Fermentation performance optimization in an ectopic fermentation system

Improvement of carbon source composition reduces antibiotic resistance genes in the ectopic fermentation system

Effectively reduce antibiotic resistance genes (ARGs) in ectopic fermentation system (EFS) is essential for practical production. In this study, three experiments were performed to explore how to remove ARGs in EFS effectively. Results demonstrated that ARGs were easily enriched in rice-husk-sawdust padding; simultaneous addition of laccase and cellulase suppressed the ARGs, mainly by increasing soluble carbohydrate concentration and promoting humic acid concentration; addition of corn stalks into rice-husk-sawdust decreased the abundance of ARGs by improving the carbon source structure and enhancing cellulase activity. In conclusion, the present study provides a guidance to reduce the threat of ARGs in EFS, which paved a potential pathway to safely utilize manure resources.

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.

Changes of bacterial and fungal communities and relationship between keystone taxon and physicochemical factors during dairy manure ectopic fermentation

BACKGROUND

Due to interactions with variety of environmental and physicochemical factors, the composition and diversity of bacteria and fungi in manure ectopic fermentation are constantly changing. The purpose of this study was to investigated bacterial and fungal changes in dairy manure ectopic fermentation, as well as the relationships between keystone species and physicochemical characteristics.

METHODS

Ectopic fermentation was carried out for 93 days using mattress materials, which was combined with rice husk and rice chaff (6:4, v/v), and dairy waste mixed with manure and sewage. Physicochemical characteristics (moisture content, pH, NH4+-N (NN), total organic carbon (TO), total nitrogen (TN) and the C/N ratio) of ectopic fermentation samples were measured, as well as enzymatic activity (cellulose, urease, dehydrogenase and alkaline phosphatase). Furthermore, the bacterial and fungal communities were studied using 16S rRNA and 18S rRNA gene sequencing, as well as network properties and keystone species were analyzed.

RESULTS

During the ectopic fermentation, the main pathogenic bacteria reduced while fecal coliform increased. The C/N ratio gradually decreased, whereas cellulase and dehydrogenase remained at lower levels beyond day 65, indicating fermentation maturity and stability. During fermentation, the dominant phyla were Chloroflexi, Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria of bacteria, and Ascomycota of fungi, while bacterial and fungal community diversity changed dramatically and inversely. The association between physicochemical characteristics and community keystone taxon was examined, and C/N ratio was negative associated to keystone genus.

CONCLUSION

These data indicated that microbial composition and diversity interacted with fermentation environment and parameters, while regulation of keystone species management of physicochemical factors might lead to improved maturation rate and quality during dairy manure ectopic fermentation. These findings provide a reference to enhance the quality and efficiency of waste management on dairy farm.

Occurrence and risk assessment of five kinds of antimicrobial in mattress on swine farm use ectopic fermentation systems in Zhejiang Province

Mattress is among the main products of ectopic fermentation system (EFS); however, the research on the data of antimicrobial residues in the mattress of EFS and risk assessments of mattress have not been conducted. This study involved a scale survey to assess the levels and distributions of 54 antimicrobial residues, including 4 tetracyclines, 19 quinolones, 22 sulfonamides, 3 amphenicols, and 6 macrolides in mattress on 12 swine farms that use ectopic fermentation systems (EFS) in Zhejiang Province. A total of 25 antimicrobials were detected in mattress, and the total residue amount of antimicrobial in mattress samples of each farm was 0.77-28.2 g/T. Chlortetracycline had the highest contribution rate, and the residue amount of antimicrobial in mattress is not entirely determined by the start-up time of EFS but is related to the use of feed containing antimicrobial, medication habits, the level of mattress management, and maintenance methods of EFS. The risk assessments of antimicrobial in the mattress were carried out. The results show that the risk of using mattress of EFS for soil is low.

Linking Microbial Community Succession With Substance Transformation in a Thermophilic Ectopic Fermentation System

Ectopic fermentation system (EFS) is an effective technology for treating mass livestock manure. However, the associations between microbial communities and substance transformation remain controversial. This study aimed to investigate chicken manure EFS lasting 170 days using 16S rRNA sequencing and electrochemical, spectroscopic, and chromatographic analyses. The results showed a noticeable transformation of protein-like substances into humus-like substances. Meanwhile, the electron–accepting capacity increased persistently, effectively reflecting the humification of organic substances. The contents of phenols that promoted electron transfer continued to increase from 2.80 to 6.00%, which could be used as a maturity indicator for EFS. During the heating period, the dominant microbial communities were Chloroflexi and Proteobacteria, whereas thermotolerant bacteria Cyanobacteria and Planctomycetes were significantly enriched from 1.64 to 50.15% during the continuous thermophilic period of EFS. The correlation analysis manifested that these thermotolerant bacteria were the major functional bacteria for the formation of phenols and the key to driving the humification of organic substances. This study provides insights into understanding the humification mechanisms and implementing regulatory strategies in EFS.

