Analysis of decomposing wood wastes in the Lagos Lagoon using terminal-restriction fragment length polymorphism and illumina sequencing platform

Abstract

Indiscriminate disposal of wood shavings and sawdust into the Lagos lagoon usually constitute environmental hazard and varying degree of threats to marine biotic communities. In this study we applied terminal-restriction fragment length polymorphism (T-RFLP) and illumina sequencing of 16S ribosomal RNA gene, to describe the microbial ecology of decomposing wood wastes in the Lagos lagoon, Nigeria. The terminal restriction fragments (TRFs) generated corresponds to over 100 bacterial genera and numerous uncultured bacterial clones. Phylogenetic analysis of the TRFs of 16S rRNA gene sequences and cultured bacterial sequences established genetic relatedness and divergent relationships. T-RFLP in combination with illumina sequencing platform identified bacterial species (Acinetobacter sp., Clostridium sp., Planctomyces sp., Escherichia coli, Pantoea agglomerans, Dyella japonica, Ochrobactrum sp., Prevotella sp., Runella slithyformis, Enterobacter aerogenes, Gordonia amicalis, Klebsiella sp., Thalassospira sp. and Serratia sp.) not previously accounted for in culture-dependent analysis. Bacterial strains such as Ruminococcus flavefaciens, Fibrobacter succinogenes, Simiduia agarivorans, Microbulbifer sp. and Cellulomonas fimi further identified in illumina sequences were found to be involved in the biodegradation of lignin and lignin derivatives. Hence, understanding of the diverse autochthonous microbiota of decomposing wood wastes in the Lagos lagoon is essential in the development of effective biotechnology programme, to tackling the menace of sawdust pollution.