Effect of Substrate on Identification of Microbial Communities in Poultry Carcass Composting and Microorganisms Associated with Poultry Carcass Decomposition

Composition and functional diversity of bacterial communities during swine carcass decomposition

OBJECTIVE

This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions.

METHODS

The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene.

RESULTS

A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms.

CONCLUSION

This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.

Performance exploration and microbial dynamics of urine diverting composting toilets in rural China

The ongoing "toilet revolution" in China provides new opportunities to improve the rural living environment and sanitation, and the introduction of new sanitation facilities such as urine diverting composting toilets (UDCTs) is conducive to the effective treatment and resource utilization of feces. This study revealed the degradation performance and microbial community dynamics of UDCTs and clarified the influence mechanism of fecal volume in aerobic composting treatment. The results showed that UDCTs could effectively decompose human feces, with an organic matter degradation rate of 25%⁓30%. The temperature, water content, NH₄⁺-N and nutrient accumulation were higher in the high fecal volume treatment than in the low fecal volume treatment. Bacterial community composition and structure in UDCTs varied with composting stage and fecal volume. The diversity and richness of bacterial community in compost were changed with different fecal volumes, but the dominant groups were similar. Redundancy analysis (RDA) showed that nitrogen and organic carbon were the main drivers of bacterial community changes during composting. Highly nutritious and non-phytotoxic compost products were suitable for agronomic uses. Based on these results, UDCTs can be an effective way to solve the problem of fecal pollution in rural areas, and fecal dosage is a potential influencing factor in the operation and maintenance of composting systems.

The nitrogen cycle and mitigation strategies for nitrogen loss during organic waste composting: A review

Composting is a promising technology to decompose organic waste into humus-like high-quality compost, which can be used as organic fertilizer. However, greenhouse gases (N₂O, CO₂, CH₄) and odorous emissions (H₂S, NH₃) are major concerns as secondary pollutants, which may pose adverse environmental and health effects. During the composting process, nitrogen cycle plays an important role to the compost quality. This review aimed to (1) summarizes the nitrogen cycle of the composting, (2) examine the operational parameters, microbial activities, functions of enzymes and genes affecting the nitrogen cycle, and (3) discuss mitigation strategies for nitrogen loss. Operational parameters such as moisture, oxygen content, temperature, C/N ratio and pH play an essential role in the nitrogen cycle, and adjusting them is the most straightforward method to reduce nitrogen loss. Also, nitrification and denitrification are the most crucial processes of the nitrogen cycle, which strongly affect microbial community dynamics. The ammonia-oxidizing bacteria or archaea (AOB/AOA) and the nitrite-oxidizing bacteria (NOB), and heterotrophic and autotrophic denitrifiers play a vital role in nitrification and denitrification with the involvement of ammonia monooxygenase (amoA) gene, nitrate reductase genes (narG), and nitrous oxide reductase (nosZ). Furthermore, adding additives such as struvite salts (MgNH₄PO₄·6H₂O), biochar, and zeolites (clinoptilolite), and microbial inoculation, namely Bacillus cereus (ammonium strain), Pseudomonas donghuensis (nitrite strain), and Bacillus licheniformis (nitrogen fixer) can help control nitrogen loss. This review summarized critical issues of the nitrogen cycle and nitrogen loss in order to help future composting research with regard to compost quality and air pollution/odor control.

Impact of Soil Microbes and Oxygen Availability on Bacterial Community Structure of Decomposing Poultry Carcasses

The impact of soil with an intact microbial community and oxygen availability on moisture content, soil pH, and bacterial communities during decomposition of poultry carcasses was investigated. Poultry carcasses were decomposed in soil with or without a microbial community, under aerobic or anaerobic conditions. The samples collected in each microcosm burial set-up were analyzed by targeted 16S rRNA amplicon sequencing and Amplicon sequence variants (ASV) method. Our results showed that moisture was high in the burial set-ups under anaerobic conditions and pH was high in the burial set-ups under aerobic conditions. Meanwhile, the Chao1 and Shannon index significantly differed between the different burial set-ups and across different time points. In addition, bacterial taxa composition during the early period of decomposition differed from that of the late period. A total of 23 phyla, 901 genera, and 1992 species were identified. Firmicutes was the most dominant phyla in all burial set-ups throughout the decomposition. At day 60, Pseudogracilibacillus was dominant in the burial set-ups under aerobic conditions, while Lentibacillus dominated in the burial set-ups under anaerobic conditions. This study demonstrated that the soil microbial community and availability of oxygen significantly affected the changes in moisture content, pH, and bacterial composition during the decomposition process.

