Dynamics of a pig slurry microbial community during anaerobic storage and management

Effects of swine manure dilution with lagoon effluent on microbial communities and odor formation in pit recharge systems

Pit recharge systems (PRS) control odor by managing organic solids in swine manure. However, there needs to be more understanding of PRS's effect on the microbiome composition and its impact on odor formation. A study was conducted to understand how recharge intervals used in PRS impact manure microbiome and odor formation. Bioreactors dynamically loaded simulated recharge intervals of 14, 10, and 4 days by diluting swine manure with lagoon effluent at varying ratios. Treatment ratios tested included 10:0 (control), 7:3 (typical Korean PRS), 5:5 (enhanced PRS #1), and 2:8 (enhanced PRS #2). Manure microbial membership, chemical concentrations, and odorant concentrations were used to identify the interactions between microbiota, manure, and odor. The initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent, respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9% or increased by 17.6%, respectively, with each unit dilution. Microbial community composition was controlled by both treatment (i.e., manure dilution ratio and barn source material) and environmental factors (i.e., solids and pH). Microbiome composition was correlated with manure odor formation profiles, but this effect was inseparable from environmental factors, which explained over 75% of the variance in odor profiles. Consequently, monitoring solids and pH in recharge waters will significantly impact odor control in PRS.

Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion

Direct application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment.

Microbial diversity dynamics during the self-acidification of dairy slurry

Slurry acidification has been shown to be effective in reducing environmentally damaging gases. However, this involved the use of concentrated acids on farms. Therefore, due to the health and safety concerns, there is an interest in self-acidification of slurry technique. This study was designed to determine the microbial dynamics leading to self-acidification of slurry. A fresh cattle slurry was amended 10% brewing sugar and stored over 30 days. This fermentable carbon source promoted self-acidification of the slurry from pH 7.0 to 4.7 within four days, and was associated with the accumulation of lactic acid and a reduction in methane and relative ammonia emissions. A metagenomics approach through next generation sequencing (NGS) using an Illumina MiSeq platform was used to determine the microbial diversity and dynamics (bacteria and archaea) in the stored amended slurry. 16S ribosomal ribonucleic acid (rRNA) sequence data revealed the presence of the Order of Lactobacillales was associated with the lactic acid production. The operational taxonomic units (OTUs) abundance indicates that the methanogenic community was dominated by hydrogenotrophic methanogens from the member Order of Methanobacteriales, Methanomicrobiales, and Methanosarcinales. The decrease in tolerance by the methanogens in the self-acidified slurry was probably the main reason for the reduced methane emission. These results confirm, at the microbial level, the mechanism of inhibiting methane production via self-acidification during storage period.

Enhanced anaerobic treatment of swine wastewater with exogenous granular sludge: Performance and mechanism

Anaerobic biotechnology has been widely used to the treatment of swine wastewater, but its organic loading rate is far lower than the expected. In this study, the fatigue effect was observed for indigenous anaerobic sludge (IAS) of anaerobic digestion system treating swine wastewater. On the contrary, the enhancement effect was demonstrated for exogenous granular sludge (EGS) originated from the internal circulation reactor treating pulping wastewater. The results showed the anaerobic digestion of swine wastewater with acclimatized EGS was much better than with IAS, 10th-day COD removal efficiency of 85% and 37% respectively. The better performance of acclimatized EGS was attributed to the more efficient degradation of volatile fatty acids (VFAs) as well as a stronger tolerance to the ammonia inhibition of swine wastewater. Revealed by molecular techniques, the acclimatized EGS contained more abundant syntrophic bacteria and methanogens than IAS. These functional microbes colonized in the acclimatized EGS could overcome the fatigue effect of IAS which contained a similar microbial community to pig gastrointestinal tract microbes. This study provides a feasible and promising way to enhance the efficiency of anaerobic digestion of swine wastewater.

Methodology for the design and economic assessment of anaerobic digestion plants to produce energy and biofertilizer from livestock waste

The generation and poor disposal of waste from livestock industries is the major cause of pollution of water sources, soil, and air. Therefore, profitable alternatives are required for their correct disposal and use. Anaerobic digestion plants are a technologically viable solution to overcome this problem. In this study, it is proposed a methodology for the design and economic assessment of projects using anaerobic digestion plants to produce electrical energy, thermal energy, and biofertilizer from livestock waste. The methodology is developed based on the assumption that the process is mainly composed of an anaerobic digester and an electric generator having a Diesel-cycle internal combustion engine. It is programmed in "MS Excel" sheet and assessed using technical and economic data from a three real anaerobic digestion plants. The methodology obtains technical parameters such as energy production efficiency with an average difference of 35% compared to the real plants data. In addition, the unit capital costs are calculated, obtaining a value of €3789/kW with a difference of 21.1%, as well as unit operating costs of €729/kW per year with a difference of 15.2%. The financial viability of the project is assessed by calculating the net present value and obtaining €577,050 with a difference of 17.8% and an internal rate of return with a percentage difference of 3%. The proposed methodology specifies the technical parameters and the basic engineering of an anaerobic digestion plant in a stationary state, where the basic streams and dimensions of primary equipment, such as anaerobic reactors and electric generators, are specified. Moreover, the methodology calculates capital and operating expenses for an anaerobic digestion plant, which may be useful to assess the technical and financial feasibility for a project of this type.

