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.

Bacterial dynamics and functions driven by biomass wastes to promote rural toilet blackwater absorption and recycling in an ectopic fermentation system

Due to high concentration of organic matter and the ease of disease transmission, blackwater pose a serious threat to both the environment and human health, especially in rural areas where wastewater treatment is dispersed. The reuse of biomass waste is also a difficult issue to be addressed urgently. In this study, an ectopic fermentation system (EFS) was used to treat toilet blackwater, and the effects of different biomass waste combinations on bacterial communities and functions during aerobic fermentation of blackwater were compared. The results showed that adding bran powder prolonged the high temperature period of 11 d, improved blackwater absorption capacity by 7.5% and was beneficial to microbial metabolic activities to enhance organic degradation. By contrast, the combination of corn straw and rice husk obtained abundant bacterial OTUs and diversity. Bacillus, Thermobifida and Thermopolyspora were the main microorganisms involved in the degradation of organic matter in EFS, and their abundance varied in different filler combinations. Bacterial communities were directly affected by environmental factors such as temperature, NH₄⁺-N and organic carbon as well as biomass materials during fermentation. This study revealed the role of corn straw, rice husk and bran powder in EFSs, provided new technical support for blackwater treatment and a new direction for the resource utilization of agricultural biomass waste.

Development of a microbial protease for composting swine carcasses, optimization of its production and elucidation of its catalytic hydrolysis mechanism

BACKGROUND

Dead swine carcass composting is an excellent method for harmless treatment and resource utilization of swine carcass. However, poor biodegradation ability of traditional composting results in poor harmless treatment effect. Researches report that the biodegradation ability of composting can be improved by inoculation with enzyme-producing microorganisms or by inoculation with enzyme preparations. At present, the researches on improving the efficiency of dead swine carcass composting by inoculating enzyme-producing microorganisms have been reported. However, no work has been reported on the development of enzyme preparations for dead swine carcass composting.

METHODOLOGY

The protease-producing strain was isolated by casein medium, and was identified by 16 S rRNA gene sequencing. The optimal fermentation conditions for maximum protease production were gradually optimized by single factor test. The extracellular protease was purified by ammonium sulfate precipitation and Sephadex G-75 gel exclusion chromatography. The potential for composting applications of the purified protease was evaluated by characterization of its biochemical properties. And based on amino acid sequence analysis, molecular docking and inhibition test, the catalytic hydrolysis mechanism of the purified protease was elucidated.

RESULTS

In this study, a microbial protease was developed for swine carcass composting. A protease-producing strain DB1 was isolated from swine carcass compositing and identified as Serratia marcescen. Optimum fermentation conditions for maximum protease production were 5 g/L glucose, 5 g/L urea, 1.5 mmol/L Mg²⁺, initial pH-value 8, inoculation amount 5%, incubation temperature 30 °C and 60 h of fermentation time. The specific activity of purified protease reached 1982.77 U/mg, and molecular weight of the purified protease was 110 kDa. Optimum pH and temperature of the purified protease were 8 and 50 °C, respectively, and it had good stability at high temperature and in alkaline environments. The purified protease was a Ser/Glu/Asp triad serine protease which catalyzed substrate hydrolysis by Glu, Arg, Ser, Asp and Tyr active residues.

CONCLUSIONS

In general, the microbial protease developed in this study was suitable for industrial production and has the potential to enhance composting at thermophilic stage. Moreover, the catalytic hydrolysis mechanism of the protease was further analyzed in this study.

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.

Planifilum fulgidum Is the Dominant Functional Microorganism in Compost Containing Spent Mushroom Substrate

The extensive accumulation of spent mushroom substrate (SMS) owing to the large-scale production of edible fungi is causing environmental problems that cannot be ignored. Co-composting is a promising method for agricultural and animal husbandry waste disposal. In this study, the composition and function of microbial communities in the process of cattle manure–maize straw composting with SMS addition were compared through an integrated meta-omics approach. The results showed that irrespective of SMS addition, the predominant fungi were Ascomycota, while the dominant bacteria were Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. High temperature promoted the evolution from Gram-negative bacteria (Bacteroides, Proteobacteria) to Gram-positive bacteria (Firmicutes, Actinomycetes). The composting process was accelerated by SMS addition, and the substrate was effectively degraded in 14 days. Metaproteomics results showed that the dominant microorganism, Planifilum fulgidum, secreted large amounts of S8, M17, and M32 proteases that could degrade macromolecular protein substrates in the presence of SMS. Planifilum fulgidum, along with Thermobifida fusca and Melanocarpus albomyces, synergistically degraded hemicellulose, cellulose, and protein. In addition, the dominant microorganisms related to the initial raw materials such as Pichia, Lactobacillus in the microbial agent and Hypsizygus in SMS could not adapt to the high-temperature environment (>60 °C) and were replaced by thermophilic bacteria after 5 days of composting.