Intercropping Alters the Soil Microbial Diversity and Community to Facilitate Nitrogen Assimilation: A Potential Mechanism for Increasing Proso Millet Grain Yield

Intercropping of cereals and legumes has been used in modern agricultural systems, and the soil microorganisms associated with legumes play a vital role in organic matter decomposition and nitrogen (N) fixation. This study investigated the effect of intercropping on the rhizosphere soil microbial composition and structure and how this interaction affects N absorption and utilization by plants to improve crop productivity. Experiments were conducted to analyze the rhizosphere soil microbial diversity and the relationship between microbial composition and N assimilation by proso millet (Panicum miliaceum L.) and mung bean (Vigna radiata L.) from 2017 to 2019. Four different intercropping row arrangements were evaluated, and individual plantings of proso millet and mung bean were used as controls. Microbial diversity and community composition were determined through Illumina sequencing of 16S rRNA and internal transcribed spacer (ITS) genes. The results indicated that intercropping increased N levels in the soil-plant system and this alteration was strongly dependent on changes in the microbial (bacterial and fungal) diversities and communities. The increase in bacterial alpha diversity and changes in unique operational taxonomic unit (OTU) numbers increased the soil N availability and plant N accumulation. Certain bacterial taxa (such as Proteobacteria) and fungal taxa (such as Ascomycota) were significantly altered under intercropping and showed positive responses to increased N assimilation. The average grain yield of intercropped proso millet increased by 13.9-50.1% compared to that of monoculture proso millet. Our data clearly showed that intercropping proso millet with mung bean altered the rhizosphere soil microbial diversity and community composition; thus, this intercropping system represents a potential mechanism for promoting N assimilation and increasing grain yield.

Composting pig manure and sawdust with urease inhibitor: succession of nitrogen functional genes and bacterial community

Understanding the relationship between nitrogen (N) cycle and N transformation-related functional genes is crucial to reduce N loss during composting process. Urease inhibitor (UI) is widely used to reduce N loss in agriculture. However, the effects of UI on N transformation and related N functional genes during composting have not been well investigated. The goal of this study was to investigate the effects of a urease inhibitor (UI) on N functional genes and bacterial community succession during pig manure composting. Results showed that the addition of UI decreased the ammonium N content during the thermophilic stage and notably increased the total N and nitrite N contents of the final compost. The UI significantly decreased the abundances of amoA, nirS, nirK, and nosZ during the initial composting stage, while the opposite trend was observed at the maturation stage. Bacterial community richness and diversity were increased after the UI amendment, but the relative abundance of the phyla Firmicutes and Proteobacteria significantly decreased compared with control during the thermophilic stage. Redundancy analysis indicated that the evaluated environmental factors and bacterial community showed a cumulative 94.7% contribution to the total variation in N functional genes. In summary, UI addition is a recommended method for N conservation during composting, but the added forms of UI, such as delayed addition, combined with adsorbing materials, or microorganism inoculant, should be further evaluated.

Effect of Cornstalk Biochar Immobilized Bacteria on Ammonia Reduction in Laying Hen Manure Composting

NH₃ emission has become one of the key factors for aerobic composting of animal manure. It has been reported that adding microbial agents during aerobic composting can reduce NH₃ emissions. However, environmental factors have a considerable influence on the activity and stability of the microbial agent. Therefore, this study used cornstalk biochar as carriers to find out the better biological immobilization method to examine the mitigation ability and mechanism of NH₃ production from laying hen manure composting. The results from different immobilized methods showed that NH₃ was reduced by 12.43%, 5.53%, 14.57%, and 22.61% in the cornstalk biochar group, free load bacteria group, mixed load bacteria group, and separate load bacteria group, respectively. Under the simulated composting condition, NH₃ production was 46.52, 38.14, 39.08, and 30.81 g in the treatment of the control, mixed bacteria, cornstalk biochar, and cornstalk biochar separate load immobilized mixed bacteria, respectively. The cornstalk biochar separate load immobilized mixed bacteria treatment significantly reduced NH₃ emission compared with the other treatments (p < 0.05). Compared with the control, adding cornstalk biochar immobilized mixed bacteria significantly decreased the electrical conductivity, water-soluble carbon, total nitrogen loss, and concentration of ammonium nitrogen (p < 0.05), and significantly increased the seed germination rate, total number of microorganisms, and relative abundance of lactic acid bacteria throughout the composting process (p < 0.05). Therefore, the reason for the low NH₃ emission might be due not only to the adsorption of the cornstalk biochar but also because of the role of complex bacteria, which increases the relative abundance of lactic acid bacteria and promotes the acid production of lactic acid bacteria to reduce NH₃ emissions. This result revealed the potential of using biological immobilization technology to reduce NH₃ emissions during laying hen manure composting.