Fate of Mycobacterium avium subsp. paratuberculosis and changes in bacterial diversity populations in dairy slurry after chemical treatments

AIMS

A major drawback of using dairy slurry as fertilizer is that it may contains pathogens such as Mycobacterium avium subsp. paratuberculosis (MAP), and it could represent a risk to animal and public health. Thus, the aim of this study was to evaluate the fate of MAP and bacterial communities in dairy slurry after chemical treatments.

METHODS AND RESULTS

Cattle slurry, naturally contaminated with MAP, was collected from a dairy herd and divided into 32 glass bottles which were assigned to eight different treatments (control, 3·0% CaO, 0·5% NaOH; 0·087%, 0·11% and 0·14% H₂ SO₄ ; and 1·0 and 2·5% KMnO₄ ). Treated dairy slurry samples were evaluated at 0, 1, 3, 7, 15, 30 and 60-days following treatment application for viable MAP and dairy slurry pH, and in addition temperature in this material was monitored continuously. Bacterial counts were estimated at each sampling time. A Bayesian zero-inflated Poisson mixed model was fitted to assess the effect of each treatment on the count of MAP cells. Model results indicated that only the 3·0% CaO treatment had a statistically important negative effect on MAP counts during the study period. For most treatments, MAP was undetectable immediately after chemical treatment but re-appeared over time, in some replicates at low concentrations. However, in those cases MAP counts were not statistically different than the control treatment. Regarding the fate of the other bacterial populations, the Firmicutes phylum was the dominant population in the un-treated slurry while Clostridia class members were among the most prevalent bacteria after the application of most chemical treatments.

CONCLUSION

Only 3% CaO treatment had a statistically important negative effect on MAP viability in cattle slurry.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides evidence of MAP partial control in dairy slurry. This information should be considered as a best management practice to reduce MAP and other pathogens for slurry management on dairy farms.

Pyrosequencing-based analysis of the complex microbiota located in the gastrointestinal tracts of growing-finishing pigs

The commensal gut microbial communities play an important role in the health and production efficiency of growing-finishing pigs. This study aimed to analyse the composition and diversity of the microbiota in the gastrointestinal tract sections (stomach, duodenum, jejunum, ileum, caecum, colon and rectum) of growing-finishing pigs. This analysis was assessed using 454 pyrosequencing targeting the V3–V6 region of the 16S rRNA gene. Samples were collected from 20, healthy pigs aged 24 weeks and weighing 115.9 ± 5.4 kg. The dominant bacterial phyla in the various gastrointestinal tract sections were Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria. At the genus level, Prevotella, unclassified Lachnospiraceae, Ruminococcus, unclassified Ruminococcaceae and Oscillospira were more abundant in the large intestine than in the stomach and the small intestine. Unclassified Peptostreptococcaceae and Corynebacterium were more abundant in the small intestine than in the stomach and the large intestine. Shuttleworthia, unclassified Veillonellaceae and Mitsuokella were more abundant in the stomach than in the small and large intestines. At the species level, M. el.s.d.enii and M. multacida were predominant in the stomach. In addition, P. stercorea, P. copri, C. butyricum, R. flavefaciens and R. bromii were significantly more abundant in the large intestine than in the stomach and the small intestine. B. pseudolongum and B. thermacidophilum were significantly more abundant in the small intestine than in the stomach and the large intestine. Principal coordinates analysis showed that the overall composition of the pig gastrointestinal microbiota could be clustered into three groups: stomach, small intestine (duodenum, jejunum and ileum) and large intestine (caecum, colon and rectum). Venn diagrams illustrated the distribution of shared and specific operational taxonomic units among the various gastrointestinal tract sections.

Temporal Dynamics of Bacterial Communities in Soil and Leachate Water After Swine Manure Application

Application of swine manure to agricultural land allows recycling of plant nutrients, but excess nitrate, phosphorus and fecal bacteria impact surface and drainage water quality. While agronomic and water quality impacts are well studied, little is known about the impact of swine manure slurry on soil microbial communities. We applied swine manure to intact soil columns collected from plots maintained under chisel plow or no-till with corn and soybean rotation. Targeted 16S-rRNA gene sequencing was used to characterize and to identify shifts in bacterial communities in soil over 108 days after swine manure application. In addition, six simulated rainfalls were applied during this time. Drainage water from the columns and surface soil were sampled, and DNA was extracted and sequenced. Unique DNA sequences (OTU) associated with 12 orders of bacteria were responsible for the majority of OTUs stimulated by manure application. Proteobacteria were most prevalent, followed by Bacteroidetes, Firmicutes, Actinobacteria, and Spirochaetes. While the majority of the 12 orders decreased after day 59, relative abundances of genes associated with Rhizobiales and Actinomycetales in soil increased. Bacterial orders which were stimulated by manure application in soil had varied responses in drainage waters over the course of the experiment. We also identified a “manure-specific core” of five genera who comprised 13% of the manure community and were not significantly abundant in non-manured control soils. Of these five genera, Clostridium sensu stricto was the only genus which did not return to pre-manure relative abundance in soil by day 108. Our results show that enrichment responses after manure amendment could result from displacement of native soil bacteria by manure-borne bacteria during the application process or growth of native bacteria using manure-derived available nutrients.

Comparison of microbial communities in swine manure at various temperatures and storage times

Objective

This study was designed to investigate the effects of temperature and storage time on the evolution of bacterial communities in swine manure.

Methods

Manure was stored at −20°C, 4°C, 20°C, or 37°C and sampled at 7-day intervals over 28 days of storage, for a total of 5 time points. To assess the bacterial species present, 16S ribosomal RNA gene sequences were analyzed using pyrosequencing.

