The maturity period is the main stage of antibiotic resistance genes reduction in aerobic composting process of swine manure in sub-scale farms

Highlights

• Maturity stage is the main reduction stage of ARGs in composting of sub-scale farm.

• ARGs was mainly affected by the community succession of potential host bacteria.

• Prolonging maturity period would inhibit the potential host bacteria of ARGs.

Abstract

This study was focused on the changes of antibiotic resistance genes (ARGs) and their potential host bacteria during the swine manure composting on sub-scale farms. Eight target ARGs increased 427% on average, with a trend of increase at early stage and decrease at later stage, and the main reduction stage appeared in maturity stage. The abundance of ARGs was mainly affected by the community succession of potential host bacteria. Composting could reduce the abundance of potential host bacteria of ARGs as well as pathogens such as Pseudomonas, and reduce the environmental risks of swine manure. N/C and S levels had a positive effect on the potential host of most ARGs. Prolonging the maturity period would inhibit the growth of potential host bacteria of ARGs during composting, therefore inhibiting the transmission of ARGs.

Introduction

Antibiotic resistance genes (ARGs) and their hosts are considered to be a major threat to global health, food safety, and social development. They are widely distributed in different ecological environments (freshwater, marine ecosystems, sediments, and soil), and anthropogenic waste (sewage, sludge, feces, and solid waste) (Martinez, 2009, Munir and Xagoraraki, 2011, Zhu et al., 2013). ARGs can result in microorganisms that are resistant to antibiotics and can spread through vertical gene transfer (VGT) and horizontal gene transfer (HGT) (Nandi et al., 2004). Vertical gene transfer is the propagation of ARGs in different environmental media such as water and soil through the self-propagation of microorganisms. Through horizontal gene transfer, under the action of mobile genetic elements (MGEs), ARGs are spread through conjugation, transduction, and transformation (von Wintersdorff et al., 2016). The potential of horizontal transfer of ARGs is directly related to their environmental risks, which may nullify the effect of antibiotics (Bengtsson-Palme and Larsson, 2015). Various antibiotic compounds are used for the treatment of animals in the livestock and poultry industries. It has been reported that these substances have been detected in animal manure, including tetracycline, aminoglycosides, macrolides, fluoroquinolones, and sulfonamides (Munir and Xagoraraki, 2011). The abuse of antibiotics has been widely reported as a cause for antibiotic resistant bacteria in the gastrointestinal tracts of livestock and poultry (Jechalke et al., 2014), which has increased the risks of antibiotics and ARGs contamination (Huang et al., 2019). In recent years, more attention has been paid to the environmental risks of antibiotics and ARGs. The World Health Organization has pointed out that countries around the world should use antibiotics more wisely to cope with increasing resistance (World Health Organization, 2015).

Composting is an environmentally acceptable way to dispose of and utilize organic wastes composts, especially livestock manure (Onwosi et al., 2017). The product of composting can take the place of soil conditioners and support the formation of humus, which is a benefit that cannot be achieved artificially (Onwosi et al., 2017). Aerobic composting, a cost-effective means of harmless treatment and resource utilization of livestock and poultry manure, is widely used around the world. Previous studies have shown that thermophilic composting can degrade 50 ~ 99% of certain antibiotics, such as tetracyclines in manure (Dolliver et al., 2008, Kim et al., 2010). Due to the differences in compost materials, physicochemical properties, and microbial community structure, the removal efficiency of ARGs varies in different types of manure. The ARG abundance in cattle manure and chicken manure could be significantly reduced after composting (Riaz et al., 2020). Previous research also shows that ARGs in swine manure could be effectively removed during the thermophilic phase of composting (Wang et al., 2016, Youngquist et al., 2016). The composting process may result in the reduction of one type of ARG but an increase in the abundance of another type of ARG (Riaz et al., 2020). The microbial community directly affects the abundance of ARGs during composting (Zhang et al., 2016), and has a greater influence on the dynamics of ARGs than the presence of antibiotics (Qian et al., 2016). The application of composting products in soil may lead to an increase in the abundance and durability of soil ARGs (Xie et al., 2018).

China is the world's largest producer and consumer of antibiotics (Xue et al., 2013). In 2013, China used 162,000 tons of antibiotics, 52% of which were used in animal husbandry (Zhang et al., 2015). Animal husbandry farmers generally add antibiotics to feed and even use antibiotics as nutritional supplements to promote growth, which increases the environmental risk of antibiotic resistant genes (Jechalke et al., 2014, Sarmah et al., 2006). The 2019 National Economic and Social Development Statistical Bulletin shows that China had 54.519 million hogs on the market and 31.041 million hogs on hand at the end of the year. With the continuous expansion of the scale of the hog breeding industry, excessive manure output has caused great pressure on waste management and disposal. According to The First National Pollution Source Census: Source and Discharge Coefficient Handbook for Livestock and Poultry Farming, the output of manure in China in 2019 was estimated to be 240 million tons. The China Animal Husbandry and Veterinary Yearbook shows that in 2016 there were 40,205,599 hog farms with less than 50 hogs in China, accounting for 94.36% of all farms.

Studies have shown that the manure composting process on large-scale farms can effectively reduce ARGs (Zhang et al., 2020), but the fate of ARGs in sub-scale farms is not clear. The abuse of antibiotics induces bacteria to develop resistance, and these bacteria which carry ARGs will be present in manure (Jechalke et al., 2014, Sarmah et al., 2006). They grow and reproduce in large quantities by natural selection, and are then discharged into the surrounding environment, causing great environmental risks. Large-scale farms generally have standardized antibiotic management regulations. However, the use of antibiotics may not be standardized in sub-scale farms. As a result, the fate of ARGs and bacteria are different from those in large-scale farms. Studying the change in the level of ARGs and bacteria communities during composting of manure on sub-scale farms aims to discover potential host bacteria of ARGs and explore conditions for controlling the growth of potential host bacteria. Besides, most of the current research focuses on the effects of physicochemical properties and microbial community structure on ARGs, while less attention has been paid to pathogenic bacteria in manure composting. Once the pathogenic bacteria acquire ARGs, it will pose greater environmental risks. In this study, manure was collected from a simulated sub-scale farm. The main objectives of this study are: (1) To determine the abundance and diversity of ARGs, MGEs, and bacteria during the composting of manure; (2) To study potential host bacteria of ARGs and evaluate pathogenic bacteria (3) To study the effects of physicochemical properties on potential host bacteria of ARGs during the composting process.