Biodegradation of skatole by Burkholderia sp. IDO3 and its successful bioaugmentation in activated sludge systems

Highlights

• The Burkholderia strain was reported to degrade skatole for the first time.

• RNA-seq analysis indicated that skatole activated the oxidative phosphorylation.

• Bioaugmentation of strain IDO3 could increase the removal of skatole.

• Burkholderia was colonized to be the predominant genus in bioaugmentation systems.

Abstract

Skatole is the key malodorous compound in livestock and poultry waste and wastewater with a low odor threshold. It not only causes serious nuisance to residents and workers, but also poses threat to the environment and human health due to its biotoxicity and recalcitrant nature. Biological treatment is an eco-friendly and cost-effective approach for skatole removal, while the bacterial resources are scarce. Herein, the Burkholderia strain was reported to efficiently degrade skatole for the first time. Results showed that strain IDO3 maintained high skatole-degrading performance under the conditions of pH 4.0–9.0, rotate speed 0–250 rpm, and temperature 30–35 °C. RNA-seq analysis indicated that skatole activated the oxidative phosphorylation and ATP production levels in strain IDO3. The oxidoreductase activity item which contained 373 differently expressed genes was significantly impacted by Gene Ontology analysis. Furthermore, the bioaugmentation experiment demonstrated that strain IDO3 could notably increase the removal of skatole in activated sludge systems. High-throughput 16S rRNA gene sequencing data indicated that the alpha-diversity and bacterial community tended to be stable in the bioaugmented group after 8 days operation. PICRUSt analysis indicated that xenobiotics biodegradation and metabolism, and membrane transport categories significantly increased, consistent with the improved skatole removal performance in the bioaugmented group. Burkholderia was survived and colonized to be the predominant population during the whole operation process (34.19–64.00%), confirming the feasibility of Burkholderia sp. IDO3 as the bioaugmentation agent in complex systems.

Introduction

Intensified livestock and poultry production generate large amounts of urine, faeces, and manure, which result in malodor emissions causing serious nuisance to nearby residents and environmental pollution (Mackie et al., 1998). The odorous compounds, which generally include volatile fatty acids, sulfur-containing compounds, ammonia, volatile amines, phenols, and indoles, resulted from microbial metabolism of dietary nutrients and endogenous products in the animal intestines and manure (Mackie et al., 1998; Deslandes et al., 2001). Skatole (3-methyindole) is amongst the most noticeable and offensive compounds with a low odor threshold of 0.00309 mg/m³ in air emissions (Liu et al., 2018; Schiffman et al., 2001). In addition to the unpleasant and disgusting smell, skatole also poses threat to the ecological system and human health. Skatole has been proven to be able to induce acute bovine pulmonary edema and emphysema, lung diseases, hemoglobinuria, and hemolysis in ruminants (Carlson et al., 1972). It may cause damage to lung Clara cells in humans via the covalent binding of its biotransformation products to pulmonary proteins (Weems et al., 2009). Skatole also has a broad bacteriostatic effect which is toxic to many microorganisms (Tittsler et al., 1935). Studies have indicated that skatole is ubiquitously presented in the wastewater and livestock waste, whose concentrations can reach as high as mg/L or mg/kg level (Lebrero et al., 2011; Zhu, 2000). Therefore, the control and removal of skatole are of great concern.

Biodegradation has been proven to be an eco-friendly and cost-effective approach in environment remediation (Yun et al., 2017; Bharti et al., 2019; Derakhshan et al., 2018). In this respect, it was reported that skatole could be transformed under anaerobic methanogenic and sulfate-reducing conditions (Gu and Berry, 1992; Gu et al., 2002). However, anaerobic transformation is time-consuming and the isolation of anaerobic-degrading strains is still a challenge. Aerobic degradation of skatole has attracted much attention for its relatively high removal efficiency in the last few decades. The initial study could be dated back to 1968, the indole-induced cells of a Gram-positive coccus were shown to be able to oxide skatole (Fujioka and Wada, 1968). Thereafter it was until 2006 that a Pseudomonas sp. Gs strain was isolated from mangrove sediment enrichment with the ability to mineralize skatole (Yin et al., 2006). Strains from Lactobacillus, Rhodopseudomonas, Cupriavidus, and Acinetobacter were successively reported for skatole removal and the degradation conditions were characterized (Meng et al., 2013; Sharma et al., 2015; Fukuoka et al., 2015; Tesso et al., 2019). However, the skatole-degrading microbial strains are still limited due to the biotoxicity and recalcitrant nature of skatole. In addition, most of previous studies focused on skatole degradation properties, there is a paucity of knowledge about genetic responses of bacteria to skatole stress, and the functional enzymes for skatole biodegradation remain unknown. Recently developed omics technology has been proven to be a powerful approach to unveil the adaptation and degradation mechanism towards aromatics (Chen et al., 2018a).

Bioaugmentation using the specific strains or consortia is considered to be a useful technique to increase bioremediation efficiency (Liang et al., 2020; Zhao et al., 2019a). The inoculated strains are able to affect the degradation performance, biomass, diversity, and structure of indigenous microbial communities (Wu et al., 2018; Huang et al., 2019). However, bacterial strains may not survive and even vanish in the complex community systems in many cases (Herrero and Stuckey, 2015). The augmented strains may be uncompetitive and difficult to adapt to indigenous communities, washed out with the effluent, or inhibited by other toxic substances. Therefore, a key factor for successful bioaugmentation is to retain the augmented strains. Up to date, only one report referred to the skatole removal in chicken manure using Acinetobacter toweneri NTA1-2A and Acinetobacter guillouiae TAT1-6A (Tesso et al., 2019), and the related microbial community information is lacked. Successful survival and colonization of an efficient skatole-degrading strain in activated sludge systems should represent an important breakthrough for practical skatole removal applications.

Burkholderia is a versatile aromatic-degrading genus and occupies diverse of niches in the environment (Coenye and Vandamme, 2003). However, there is no studies describing skatole degradation by Burkholderia to the best of our knowledge. Burkholderia sp. IDO3 was previously isolated from the activated sludge which could degrade indole (Ma et al., 2019a, 2019b). We have found that this strain can also utilize skatole as the sole carbon source. The objectives of the present study are (i) to evaluate the skatole biodegradation performance of strain IDO3 under various conditions; (ii) to determine the mRNA expression profile of strain IDO3 in response to skatole; (iii) and to validate the feasibility of the strain IDO3 for bioaugmentation in sludge systems.