Results

After normalization, 113,934 sequence reads were obtained, with an average length of 466.6±4.4 bp. The diversity indices of the communities reduced as temperature and storage time increased, and the slopes of rarefaction curves decreased from the second week in samples stored at −20°C and 4°C. These results indicate that the richness of the bacterial community in the manure reduced as temperature and storage time increased. Firmicutes were the dominant phylum in all samples examined, ranging from 89.3% to 98.8% of total reads, followed by Actinobacteria, which accounted for 0.6% to 7.9%. A change in community composition was observed in samples stored at 37°C during the first 7 days, indicating that temperature plays an important role in determining the microbiota of swine manure. Clostridium, Turicibacter, Streptococcus, and Lactobacillus within Firmicutes, and Corynebacterium within Actinobacteria were the most dominant genera in fresh manure and all stored samples.

Conclusion

Based on our findings, we propose Clostridium as an indicator genus of swine manure decomposition in an anaerobic environment. The proportions of dominant genera changed in samples stored at 20°C and 37°C during the fourth week. Based on these results, it was concluded that the microbial communities of swine manure change rapidly as storage time and temperature increase.

Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process

Temperature plays crucial roles in microbial interactions that affect the stability and performance of anaerobic digestion. In this study, the microbial interactions and their succession in the anaerobic digestion process were investigated at three levels, represented by (1) present and (2) active micro-organisms, and (3) gene expressions under a temperature gradient from 25 to 55 °C. Network topological features indicated a global variation in microbial interactions at different temperatures. The variations of microbial interactions in terms of network modularity and deterministic processes based on topological features, corresponded well with the variations of methane productions, but not with temperatures. A common successional pattern of microbial interactions was observed at different temperatures, which showed that both deterministic processes and network modularity increased over time during the digestion process. It was concluded that the increase in temperature-mediated network modularity and deterministic processes on shaping the microbial interactions improved the stability and efficiency of anaerobic digestion process.

Effect of Storage Period on the Changes of Odorous Compound Concentrations and Bacterial Ecology for Identifying the Cause of Odor Production from Pig Slurry

Odor from buildings where pigs are housed is generated by anaerobic fermentation of undigested materials in pig slurry stored for several weeks in pit. The objective of this study was to investigate the effect of storage period on the level of odorous compounds in pig slurry and on its bacterial community. A slurry sample (15 L) was taken from the pit of a finisher pig building and incubated in acryl chambers for six- weeks. Slurry for analysis was sampled every two-week. Levels of odorous compounds in the slurry sample were drastically changed after two weeks of storage period; levels of phenols and short chain fatty acids (SCFAs) were decreased (P<0.05), whereas indoles and branched-chain fatty acids (BCFAs) were increased (P<0.05). Among dominant bacteria, Bacteroides and Porphyromonadacese_uc_g revealed a strong positive correlation with the levels of phenols and SCFAs. Populations of AC160630_g, Acholeplasmatales_uc_g, Mollicutes_uc_g and Cloacamonas_f_uc_g positively correlated with indole and BCFAs content. Taken together, levels of odorous compounds were increased after two weeks of storage, possibly because of changes in the predominant bacterial groups to those that use protein as a carbon source in the hypo-carbohydrate conditions.

Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil

Anaerobic digestion is an alternative method for the treatment of animal manure and wastewater. The anaerobic bioconversion of biomass requires a multi-step biological process, including microorganisms with distinct roles. The diversity and composition of microbial structure in pilot-scale anaerobic digestion operating at ambient temperature in Brazil were studied. Influence of the seasonal and temporal patterns on bacterial and archaeal communities were assessed by studying the variations in density, dynamic and diversity and structure. The average daily biogas produced in the summer and winter months was 18.7 and 16 L day(-1), respectively, and there was no difference in the average methane yield. Quantitative PCR analysis revealed that no differences in abundances and dynamics were found for bacterial communities and the total number of Archaea in different seasons. Analysis of bacterial clone libraries revealed a predominance of Firmicutes (54.5 %/summer and 46.7 %/winter) and Bacteroidetes (31.4 %/summer and 44.4 %/winter). Within the Archaea, the phylum Euryarchaeota was predominant in both digesters. Phylogenetic distribution showed changes in percentage between the phyla identified, but no alterations were recorded in the quality and amount of produced methane or community dynamics. The results may suggest that redundancy of microbial groups may have occurred, pointing to a more complex microbial community in the ecosystem related to this ambient temperature system.

Biotic and abiotic roles of leachate recirculation in batch mode solid-state anaerobic digestion of cattle manure

Solid state anaerobic digestion, with leachate recirculation, is suitable for exploiting manure with a high solid content. The biotic and abiotic effects of the leachates were studied in lab-scale leach bed reactors (LBRs). LBRs were fed with cow manure and four leachates either biologically active or inert. The biotic impact of leachate was assessed by monitoring the microbial communities in the manure and in the leachates. LBRs with biologically active leachates, regardless to their origin, produced equivalent methane volumes (114.52±19.05 and 99.79±6.4NL/kgVS) while LBRs with inert leachates produced half less methane (60.22±5.71 and 58.87±13.2NL/kgVS) attesting to the biotic role of leachate. Moreover, its beneficial abiotic role is mainly due to its initial nutrient content, pH, and buffering capacity. The microbial community in the manure was strongly involved in methane production, and no transfer of microorganisms from the liquid phase was found (p<0.05).