Proliferation of antibiotic-resistant microorganisms and associated genes during composting: An overview of the potential impacts on public health, management and future

Antibiotic residues together with non-antibiotic drugs and heavy metals act as a selective pressure for the spread of antibiotic-resistant microorganisms (ARMs), antibiotic-resistant genes (ARGs), and mobile genetic elements (MGEs) during composting of livestock manure. ARMs, ARGs and MGEs have become emerging contaminants since they are regularly implicated in the majority of compost produced from livestock manure. The prevalence of these contaminants in agricultural soil receiving compost has drawn huge attention globally due to the risks they pose to the total environment. Although a large body of literature exists on the application of composting methods in minimizing the relative abundance of these contaminants, there is a paucity of information on the robustness, limitations and opportunities and threats of various composting protocols currently deployed. To address this knowledge gap, the current review compiled literature on the origin and mechanisms of the proliferation of ARMs, ARGs, and MGEs during composting of livestock manure. The effectiveness of current composting protocols in the reduction or removal of emerging contaminants was evaluated. Furthermore, the potential environmental impacts and human health risks of these contaminants following land application of compost were also presented. Finally, we propose some strategic approaches for the reduction of ARGs and MGEs during composting of livestock manure.

Adding a complex microbial agent twice to the composting of laying-hen manure promoted doxycycline degradation with a low risk on spreading tetracycline resistance genes

Poultry manure is a reservoir for antibiotics and antibiotic resistance genes and composting is an effective biological treatment for manure. This study explored the effect of using two methods of adding a complex microbial agent to the composting of laying-hen manure on doxycycline degradation and tetracycline resistance genes elimination. The results showed that incorporating a complex microbial agent at 0.8% (w/w) on the 0^th and 11th day (group MT2) effectively degraded doxycycline with a final degradation rate of 46.83 ± 0.55%. The half-life of doxycycline in this group was 21.90 ± 0.00 days and was significantly lower than that of group MT1 (1.6% (w/w) complex microbial agent added on the 0^th day) and group DT (compost without complex microbial agent). But there was no significant difference in the final degradation rate of doxycycline between group DT and group MT1. The addictive with the complex microbial agent changed the microbial community structure. Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla during composting. Aerococcus, Desemzia, Facklamia, Lactobacillus, Streptococcus, and Trichococcus were the bacteria related to the degradation of doxycycline. Moreover, the incorporation of a complex microbial agent could decrease the risk on spreading tetracycline resistance genes. The single addition promoted the elimination of tetM, whose possible hosts were Enterococcus, Lactobacillus, Staphylococcus, and Trichococcus. Adding the complex microbial agent twice promoted the elimination of tetX, which was related to the low abundance of Chryseobacterium, Flavobacterium and Neptunomonas in group MT2. Redundancy analysis showed that the bacterial community, residual doxycycline and physiochemical properties have a potential effect on the variation in tetracycline resistance genes levels. Overall, adding the complex microbial agent twice is an effective measure to degrade doxycycline.

Effect of thermotolerant bacterial inoculation on the microbial community during sludge composting

A thermophilic bacterium (Geobacillus stearothermophilus CHB1) was inoculated in a sludge compost, and the effects of the inoculation on the abundance and structure of the bacterial community in the sludge compost were investigated using quantitative PCR and Illumina MiSeq sequencing. The results showed that the high-temperature stage (>50 °C) of the CHB1 and CK (control without inoculum) piles started on days 5 and 8, respectively, and lasted for 7 and 2 days, respectively, indicating the extension of the thermophilic phase by CHB1 inoculation in the sludge compost. At the end of composting, the CHB1 piles showed a higher loss of total organic carbon, lower C/N ratio, and lower moisture content. The abundance of bacteria in the CHB1 piles was significantly higher in the heating and thermophilic phase of composting but were lower than those of the CK in the cooling phase. The richness and diversity of the bacterial community in the thermophilic phase increased after inoculation with CHB1. After inoculation of CHB1, there were higher relative abundances of Firmicutes, Thermopolyspora, Thermobacillus, Thermomonas, Thermomonospora, and Thermovum, which can grow in a high-temperature environment. Furthermore, redundancy analysis indicated that total organic carbon, total nitrogen, C/N ratio, pH, temperature, and moisture were the significant parameters that affected the bacterial community structure during sludge composting. Our findings suggested that inoculation with CHB1 would enhance the quality and efficiency of composting.