Microbial community changes during co-composting of oil palm empty fruit bunch with palm oil mill effluent anaerobic sludge

The oil palm industry in Malaysia produces residues such as oil palm empty fruit bunch (OPEFB) and palm oil mill effluent (POME) anaerobic sludge which can be transformed into high value-added products. The utilization of these residues in the form of decomposed biomass for agricultural used create interest in improving the composting process to be more efficient and sustainable. During the composting process, organic materials including lignocellulose are broken down by the bacterial communities which develop in line with the symbiotic relationship among the species present. Recently, the enhanced co-composting of OPEFB and POME anaerobic sludge process has spurred increase attention into finding how microbial diversity influence the degradation process and what microbes are involved during the process. Hence, the overall objective of this study was to elucidate the bacterial communities participating in the enhanced composting process through isolation and characterization of cultivated microbes, polymerase chain reaction- denaturing gradient gel electrophoresis (PCR-DGGE), 16S rRNA clone library techniques and next generation sequencing (pyrosequencing). In the first study, 27 cellulolytic and hemicellulolytic bacteria strains were isolated at different stages of composting of which 23 strains were identified as closely related to Bacillus subtilis, Bacillus firmus, Thermobifida fusca, Thermomonospora sp. S22-23, Cellulomonas sp. ANA-WS2, Ureibacillus thermosphaericus, Paenibacillus barengoltzii, Paenibacillus campinasensis BL11, Geobacillus thermodenitrificans and Pseudoxanthomonas byssovorax. All of these were known to be commonly involved in lignocellulose degradation. Four strains related to Exiguobacterium acetylicum and Rhizobium sp which are previously not known as lignocellulosic degraders were found with cellulolytic and hemicellulolytic activities. Consequently, PCR-DGGE and 16s rRNA clone library methods were used to visualize the shift in microbial community and to identify the bacterial community species. PCR-DGGE showed that the bacterial community drastically shifted and the banding patterns correlate with the abundance of phyla Actinobacteria (high G+C content DNA bacterium) and Firmicutes (low G+C content DNA bacterium) during thermophilic, cooling and maturing stages as detected in the clone library. 16S rRNA clones belonging to the genera Bacillus, Exiguobacterium, Desemzia, and Planococcus were the dominant group with species closely related to Solibacillus silvestris was found to be major contributors to the changes in the lignocellulosic component throughout composting. Clones identified as Thermobacillus xylanilyticus, Brachybact- erium faecium, Cellulosimicrobium cellulans, Cellulomonas sp., and Thermobifida fusca, which are known to be lignocellulosic-degrading bacteria, were also detected. The results were in line with identification of isolated cellulolytic and hemicellulolytic bacteria and revealed the presence of these bacteria types at different stages of composting. In depth analysis of the bacterial community structure and shift in microbial abundance using pyrosequencing showed that the largest bacterial communities were belonged to phyla Firmicutes and Proteobacteria, in which their species related to Devosia yakushimensis and Planoccocus rifietoensis were found during thermophilic, cooling and maturing stages. It is of interest to report for the first time that sequence related to Devosia yakushimensis was found to be a dominant bacterial species during thermophilic stage which was not discovered in the analysis of clone library. The data obtained suggests that clone libraries can overlook important groups of bacteria, hindering the link between the microbial diversity to operational performance. The results of the present study clearly demonstrate the ensuing changes that take place in the microbial community during co-composting of oil palm empty fruit bunch with palm oil mill effluent anaerobic sludge