Prokaryote community dynamics in anaerobic co-digestion of swine manure, rice straw and industrial clay residuals

The aim of this study was to analyze the effect of the addition of rice straw and clay residuals on the prokaryote methane-producing community structure in a semi-continuously stirred tank reactor fed with swine manure. Molecular techniques, including terminal restriction fragment length polymorphism and a comparative nucleotide sequence analyses of the prokaryotic 16S rRNA genes, were performed. The results showed a positive effect of clay addition on methane yield during the co-digestion of swine manure and rice straw. At the digestion of swine manure, the bacterial phylum Firmicutes and the archaeal family Methanosarcinaceae, particularly Methanosarcina species, were predominant. During the co-digestion of swine manure and rice straw the microbial community changed, and with the addition of clay residual, the phylum Bacteroidetes predominated. The new nutritional conditions resulted in a shift in the archaeal family Methanosarcinaceae community as acetoclastic Methanosaeta species became dominant.

Assessment of Bacterial Community Assembly Patterns and Processes in Pig Manure Slurry

The bacterial community assembly patterns and processes are poorly understood in pig manure slurry. We collected pig manure slurry samples during the winter and summer seasons from eight commercial pig farms in South Korea. The V3 region of 16S rRNA genes was PCR amplified and sequenced using paired-end Illumina technology for in-depth characterization of bacterial community. Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Tenericutes were the predominant bacterial phyla present in slurry samples. Bacterial taxonomic community composition was not influenced by the season; however, phylogenetic community composition was affected by seasonal variations. The community composition and diversity patterns were strongly influenced by pH. The bacterial diversity indices showed a unimodal relationship with pH. Phylogenetic signals were detected over only short phylogenetic distances, revealing that closely related bacterial operational taxonomic units (OTUs) tend to co-occur in the same environment; hence, they are ecologically similar. Across all samples, a niche-based process, through strong environmental filtering imposed by pH, primarily governed bacterial community assembly; however, in samples close to the neutral pH range, the role of environmental filtering was decreased due to neutral community assembly. In summary, pH emerged as the major physico-chemical variable in pig manure slurry that regulates the relative importance of niche-based and neutral processes in shaping the community assembly of bacteria.

Assessment of bacterial and archaeal community structure in Swine wastewater treatment processes

Microbial communities from two field-scale swine wastewater treatment plants (WWTPs) were assessed by pyrosequencing analyses of bacterial and archaeal 16S ribosomal DNA (rDNA) fragments. Effluent samples from secondary (anaerobic covered lagoons and upflow anaerobic sludge blanket [UASB]) and tertiary treatment systems (open-pond natural attenuation lagoon and air-sparged nitrification-denitrification tank followed by alkaline phosphorus precipitation process) were analyzed. A total of 56,807 and 48,859 high-quality reads were obtained from bacterial and archaeal libraries, respectively. Dominant bacterial communities were associated with the phylum Firmicutes, Bacteroidetes, Proteobacteria, or Actinobacteria. Bacteria and archaea diversity were highest in UASB effluent sample. Escherichia, Lactobacillus, Bacteroides, and/or Prevotella were used as indicators of putative pathogen reduction throughout the WWTPs. Satisfactory pathogen reduction was observed after the open-pond natural attenuation lagoon but not after the air-sparged nitrification/denitrification followed by alkaline phosphorus precipitation treatment processes. Among the archaeal communities, 80% of the reads was related to hydrogeno-trophic methanogens Methanospirillum. Enrichment of hydrogenotrophic methanogens detected in effluent samples from the anaerobic covered lagoons and UASB suggested that CO2 reduction with H2 was the dominant methanogenic pathway in these systems. Overall, the results served to improve our current understanding of major microbial communities' changes downgradient from the pen and throughout swine WWTP as a result of different treatment processes.

Chaotropicity: a key factor in product tolerance of biofuel-producing microorganisms

Fermentation products can chaotropically disorder macromolecular systems and induce oxidative stress, thus inhibiting biofuel production. Recently, the chaotropic activities of ethanol, butanol and vanillin have been quantified (5.93, 37.4, 174kJ kg(-1)m(-1) respectively). Use of low temperatures and/or stabilizing (kosmotropic) substances, and other approaches, can reduce, neutralize or circumvent product-chaotropicity. However, there may be limits to the alcohol concentrations that cells can tolerate; e.g. for ethanol tolerance in the most robust Saccharomyces cerevisiae strains, these are close to both the solubility limit (<25%, w/v ethanol) and the water-activity limit of the most xerotolerant strains (0.880). Nevertheless, knowledge-based strategies to mitigate or neutralize chaotropicity could lead to major improvements in rates of product formation and yields, and also therefore in the economics of biofuel production.

Detection of pathogens, indicators, and antibiotic resistance genes after land application of poultry litter

Poultry litter (PL) is a by-product of broiler production. Most PL is land applied. Land-applied PL is a valuable nutrient source for crop production but can also be a route of environmental contamination with manure-borne bacteria. The objective of this study was to characterize the fate of pathogens, fecal indicator bacteria (FIB), and bacteria containing antibiotic resistance genes (ARGs) after application of PL to soils under conventional till or no-till management. This 2-yr study was conducted in accordance with normal agricultural practices, and microbial populations were quantified using a combination of culture and quantitative, real-time polymerase chain reaction analysis. Initial concentrations of in PL were 5.4 ± 3.2 × 10 cells g PL; sp. was not detected in the PL but was enriched periodically from PL-amended soils. was detected in PL (1.5 ± 1.3 × 10 culturable or 1.5 ± 0.3 × 10 genes g) but was rarely detected in field soils, whereas enterococci (1.5 ± 0.5 × 10 cells g PL) were detected throughout the study. These results suggest that enterococci may be better FIB for field-applied PL. Concentrations of ARGs for sulfonamide, streptomycin, and tetracycline resistance increased up to 3.0 orders of magnitude after PL application and remained above background for up to 148 d. These data provide new knowledge about important microbial FIB, pathogens, and ARGs associated with PL application under realistic field-based conditions.