Composting swine carcasses with nitrogen transformation microbial strains: Succession of microbial community and nitrogen functional genes

In this study, nitrogen transformation strains, including three ammonium transformation strains, one nitrite strain and one nitrogen fixer, were inoculated at different swine carcass composting stages to regulate the nitrogen transformation and control the nitrogen loss. The final total nitrogen content was significantly increased (p < 0.01). The bacterial communities were assessed by amplicon sequencing and association analysis. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were the four most dominant phyla.,Brevibacterium, Streptomyces and Ochrobactrum had a significant (p < 0.05) and positive correlation with total nitrogen and ammonium nitrogen content in both groups. The quantitative results of nitrogen transformation genes showed that ammonification, nitrification, denitrification and nitrogen fixation were simultaneously present in the composting process of swine carcasses, with the latter two accounting for a higher proportion. The ammonium transformation strains significantly (p < 0.05) strengthened nitrogen fixation and remarkably (p < 0.01) weakened nitrification and denitrification, which, however, were notably (p < 0.05) enhanced by the nitrite strain and nitrogen fixer. In this research, the inoculated strains changed the bacterial structure by regulating the abundance and activity of the highly connected taxa, which facilitated the growth of nitrogen transformation bacteria and regulated the balance/symbiosis of nitrogen transformation processes to accelerate the accumulation of nitrogen.

Influence and characteristics of Bacillus stearothermophilus in ammonia reduction during layer manure composting

Ammonia emissions is an important issue during composting because it can cause secondary pollution and a significant of nitrogen loss. Based on research adding Bacillus stearothermophilus can reduce ammonia emissions during composting because it can use sugar in organic matter fermentation to produce organic acids over 50 °C. This study conducted the batch experiments by adding different concentrations of Bacillus stearothermophilus to reduce the ammonia emissions and find out its characteristic during layer manure composting by using an aerobic composting reactor with sawdust as a bulking agent. The results show that the application of Bacillus stearothermophilus can accelerate the rate of temperature and significantly decrease pH, the warming period was 2 days in the treatment with Bacillus stearothermophilus, while it was 4 days in the treatment without Bacillus stearothermophilus. Ammonia emissions were mainly occurred in warming and high temperature period during composting. The ammonia emissions in the treatment with 8.00 g/kg initial Bacillus stearothermophilus were significantly lower than the other lower Bacillus stearothermophilus treatment and control during composting (p < 0.05), and it can significantly increase ammonium-nitrogen and nitrate-nitrogen concentration, reduce pH (p < 0.05), but the average number of Bacillus stearothermophilus copies in treatment with different initial Bacillus stearothermophilus concentration had no significant difference (p > 0.05). MiSeq System Sequencing results find that the addition of Bacillus stearothermophilus changed the bacterial community structure under warming and high-temperature periods during composting, increased the relative abundance of lactic acid bacillus and nitrification bacteria. Therefore, the reason for the low ammonia emission in 8.00 g/kg initial Bacillus stearothermophilus treatments might be not only due to the Bacillus stearothermophilus itself, but also Bacillus stearothermophilus can change the indigenous microorganism community, including increase the relative content of lactic acid Bacillus and nitrification bacteria, thus reducing the pH and promoting nitrification, and reducing ammonia emissions.

Effect of Different Proportions of Three Microbial Agents on Ammonia Mitigation during the Composting of Layer Manure

Odor emissions represent one of the important issues of aerobic composting. The addition of microbial agents to compost is an important method for solving this problem, but this process is often unstable when a single microbial agent is added to the compost. Therefore, in this study, five treatments comprising different proportions of Bacillus stearothermophilus, Candida utilis, and Bacillus subtilis were tested to determine the best combination of the three microbial agents for ammonia reduction, as follows: control group (CK), 2:1:1 (A), 1:1:2 (B), 1:2:1 (C), and 1:1:1 (D). Compared with the CK group, the A, B, C, and D groups reduced ammonia emissions by 17.02, 9.68, 53.11, and 46.23%, respectively. The total ammonia emissions were significantly lower in C and D than in CK (p < 0.05). These two treatment groups had significantly increased nitrate nitrogen concentrations and decreased pH values and ammonium nitrogen concentrations (p < 0.05). Throughout the composting process, the total bacterial number was significantly higher in C and D than in CK (p < 0.05). Therefore, it is likely that B. stearothermophilus, C. utilis, and B. subtilis compounded from 1:2:1 (C) to 1:1:1 (D) reduced the ammonia emissions due to (1) a reduction in the pH and (2) the promotion of the growth of ammonia-oxidizing bacteria and the conversion of ammonium nitrogen to nitrate nitrogen. This study provides a theoretical basis and technical support for the odor problem of layer manure compost and promotes the development of composting technology.

