. The results showed that the initial ammonia flux ranged from 5.80 mg m(-2)h(-1) for the surface spray method to 1.80 mg m(-2)h(-1) for the row injection method. The initial fluxes of methane ranged from 8.75 mg m(-2)h(-1) for surface spray to 2.27 mg m(-2)h(-1) for Aerway injection, carbon dioxide ranged from 4357 mg m(-2)h(-1) for surface spray to 60 mg m(-2)h(-1) for row injection, and nitrous oxide ranged from 0.89 mg m(-2)h(-1) for surface spray to 0.22 mg m(-2)h(-1) for row injection. However, the Aerway injection method seemed to create the highest gas (GHG) concentrations inside the monitoring chambers at the initial application and produced the highest gas fluxes at subsequent sampling time (e.g., 72h after application). Nevertheless, the surface spray method appeared to produce the highest gas fluxes, and the row injection method appeared to emit the least amount of greenhouse gases into the atmosphere. Gas fluxes decreased over time and did not depend on the initial headspace concentration in the monitoring flux chambers.

The effect of stratification and seasonal variability on the profile of an anaerobic swine waste treatment lagoon.

In this study, the characterization of an anaerobic swine waste treatment lagoon from a farrowing operation (approximately 2000 sows) was carried out to examine the dynamics of the system due to stratification and seasonal variability. Swine waste samples were taken at different depths with a pulley system equipped with a special sampler that allows for sampling exclusively at certain depth. Chemicals and microbial dynamics were monitored throughout a one-year-period. Results showed that nutrient (C, N, P, S) concentrations varied according to stratified lagoon layers and season. Trace minerals (Al, Ca, Fe, and Mg), on the other hand, appeared to be affected more by stratification than seasonal variability. Molecular analysis also showed that microbial community structure appeared to be affected by the stratification and seasonal variability. Based on these data, it is important to consider the effect of stratification and seasonal variability in managing these open lagoons.

Effect of alum treatment on the concentration of total and ureolytic microorganisms in poultry litter.

Microbial mineralization of urea and uric acid in poultry litter results in the production of ammonia, which can lead to decreased poultry performance, malodorous emissions, and loss of poultry litter value as a fertilizer. Despite the fact that this is a microbial process, little is known about how the microbial populations, especially ammonia-producing (ureolytic) organisms in poultry litter, respond to litter amendments such as aluminum sulfate (Al(2)(SO(4))(3).14H(2)O; alum). The goal of this study was to measure the temporal changes in total bacterial and fungal populations and urease-producing microorganisms in nontreated litter or litter treated with 10% alum. Quantitative real-time polymerase chain reaction was used to target the bacterial 16S rRNA gene, the fungal 18S rRNA gene, or the urease gene of bacterial and fungal ammonia producers in a poultry litter incubation study. Nontreated poultry litter had relatively high total (2.8 +/- 0.8 x 10(10) cells g(-1) litter) and ureolytic (2.8 +/- 1.3 x 10(8) cells g(-1) litter) bacterial populations. Alum treatment reduced the total bacterial population by 50% and bacterial urease producers by 90% within 4 wk. In contrast, at 16 wk after alum treatment, the fungal population was three orders of magnitude higher in alum-treated litter than in nontreated litter (3.5 +/- 0.8 x 10(7) cells g(-1) litter and 5.5 +/- 2.5 x 10(4) cells g(-1) litter, respectively). The decrease in pH produced by alum treatment is believed to inhibit bacterial populations and favor growth of fungi that may be responsible for the mineralization of organic nitrogen in alum-treated litters.

The impact of alum addition on organic P transformations in poultry litter and litter-amended soil.

Poultry litter treatment with alum (Al(2)(SO(4))(3) . 18H(2)O) lowers litter phosphorus (P) solubility and therefore can lower litter P release to runoff after land application. Lower P solubility in litter is generally attributed to aluminum-phosphate complex formation. However, recent studies suggest that alum additions to poultry litter may influence organic P mineralization. Therefore, alum-treated and untreated litters were incubated for 93 d to assess organic P transformations during simulated storage. A 62-d soil incubation was also conducted to determine the fate of incorporated litter organic P, which included alum-treated litter, untreated litter, KH(2)PO(4) applied at 60 mg P kg(-1) of soil, and an unamended control. Liquid-state (31)P nuclear magnetic resonance indicated that phytic acid was the only organic P compound present, accounting for 50 and 45% of the total P in untreated and alum-treated litters, respectively, before incubation and declined to 9 and 37% after 93 d of storage-simulating incubation. Sequential fractionation of litters showed that alum addition to litter transformed 30% of the organic P from the 1.0 mol L(-1) HCl to the 0.1 mol L(-1) NaOH extractable fraction and that both organic P fractions were more persistent in alum-treated litter compared with untreated litter. The soil incubation revealed that 0.1 mol L(-1) NaOH-extractable organic P was more recalcitrant after mixing than was the 1.0 mol L(-1) HCl-extractable organic P. Thus, adding alum to litter inhibits organic P mineralization during storage and promotes the formation of alkaline extractable organic P that sustains lower P solubility in the soil environment.