Experimental study of the impact of antimicrobial treatments on Campylobacter, Enterococcus and PCR-capillary electrophoresis single-strand conformation polymorphism profiles of the gut microbiota of chickens

An experiment was conducted to compare the impact of antimicrobial treatments on the susceptibility of Campylobacter, Enterococcus faecium and Enterococcus faecalis, and on the diversity of broiler microbiota. Specific-pathogen-free chickens were first orally inoculated with strains of Campylobacter and Enterococcus faecium. Birds were then orally treated with recommended doses of oxytetracycline, sulfadimethoxine/trimethoprim, amoxicillin or enrofloxacin. Faecal samples were collected before, during and after antimicrobial treatment. The susceptibility of Campylobacter, Enterococcus faecium and Enterococcus faecalis strains isolated on supplemented or non-supplemented media was studied and PCR-capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) profiles of the gut microbiota were analysed. Enrofloxacin-resistant Campylobacter were selected in the enrofloxacin-treated group and showed the Thr86Ile mutation in the gyrA gene. Acquisition of the tetO gene in Campylobacter coli isolates was significantly more frequent in birds given oxytetracycline. No impact of amoxicillin treatment on the susceptibility of Campylobacter could be detected. Ampicillin- and sulfadimethoxine/trimethoprim-resistant Enterococcus faecium were selected in amoxicillin-treated broilers, but no selection of the inoculated vancomycin-resistant Enterococcus faecium could be detected, although it was also resistant to tetracycline and sulfadimethoxine/trimethoprim. PCR-CE-SSCP revealed significant variations in a few peaks in treated birds as compared with non-treated chickens. In conclusion, antimicrobial treatments perturbed chicken gut microbiota, and certain antimicrobial treatments selected or co-selected resistant strains of Campylobacter and Enterococcus.

Comparison of DNA extraction kits and modification of DNA elution procedure for the quantitation of subdominant bacteria from piggery effluents with real-time PCR

Four commercial DNA extraction kits and a minor modification in the DNA elution procedure were evaluated for the quantitation of bacteria in pig manure samples. The PowerSoil®, PowerFecal®, NucleoSpin® Soil kits and QIAamp® DNA Stool Mini kit were tested on raw manure samples and on lagoon effluents for their ability to quantify total bacteria and a subdominant bacteria specific of pig manure contamination: Lactobacillus amylovorus. The NucleoSpin® Soil kit (NS kit), and to a lesser extent the PowerFecal® kit were the most efficient methods. Regardless of the kit utilized, the modified elution procedure increased DNA yield in the lagoon effluent by a factor of 1.4 to 1.8. When tested on 10 piggery effluent samples, compared to the QIAamp kit, the NS kit combined with the modified elution step, increased by a factor up to 1.7 log₁₀ the values of the concentration of L. amylovorus. Regardless of the type of manure, the best DNA quality and the highest concentrations of bacteria were obtained using the NS kit combined with the modification of the elution procedure. The method recommended here significantly improved quantitation of subdominant bacteria in manure.

Spatial and temporal variations of microbial community in a mixed plug-flow loop reactor fed with dairy manure

Mixed plug-flow loop reactor (MPFLR) has been widely adopted by the US dairy farms to convert cattle manure to biogas. However, the microbiome in MPFLR digesters remains unexplored. In this study, the microbiome in a MPFLR digester operated on a mega-dairy farm was examined thrice over a 2 month period. Within 23 days of retention time, 55-70% of total manure solid was digested. Except for a few minor volatile fatty acids (VFAs), total VFA concentration and pH remained similar along the course of the digester and over time. Metagenomic analysis showed that although with some temporal variations, the bacterial community was rather stable spatially in the digester. The methanogenic community was also stable both spatially and temporally in the digester. Among methanogens, genus Methanosaeta dominated in the digester. Quantitative polymerase chain reaction (qPCR) analysis and metagenomic analysis yielded different relative abundance of individual genera of methanogens, especially for Methanobacterium, which was predominant based on qPCR analysis but undetectable by metagenomics. Collectively, the results showed that only small microbial and chemical gradients existed within the digester, and the digestion process occurred similarly throughout the MPFLR digester. The findings of this study may help improve the operation and design of this type of manure digesters.

Dynamics of soil bacterial communities in response to repeated application of manure containing sulfadiazine

Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ) which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as Devosia, Shinella, Stenotrophomonas, Clostridium, Peptostreptococcus, Leifsonia, Gemmatimonas, were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera Pseudomonas and Lysobacter, Hydrogenophaga, and Adhaeribacter decreased in response to the repeated application of manure and SDZ.