Effects of exogenous microbial inoculum on the structure and dynamics of bacterial communities in swine carcass composting

Composting is a widely accepted method for the disposal of deceased livestock. It is a biological self-heating process during which animal carcasses are converted to fertilizer products. Additional inoculants can facilitate the composting progress. This study investigated how the addition of microbial inoculants could improve the composting effectiveness and could change the structure and dynamics of bacterial communities in the carcass composting process. Four strains of Bacillus were inoculated into the swine carcass composting piles. The groups with the additional inoculants showed a higher temperature in the thermophilic phase and higher germination indices in the composted products. The sequencing results showed that the dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria, and the dominant classified genera were Brevibacterium and Bacillus. Canonical correlation analysis showed that temperature and moisture exerted a stronger influence on the bacterial community diversity. The interaction network of dominant genera and the abundance variation of the bacterial community demonstrated that the inoculated bacterial agent changed the structure of bacterial communities and enriched the diversity of the species due to antagonism and symbiosis among the dominant bacterial communities.

Evaluation of compost, vegetable and food waste as amendments to improve the composting of NaOH/NaClO-contaminated poultry manure

Regular usage of NaOH/NaClO disinfectants results in high sodium salt and alkalinity of poultry manure. This study compared three amendments: vegetable waste (V), food waste (F) and mature compost (C) for their ability to improve the composting of NaOH/NaClO-contaminated poultry manure. C compost resulted in the highest compost temperatures (p<0.001) and greatest reduction in OM, TC, TN and NH₄-N (p<0.05). C and V composts were more efficient at lowering extractable-Na (ext-Na) and electrical conductivity (EC) than F (p<0.05). Maturity was primarily indicated by NH₄-N, EC and ext-Na. Bacterial dynamics was profoundly influenced by NH₄-N, EC and TC, with the decrease leading to discriminate genera shift from Sinibacillus and Thiopseudomonas to Brevbacterium, Brachybacterium, and Microbacterium. These findings suggest that mature compost was more desirable amendment than vegetable and food waste in the composting of NaOH/NaClO-contaminated poultry manure, and the decrease of ext-Na indicated compost maturity but did not influence bacterial dynamics.

Effects of different types of biochar on methane and ammonia mitigation during layer manure composting

Biochar, because of its unique physiochemical properties and sorption capacity, may be an ideal amendment in reducing gaseous emissions during composting process but there has been little information on the potential effects of different types of biochar on undesired gaseous emissions. The objective of this study was to examine the ability and mechanism of different types of biochar, as co-substrate, in mitigating gaseous emission from composting of layer hen manure. The study was conducted in small-scale laboratory composters with the addition of 10% of one of the following biochars: cornstalk biochar, bamboo biochar, woody biochar, layer manure biochar and coir biochar. The results showed that the cumulative NH₃ production was significantly reduced by 24.8±2.9, 9.2±1.3, 20.1±2.6, 14.2±1.6, 11.8±1.7% (corrected for initial total N) in the cornstalk biochar, bamboo biochar, woody biochar, layer manure biochar and coir biochar treatments, respectively, compared to the control. Total CH₄ emissions was significantly reduced by 26.1±2.3, 15.5±2.1, 22.4±3.1, 17.1±2.1% (corrected for the initial total carbon) for cornstalk biochar, bamboo biochar, woody biochar and coir biochar treatments than the control. Moreover, addition of cornstalk biochar increased the temperature and NO₃^--N concentration and decreased the pH, NH₄⁺-N and organic matter content throughout the composting process. The results suggested that total volatilization of NH₃ and CH₄ in cornstalk biochar treatment was lower than the other treatments; which could be due to (i) decrease of pH and higher nitrification, (ii) high sorption capacity for gases and their precursors, such as ammonium nitrogen from composting mixtures, because of the higher surface area, pore volumes, total acidic functional groups and CEC of cornstalk biochar.