Mechanisms of nitrogen transformation driven by functional microbes during thermophilic fermentation in an ex situ fermentation system

In this study, we explored the pathways and mechanisms of nitrogen (N) transformation driven by functional microbes carrying key genes in an ex situ fermentation system (EFS). Temperature and N content were found to be the most important factors driving variation in bacterial and fungal communities, respectively; Bacillus became the most abundant bacteria and Batrachochytrium became the most abundant fungi. Co-occurrence network analysis showed that some bacteria including Halomonas, Truepera, and Gemmatimonas species carry genes that promote mineralization, nitrification, dissimilatory/assimilatory nitrate reduction, denitrification, anammox reactions, and N fixation. The maximum rate of total mineralization reached 136.60 μg N g^-1 d^-1. Functional microbes promoted various N conversion processes at different rates in the EFS, with levels increasing by at least 0.23 μg N g^-1 d^-1. These results provide a theoretical basis for feasible optimization measures to address N loss during fermentation.

Comprehensive analysis of environmental factors mediated microbial community succession in nitrogen conversion and utilization of ex situ fermentation system

An ex situ fermentation system (EFS) can efficiently transform and utilize nitrogen in swine wastewater and reduce environmental pollution. High-throughput sequencing was used to study the relationship between the succession of total bacteria, fungi, and functional bacteria in a swine wastewater EFS, as well as nitrogen metabolism and environmental factors. During the fermentation process, inorganic nitrogen gradually accumulated and the pH changed rapidly from weakly acidic to alkaline. The dominant genera of bacteria, fungi and functional bacteria carrying amoA, nirK, and nosZ genes changed gradually, and Clostridium sensu stricto 1, Thermomyces, Nitrosomonas, Mesorhizobium, and Pseudomonas genera became the most abundant, which showed positive correlations with temperature, pH, and nitrogen levels. Other changed populations showed different correlations with environmental factors, and physical-chemical factors explained more variation of microorganisms than nitrogen resources. These findings contribute to a comprehensive understanding of nitrogen metabolism in EFSs from a molecular micro-ecology perspective.

Insights into functional microbial succession during nitrogen transformation in an ectopic fermentation system

The ectopic fermentation system (EFS) is an advanced technology for treating farm wastewater, and it reduces ammonia nitrogen emission and nitrogen loss of fermentation products. This study observed the functional bacteria succession related to nitrogen metabolism in EFS by high throughput sequencing, and evaluated their associations with environmental factors. Results revealed that with the changes of temperature, pH, moisture content, and nitrogen content during fermentation, the species richness and diversity of ammonia oxidizing bacteria (AOB) with amoA increased, but those of denitrifying bacteria carrying nirK and nosZ decreased. During the fermentation process, the dominant bacterial populations of AOB and denitrifying bacteria changed significantly, and different bacterial populations showed different positive/negative correlations with the environmental factors. This study revealed the role of functional bacteria in ammonia removal and nitrogen conservation of EFS, and provided a theoretical basis for the improvement of microbial agents and EFS application.

Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments

Shikimic acid is an important intermediate for the manufacture of the antiviral drug oseltamivir (Tamiflu®) and many other pharmaceutical compounds. Much of its existing supply is obtained from the seeds of Chinese star anise (Illicium verum). Nevertheless, plants cannot supply a stable source of affordable shikimate along with laborious and cost-expensive extraction and purification process. Microbial biosynthesis of shikimate through metabolic engineering and synthetic biology approaches represents a sustainable, cost-efficient, and environmentally friendly route than plant-based methods. Metabolic engineering allows elevated shikimate production titer by inactivating the competing pathways, increasing intracellular level of key precursors, and overexpressing rate-limiting enzymes. The development of synthetic and systems biology-based novel technologies have revealed a new roadmap for the construction of high shikimate-producing strains. This review elaborates the enhanced biosynthesis of shikimate by utilizing an array of traditional metabolic engineering along with novel advanced technologies. The first part of the review is focused on the mechanistic pathway for shikimate production, use of recombinant and engineered strains, improving metabolic flux through the shikimate pathway, chemically inducible chromosomal evolution, and bioprocess engineering strategies. The second part discusses a variety of industrially pertinent compounds derived from shikimate with special reference to aromatic amino acids and phenazine compound, and main engineering strategies for their production in diverse bacterial strains. Towards the end, the work is wrapped up with concluding remarks and future considerations.