Microbial examination of anaerobic sludge adaptation to animal slurry

The objective of this study was to evaluate changes in the microbial population of anaerobic sludge digesters during the adaptation to pig slurry (PS) using quantitative real-time polymerase chain reaction (qPCR) and qualitative scanning electron microscopy (SEM). Additionally, the relationship between microbial parameters and sludge physicochemical composition and methane yield was examined. Results showed that the addition of PS to an unadapted thermophilic anaerobic digester caused an increase in volatile fatty acids (VFA) concentration, a decrease in removal efficiency and CH4 yield. Additionally, increases in total bacteria and total archaea were observed using qPCR. Scanning electron micrographs provided a general overview of the sludge's cell morphology, morphological diversity and degree of organic matter degradation. A change in microbial morphotypes from homogeneous cell morphologies to a higher morphological diversity, similar to that observed in PS, was observed with the addition of PS by SEM. Therefore, the combination of qPCR and SEM allowed expanding the knowledge about the microbial adaptation to animal slurry in thermophilic anaerobic digesters.

Bacterial communities in manures of piglets and adult pigs bred with different feeds revealed by 16S rDNA 454 pyrosequencing

Pyrosequencing-based analysis was used to characterize and compare bacterial communities in manure samples of piglets (GSPM) and adult pigs (GBPM) bred with green feeds without additives, and piglets (ASPM) and adult pigs (ABPM) bred with synthetic feeds containing additives. For each sample, 5,010 effective sequences were selected and utilized to do the bacterial composition analysis, respectively. In total, 1,489, 1,327, 941, and 883 operational taxonomic units were obtained at 5 % distance cutoff in GBPM, GSPM, ABPM, and ASPM, respectively. Bacterial phylotype richness in GBPM was higher than the other samples, and ASPM had the least richness. The most dominant class in the four samples is Bacteroidia. Approximately 41 % sequences in GBPM were affiliated with the Clostridiales order. Campylobacter, Clostridium and Streptococcus genera containing pathogenic bacteria were detected in the four samples. Bacterial diversity and abundance in swine manures varied with piglets, adult pigs, and feeds. In the four samples, higher bacterial diversity but less potentially pathogenic bacterial genera in manures of adult pigs bred with green feeds were found, which indicated that those manures were more suitable for resource utilization. This study also provides evidence for the reasonableness of pig farming with green feeds.

Monitoring the performance and microbial diversity dynamics of a full scale anaerobic wastewater treatment plant treating sugar factory wastewater

Microbial community dynamics and the overall system performance of a real scale anaerobic wastewater treatment plant treating sugar industry wastewater were studied. Dominant bacterial and archaeal communities were monitored by 16S rRNA gene targeted PCR amplification and single strand conformation polymorphism analysis (SSCP). Chemical oxygen demand (COD) removal efficiency and operational parameters such as pH, temperature, alkalinity, volatile fatty acids in the methanogenic reactor remained within respective optimal ranges. All bacterial profiles in acidogenic and methanogenic reactors and in the lamella separator presented complex patterns; and the bacterial diversity, measured as SSCP profile richness and structure, was quite chaotic. In contrast to the results obtained for the bacterial community, archaeal 16S rDNA patterns in acidogenic and methanogenic reactors and the lamella separator remained relatively stable over the whole operation period of the anaerobic wastewater treatment plant. Evaluation of microbial community dynamics and overall system performance using the Mantel test revealed that there was no correlation between the dynamics of the microbial communities and the abiotic parameters.

Homogeneity and synchronous dynamics of microbial communities in particulate biofilms: from major populations to minor groups

Natural or engineered microbial populations often show variations over time. These variations may be due to environmental fluctuations or intrinsic factors. Thus, studying the dynamics of microbial diversity for different communities living in a spatially homogeneous landscape is of interest. As a model ecosystem, nitrifying biofilm communities were grown in a two litre inverse turbulent bed reactor (ITBR) containing an estimated 200 million small particles (about 150 μm in diameter). Each particulate biofilm is considered as a distinct community growing in the neighborhood of other similar particles, in a homogeneous and well-controlled environmental context. A molecular approach was adopted to test how microbial community structures might evolve: either in synchrony, converging or diverging. The shape of biofilm was observed by microscopy for each particle. The biomass content was evaluated by quantitative PCR and showed similar values for each particle. The microbial community structure was evaluated by Capillary Electrophoresis-Single Strand Conformation Polymorphism (CE-SSCP) fingerprinting and showed extraordinary homogeneity between particles, even though transitory community structures were observed when reactor operating conditions were modified. This homogeneity was observed for the Bacteria primer set but, more interestingly, was also observed when minor non-nitrifying bacteria making up the biofilm, representing about 5% and 10% of total cells, were targeted.

Identification of Methanoculleus spp. as active methanogens during anoxic incubations of swine manure storage tank samples

Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-(13)C]acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of (13)C into DNA was detectable at in situ acetate concentrations (~7 g/liter). Fingerprints of DNA retrieved from heavy fractions of the (13)C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.

Capillary electrophoresis single-strand conformation polymorphism for the monitoring of gastrointestinal microbiota of chicken flocks

The objective of the present study was to evaluate the capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) to characterize poultry gut microbiota and the ability of this molecular method to detect modifications related to rearing conditions to be used as an epidemiological tool. The V3 region of the 16S rRNA gene was selected as the PCR target. Our results showed that this method provides reproducible data. The microbiota analysis of individuals showed that variability between individual fingerprints was higher for ileum and cloaca than for ceca. However, pooling the samples decreased this variability. To estimate the variability within and between farms, we compared molecular gut patterns of animals from the same hatchery reared under similar conditions and fed the same diet in 2 separate farms. Total aerobic bacteria, coliforms, and lactic acid bacteria were enumerated using conventional bacteriological methods. A significant difference was observed for coliforms present in the ceca and the cloaca depending on the farm. Ileal contents fingerprints were more closely related to those of cloacal contents than to those of ceca contents. When comparing samples from the 2 farms, a specific microbiota was highlighted for each farm. For each gut compartment, the microbiota fingerprints were joined in clusters according to the farm. Thus, this rapid and potentially high-throughput method to obtain gut flora fingerprints is sensitive enough to detect a "farm effect" on the balance of poultry gut microbiota despite the birds being fed the same regimens and reared under similar conditions.

