Heavy metals, antibiotics and nutrients affect the bacterial community and resistance genes in chicken manure composting and fertilized soil

Highlights

• Compost is effective for reducing pathogenic bacteria, antibiotics and ARGs.

• Antibiotics, heavy metals and nutrients could affect bacterial community and ARGs.

• Heavy metals in chicken manure is the main factor that affects bacterial composition.

• The application of compost lead to a decrease in pathogens and ARGs in soil.

Abstract

Succession of bacterial communities involved in the composting process of chicken manure, including first composting (FC), second composting (SC) and fertilizer product (Pd) and fertilized soil (FS), and their associations with nutrients, heavy metals, antibiotics and antibiotic resistance genes (ARGs) were investigated. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla observed during composting. Overall, potential pathogenic bacteria decreased from 37.18% (FC) to 3.43% (Pd) and potential probiotic taxa increased from 5.77% (FC) to 7.12% (Pd). Concentrations of heavy metals increased after second composting (SC), however, no significant differences were observed between FS and CS groups. Alpha diversities of bacterial communities showed significant correlation with heavy metals and nutrients. All investigated antibiotics decreased significantly after the composting process. The certain antibiotics, heavy metals, or nutrients was significantly positive correlated with the abundance of ARGs, highlighting that they can directly or indirectly influence persistence of ARGs. Overall, results indicated that the composting process is effective for reducing potential pathogenic bacteria, antibiotics and ARGs. The application of compost lead to a decrease in pathogens and ARGs, as well as an increase in potentially beneficial taxa and nutrients in soil.

Introduction

Livestock husbandry is considered a significant contributor to current environmental problems (Steinfeld et al., 2012). Specifically, livestock manure is considered the main contributor (Ma et al., 2018). The growing demand for chicken meat and eggs has led to an increase in chicken husbandry in China, producing around 1.0 million tons of chicken manure daily. Uncontrolled discharge of manure can lead to serious environmental pollution as well as dissemination of pathogens and infectious agents.

Antibiotics are commonly used to treat animal diseases or added to animal feed as supplements to promote growth of food animals. However, most antibiotics are poorly metabolized by animals after ingestion, and as a result substantial amounts of antibiotics are excreted in feces (Zhu et al., 2013a; Awad et al., 2013). Consequently, soil is the primary receiver of the poorly absorbed or metabolized antibiotics through land application of manure (Chen et al., 2018). Heavy metals, such as copper (Cu), zinc (Zn), chromium (Cr) and manganese (Mn), are also widely used as feed additive in food animals (Zhang et al., 2012) for their antimicrobial and growth-stimulating effects (Hölzel et al., 2012; Deka et al., 2015; Vacchina et al., 2013). However, adsorption rates of Zn, Cu and Mn in broiler chicks were only 50–60%, 30–40% and 5–15%, respectively (Bao et al., 2010), causing high levels of heavy metals in animal manure and long-term contamination of soils (Wang et al., 2013; Yang et al., 2017a). Other nonessential elements such as cadmium (Cd), nickel (Ni), and lead (Pb) are introduced during livestock rearing, via industrial wastewater and feed pollution (Zhang et al., 2012; Wang et al., 2013).

Composting has been considered as a way of achieving stabilized substrates from animal manure which can serve as agriculture fertilizer (Gabhane et al., 2012; Ding et al., 2016a). Previous studies suggested that composting is a suitable method of eliminating antibiotics, pathogens and antibiotic resistance genes (ARGs) in manure (Chen et al., 2018; Xie et al., 2016), thereby reducing the dissemination of antibiotics and ARGs into soil environments. However, given the potential benefit of composting, there is still concern about the efficacy of the composting process of chicken manure with regard to reducing or eliminating antimicrobial resistance. The composting technique may not always be sufficient to ensure complete inactivation of pathogens and reduction in ARGs within the entire compost mass (Islam et al., 2004; Ezzariai et al., 2018). Additionally, unlike antibiotics and AGRs, heavy metals are not subject to degradation and/or removal and can become concentrated during the composting process, thus potentially representing a long-term selection pressure (Yang et al., 2017a). The presence of the antibiotics created a selection pressure that accelerated emergence of both ARGs and antibiotic resistant bacteria (ARB) in manure and manure-amended soils (Chen and Zhang, 2013; Wichmann et al., 2014). Notably, an increasing number of studies have highlighted the role of heavy metals in proliferation of antibiotic resistance through co-selection (Baker-Austin et al., 2006), and nutrients have the potential to enhance the effect of selective pressures of ARGs (Berendonk et al., 2015). Moreover, the combined effects of nutrients, heavy metals and microbial communities were observed to drive the distribution of ARGs in mariculture sediments (Zhao et al., 2017a). Thus, additional researches are needed, gathering chemical and microbiological data to better understand the interactions between various environmental factors and ARGs elimination.

The composting process involves numerous interacting factors including nutrients, moisture, temperature and diverse bacteria (Li et al., 2014), with bacterial succession playing a role in material transformation and maturity during the composting process (Zhong et al., 2018). Bacterial diversity varied at the thermophilic and maturity phase of composting (Wang et al., 2017), and bacterial community composition during composting could be also driven by alterations in the environmental condition (Sun et al., 2012). However, there is still a limited understanding of the associations between bacterial populations and the environment factors of composting process, including nutrients, heavy metals and antibiotic levels and how these factors affect ARG mitigation during chicken manure composting and after fertilization in soil.

Here, bacterial community dynamics and diversity were monitored throughout the composting processes using high-throughput sequencing. The effect of environmental factors on bacterial communities and relative abundances of ARGs was also determined. Our goal was to investigate the interaction among bacterial community, nutrients, heavy metals, antibiotics, and ARGs during the composting process and in soil after fertilization.