Characterization of Bacterial Community Dynamics During the Decomposition of Pig Carcasses in Simulated Soil Burial and Composti
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J. Microbiol. Biotechnol. (2017), 27(12), 2199–2210 https://doi.org/10.4014/jmb.1709.09032 Research Article Review jmb Characterization of Bacterial Community Dynamics during the Decomposition of Pig Carcasses in Simulated Soil Burial and Composting Systems S Bo-Min Ki1, Yu Mi Kim2, Jun Min Jeon3, Hee Wook Ryu2*, and Kyung-Suk Cho1* 1Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea 2Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea 3Green Environmental Complex Center, Suncheon 57992, Republic of Korea Received: September 18, 2017 Revised: September 30, 2017 Soil burial is the most widely used disposal method for infected pig carcasses, but composting Accepted: October 10, 2017 has gained attention as an alternative disposal method because pig carcasses can be First published online decomposed rapidly and safely by composting. To understand the pig carcass decomposition October 14, 2017 process in soil burial and by composting, pilot-scale test systems that simulated soil burial and *Corresponding authors composting were designed and constructed in the field. The envelope material samples were K.-S.C. collected using special sampling devices without disturbance, and bacterial community Phone: +82-2-3277-2393; Fax: +82-2-3277-3275; dynamics were analyzed by high-throughput pyrosequencing for 340 days. Based on the odor E-mail: [email protected] gas intensity profiles, it was estimated that the active and advanced decay stages were reached H.W.R. earlier by composting than by soil burial. The dominant bacterial communities in the soil were Phone: +82-2-820-0611; Fax: +82-2-812-5378; aerobic and/or facultatively anaerobic gram-negative bacteria such as Pseudomonas, Gelidibacter, E-mail: [email protected] Mucilaginibacter, and Brevundimonas. However, the dominant bacteria in the composting system were anaerobic, thermophilic, endospore-forming, and/or halophilic gram-positive bacteria such as Pelotomaculum, Lentibacillus, Clostridium, and Caldicoprobacter. Different S upplementary data for this paper are available on-line only at dominant bacteria played important roles in the decomposition of pig carcasses in the soil and http://jmb.or.kr. compost. This study provides useful comparative date for the degradation of pig carcasses in pISSN 1017-7825, eISSN 1738-8872 the soil burial and composting systems. Copyright© 2017 by Keyword: Pig carcass disposal, soil burial, composting, bacterial community dynamics, The Korean Society for Microbiology and Biotechnology sampling device Introduction [1]. Confirmed cases of FMD were recorded on 3,748 farms during 144 days, from 28 November 2010 to 21 April 2011 Foot-and-mouth disease (FMD), a highly transmissible [1]. The Republic of Korea implemented a policy to viral disease of cloven-hoofed animals, is one of the most depopulate infected animals [4]. serious and economically significant diseases in the livestock Even though various methods have been used for carcass industry [1]. Once FMD is introduced into an FMD-free disposal, including burial, burning, incineration, rendering, country, the country makes great efforts to eradicate the anaerobic digestion, alkaline hydrolysis, and composting disease by enforcing strict control measures, such as [5-8], the most widely used disposal method has been culling and the disposal of animals on infected farms [2]. burial in soil. Burial is a relatively economical option for According to an OIE report, the Republic of Korea had 21 carcass disposal compared with other available methods; outbreaks of FMD in 2016, 188 in 2014, and 175 in 2010 [3]. it is convenient, logistically simple, and relatively quick, Unfortunately, the epidemic that occurred during the especially for daily mortalities, as the equipment necessary winter of 2010–2011 was the biggest ever recorded in Korea is widely available, and the technique is relatively straight- December 2017 ⎪ Vol. 27⎪ No. 12 2200 Ki et al. forward. If performed on-farm or on-site, trench burial also bacterial diversity during pig leg decomposition. Xu et al. eliminates the need for transportation of potentially [22] evaluated field-scale composting in cattle, quantifying infectious material. However, there is potential for bacterial 16S rDNA fragments using real-time PCR. detrimental environmental effects, specifically water quality Recently, the bacterial communities associated with carcass issues, as well as the risk that disease agents will persist in decomposition were investigated using an advanced the environment owing to the limited environmental sequencing technique to monitor the temporal changes of controls in place [9]. entire microbial communities [23]. Yang et al. [24] used high- As a consequence of those disadvantages of burial, throughput nucleotide sequencing analysis to investigate the alternative methods are required for the safe and rapid bacterial communities in leachates from the decomposition degradation of animal carcasses. Composting of infected of pig carcasses. Pechal et al. [25] studied skin and mouth livestock carcasses has been adopted as an environmentally bacterial communities during the decomposition of three sound method for carcass disposal in recent disease swine carcasses over 5 days. Metcalf et al. [23] conducted a outbreaks in Australia and North America [6]. Composting laboratory experiment to characterize temporal changes in has many different methods, such as aerobic, anaerobic, microbial communities associated with mouse carcasses as mechanical mixing, and microbial culture-added composting they decomposed on soil under controlled conditions for [5]. Recently, studies of pig carcass composting for emergency 48 days. Lindblad [26] monitored the change of the microbial disposal were conducted [10-13]. Akdeniz et al. [10] community during composting of pig carcasses for 13 monitored gas profiles during pig carcass composting for 6 months. However, previous studies have focused on the months. The safe disposal of carcasses during a disease changes in soil or compost bacterial community structure outbreak is a significant environmental and health issue for during the decomposition of carcasses through artificial both humans and other livestock. Composting carcasses situations using small quantities of tissue in the laboratory, and manure with bulking materials uses bacterial activity rather than whole organisms on the field-scale. to decompose the carcass tissues and generate heat, which For continual monitoring of the bacterial community can lead to temperatures high enough to kill targeted during pig carcass decomposition in a soil pit or compost bin, pathogenic microorganisms [6]. repetitive sampling of the envelope materials is necessary. The decomposition of carcasses causes a change in gas Dredging soil or compost is the most representative sampling profiles and bacterial community structures during both method, but it causes significant microenvironmental soil burial and composting [14]. A variety of odor gases, changes. Samples from a soil burial site were taken by including sulfur and nitrogen compounds, acids, aldehydes, careful excavation at several locations close to pig carcasses and cyclic hydrocarbons, are released by decaying pig avoiding as far as possible sites of disturbance [27]. carcasses [13-16]. Some researchers have been evaluating Envelope material samples were collected through ports the availability of volatile organic compounds (VOCs) as installed in the sidewalls of a compost bin to minimize markers for the diagnosis of pig carcass decomposition disturbance [13]. Bergmann et al. [21] collected samples processes [10, 14]. To collect odor gases from soil burial through port side perforations. These methods have sites and compost bins, passive sampling devices that use a limitations in collecting envelope materials from a soil diffusive sampler have been developed to replace special burial site or composting apparatus. In this study, we air sampling probes inside the pits and bins [14]. proposed special sampling devices designed to collect The bacterial community is another important factor samples from a soil burial pit or compost bin without influencing the decomposition of carcasses [17, 18]. Several disturbance. studies have focused on bacterial ecology at burial and Although soil burial and composting methods have been composting processes. Lipolytic bacteria were quantitatively widely used for pig carcass disposal, there is still insufficient evaluated by quantitative polymerase chain reaction using information on the temporal trends of the bacterial lipase-specific primers and lipolytic bacterial counts [19]. community during pig decomposition in these methods. To Bacterial community dynamics during pig leg decomposition characterize the temporal trends, pilot-scale test systems to in soil were studied using 16S rDNA polymerase chain simulate soil burial and composting with passive aeration reaction-denaturing gradient gel electrophoresis (PCR- were constructed in the field, and the changes in gas DGGE) [20]. Bergmann et al. [21] used real-time PCR-DGGE profiles inside the systems were monitored for 340 days. based on 16S rRNA to characterize the change in soil Moreover, the internal soil and compost from the systems J. Microbiol. Biotechnol. Bacterial Community Dynamics in Pig Carcass Decomposition 2201 were sampled using the special sampling devices, and then slaughterhouse in Suncheon, Korea. Animal ethics approval was their bacterial community