Bacterial community dynamics in aerated cow manure slurry at different aeration intensities

AIMS

This study aimed to characterize microbial community dynamics in aerated cow manure slurry at different aeration intensities.

METHODS AND RESULTS

Batch aerobic treatments were set up in 5-l jar fermentor, each containing 3 l of manure slurry; the slurries were subjected to low, medium and high (50, 150 and 250 ml min(-1), respectively) aeration for 9 days. Microbial community composition was determined using terminal restriction fragment length polymorphism and a clone library targeting 16S rRNA genes. High and medium aeration accelerated organic carbon degradation in parallel with the degree of aeration intensity; however, 90% of the initial total organic carbon was retained during low-aeration treatment. During the active stages of organic carbon decomposition, clones belonging to the class Bacilli accumulated. Moreover, Bacilli accumulation occurred earlier under high aeration than under medium aeration.

CONCLUSIONS

Organic matter degradation was mainly governed by a common microbial assemblage consisting of many lineages belonging to the class Bacilli. The timing of community development differed depending on aeration intensity.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study reports on changes in several environmentally important parameters and the principal microbial assemblage during the pollution-reducing phase of cattle manure aeration treatment.

Effect of oxygen and temperature on the dynamic of the dominant bacterial populations of pig manure and on the persistence of pig-associated genetic markers, assessed in river water microcosms

AIMS

The aim is to evaluate the dynamic of Bacteroides-Prevotella and Bacillus-Streptococcus-Lactobacillus populations originating from pig manure and the persistence of pig-associated markers belonging to these groups according to temperature and oxygen.

METHODS AND RESULTS

River water was inoculated with pig manure and incubated under microaerophilic and aerobic conditions, at 4 and 20°C over 43 days. The diversity of bacterial populations was analysed by capillary electrophoresis-single-strand conformation polymorphism. The persistence of the pig-associated markers was measured by real-time PCR and compared with the survival of Escherichia coli and enterococci. Decay was characterized by the estimation of the time needed to produce a 1-log reduction (T90). The greatest changes were observed at 20°C under aerobic conditions, leading to a reduction in the diversity of the bacterial populations and in the concentrations of the Pig-1-Bac, Pig-2-Bac and Lactobacillus amylovorus markers with a T90 of 10·5, 8·1 and 17·2 days, respectively.

CONCLUSIONS

Oxygen and temperature were found to have a combined effect on the persistence of the pig-associated markers in river waters.

SIGNIFICANCE AND IMPACT OF THE STUDY

The persistence profiles of the Pig-1-Bac, Pig-2-Bac and Lact. amylovorus markers in addition to their high specificity and sensitivity support their use as relevant markers to identify pig faecal contamination in river waters.

Effect of temperature on microbial population and performance of an aerobic thermophilic reactor treating cattle slurry and waste food

This study was carried out to quantify and identify the presence of somatic coliphages, RNA coliphages, sulphite-reducing clostridia, Clostridium tyrobutyricum or its related clostridia, faecal coliforms, enterococci and heterotrophs in a mixture of cattle slurry and waste food (whey and jam) that had undergone aerobic thermophilic treatment (ATT). We also investigated the influence of different factors, including pH, COD, temperature, odour removal, addition of waste food (whey and jam) and nitrogen losses, on the long-term ATT process. The processes were conducted semi-continuously with retention time of five days and with the waste food and slurry mixture (1:4) being added daily into the reactor. The experiments lasted seven days for each thermophilic temperature (50, 60 and 70 degrees C). Our work showed that, at the higher temperature of the ATT operation, the number of microorganisms declined much more rapidly than at the lower temperature and the final product was hygienically safe. The use of waste food (whey and jam) was beneficial because it buffered pH.

Nutrients and bacteria in common contiguous Mississippi soils with and without broiler litter fertilization

In Mississippi, spent poultry litter is used as fertilizer. Nutrient and bacterial levels in litter and nutrient levels in litter-fertilized (L+) soil are known, but less is known of bacterial levels in L+ soil. This study compared contiguous L+ and non-litter-fertilized (L-) soils comprising 15 soil types on five farms in April through May 2009. Levels of pH; NO-N; and Mehlich-3-extractable (M3) and water-extractable (WE) P, Ca, K, and Cu were higher in L+ than in L- soil. Total C; total N; NH-N; and M3 and WE Na, Fe, and Zn did not differ in L+ and L- soil. Bacterial levels were higher in 0- to 5-cm than in 5- to 10-cm cores. Levels were higher in L+ than in L- soil for culturally determined heterotrophic plate counts and staphylococci and were lower for total bacteria estimated by quantitative polymerase chain reaction (qPCR) of 16S rRNA, but cultural levels of thermotolerant coliforms, , , and enterococci were not different. Cultural presence/absence (CPA) tests and qPCR for spp., spp., and spp. detected only spp., which did not differ in L+ (CPA = 77% positive samples; mean qPCR = 0.65 log genomic units [gu] g) and L- (CPA = 70% positive samples; mean qPCR = 0 log gu g) soils. Litter applications were associated with higher levels of pH, P, Cu, heterotrophic plate counts, and staphylococci. Fecal indicator and enteric pathogen levels were not affected. We conclude that, although some litter-derived nutrients and bacteria persisted between growing seasons in L+ soils, enteric pathogens did not.

Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape

Background

The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution.

Methodology/Principal Findings

Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity.

Conclusions/Significance

Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.

Microbial population dynamics and changes in main nutrients during the acidification process of pig manures

This study evaluated the impact of pig manure acidification on anaerobic treatment and composition of the fecal microbial community. According to the different chemical oxygen demand (COD) in the anaerobic treatment processes, pig manure was diluted 4 times (x4), 16 times (x16), or 64 times (x64) and subjected to acidification. During the acidification process, pH, soluble chemical oxygen demand (SCOD), volatile fatty acids (VFAs), nitrogen (N), phosphorus (P) and potassium (K) were determined along with microbial population dynamics. The pH of the three dilutions first declined, and then slowly increased. The total VFAs of x4 and x16 dilutions peaked on day 15 and 20, respectively. The content of acetic acid, propanoic acid, butanoic acid and valeric acid of the x4 dilution were 23.6, 11.4, 8.8 and 0.6 g/L respectively, and that of the x16 dilution was 5.6, 2.3, 0.9 and 0.2 g/L respectively. Only acetic acid was detected in the x64 dilution, and its level peaked on day 10. The results showed that the liquid pig manure was more suitable to enter the anaerobic methanogenic bioreactors after two weeks of acidification. During the acidification process, total P concentration increased during the first ten days, then dropped sharply, and rose again to a relatively high final concentration, while total N concentration rose initially and then declined. Based on the analysis of denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library, we concluded that the acidification process reduced the number of pathogenic bacteria species in pig manure.

Microbial community fingerprinting by differential display-denaturing gradient gel electrophoresis

Complex microbial communities exhibit a large diversity, hampering differentiation by DNA fingerprinting. Herein, differential display-denaturing gradient gel electrophoresis is proposed. By adding a nucleotide to the 3' ends of PCR primers, 16 primer pairs and fingerprints were generated per community. Complexity reduction in each partial fingerprint facilitates sample comparison.

Active community profiling via capillary electrophoresis single-strand conformation polymorphism analysis of amplified 16S rRNA and 16S rRNA genes

Here, we report the validation and advancement of a high-throughput method for fingerprinting the active members of a microbial community. This method, termed active community profiling (ACP), provides information about both the composition and the activity of mixed microbial cultures via comparative measurements of amplified 16S rRNA (RNA) and 16S rRNA genes (DNA). Capillary electrophoresis is used to resolve single-strand conformation polymorphisms of polymerase chain reaction (PCR) and reverse transcription PCR (RT-PCR) products, producing electropherograms representative of the community structure. Active members of the community are distinguished by elevated RNA:DNA peak area ratios. Chemostat experiments with defined populations were conducted to validate the ACP approach. Using a pure culture of Escherichia coli, a direct correlation was found between the growth rate and the RNA:DNA peak ratio. In a second validation experiment, a binary culture of E. coli and Pseudomonas putida was subjected to a controlled environmental change consisting of a shift to anaerobic conditions. ACP revealed the expected cessation of growth of P. putida, an obligate aerobe, while the corresponding DNA-only analysis indicated no change in the culture. Finally, ACP was applied to a complex microbial community, and a novel binning approach was demonstrated for integrating the RNA and DNA electropherograms. ACP thus represents a significant advance from traditional DNA-based profiling techniques, which do not distinguish active from inactive or dead cells, and is well suited for high-throughput community analysis.

Comparison of selected nutrients and bacteria from common contiguous soils inside and outside swine lagoon effluent spray fields after long-term use

Swine (Sus scofa domestica) lagoon effluent is a valuable resource. In the U.S. Mid-South it is applied from April to September to fertilize grass hay in spray-irrigated fields. Lagoon levels of nutrients and bacteria, and soil levels of nutrients have been documented, but little was known of effluent bacterial levels in soil. The present study examined levels of selected effluent bacteria and nutrients in soils inside and outside spray fields after >15 yr of effluent irrigation. Samples were collected February to March 2009 from contiguous soils spanning adjacent irrigated and nonirrigated areas. Separate soil cores for bacterial and nutrient tests were collected in pairs <10 cm apart. Five cores each were collected at 15-m intervals and combined, respectively, to comprise inside and outside samples from each of 20 soils (four each from five farms/spray fields). Analyses of data combined across all soils showed higher pH and Mehlich-3-extracrable (M3-) P, Mg, K, Na, Cu, and Zn inside than outside spray fields, while total N, total C, M3-Ca, and M3-Mn did not differ. Bacterial levels were higher inside than outside spray fields for heterotrophic plate counts, thermotolerant coliforms, Staphylococcus spp., and Clostridium perfringens, but levels of Escherichia coli and Enterococcus spp. were not different. Cultural presence/absence tests for three pathogens (Listeria spp., Campylobacter spp., and Salmonella spp.) detected only Listeria spp., which did not differ inside (23% positive samples) and outside (28% positive). Molecular tests detected all three pathogens at low levels that were not different inside and outside. We found no evidence of cumulative buildup of Campylobacter spp., Listeria spp., or Salmonela s. in spray field soils.