Isolation and molecular characterization of composting bacteria from municipal solid waste disposal sites in two Kenyan cities, Nairobi and Kisumu

Advancement in civilization in developing countries with unmatched capacity to dispose of the vast amounts of wastes generated poises public health concerns and adds strain on diminishing land space in emerging urban centers. A sustainable efficient way of waste management is needful, to which end, enhanced composting through employment of appropriate biopreparations offers environmentally safe strategy. This work sought to improve the management of Municipal Solid Waste (MSW) by assessing the physical dumps site conditions, evaluation of the effects of addition of exogenous microbes on rate of waste composting, isolation and characterization of aerobic bacteria to identify suitable ones with biotechnological potentials. Crude wastes microbes were sampled from three dump sites in two Kenyan cities, Nairobi and Kisumu and their effects on biodegradation of institutional wastes of Kenyatta University were assessed in comparison with commercial microbial preparations. Aerobic bacteria were isolated from the MSW samples on culture media and characterized using both physical and molecular techniques. Physical characterization was based on colony morphologies, microscopic appearances of the bacteria and Gram staining. Molecular characterization involved sequencing of PCR amplified 16S rRNA bacterial genes and their identification using bioinformatics tools. The composting of the institutional wastes was enhanced through the addition of crude compost materials from the two Nairobi dump sites as well as the addition of commercial microbial preparations. The inoculation with Kisumu crude compost materials indicated negative effect on Nairobi based waste. Media plating yielded 356 distinct bacterial isolates, which upon physical and molecular discrimination enabled selection of 53 isolates for full analysis. Full gene sequencing yielded an average size of complete and nearly complete 16S rDNA sequence lengths of 1486bp. The BLAST search using the full gene sequences yielded 13% of the isolates with 100% identical matches with the organisms in the GenBank. The majority, 38 out of 53 samples (71.7%) of the sequences had 99% identity and four (7.5%) each had 98% and 97% identities. This enabled grouping of the 53 isolated into 3 bacterial taxa (Firmicutes, Actinobacteria and Proteobacteria) and their definition to the genus, with the majority defined up to the species level. The bulk of the isolates were of the genus Bacillus (68%). Others included species of Paenibacillus, Planococcus, Pseudomonas and a mixture of other bacteria (Stenotrophomonas maltophilia, Caryophanon sp., Ochrobactrum intermedium, Brevibacterium frigoritolerans and Blackwater bioreactor bacterium). Three were novel isolates, which, hither to had never been cultured before, requiring further classification. Available documentation on the 53 characterized and identified isolates and their closest relatives indicated that, the majority were directly attributable to MSW degradation. Some had wide range of temperature adoptability, while others produced wide range of appropriate enzymes. Additionally, some isolates produce plant growth promoting enzymes with additional ones having plant pathogen suppression properties. These are desirable qualities exploitable for efficient degradation of MSW for agriculturally applicable compost. However, a number of the isolates are pathogenic to humans and others to plants and animals. A total of 34 isolates were selected, being considerably safe bacteria with the desired biotechnological qualities for constituting the microbiological composite. With proper policy framework, the demonstrated efficient composting process and use of safe desirable isolates can be adopted by urban/ periurban communities and up-scaled for efficient MSW composting for clean environment, better crop yield and income generation for a more healthy urban dwellers.