A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda

Background

Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteria while reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system.

Material and methods

The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste. On Day 172, the compost was terminated and compost samples were collected from three layers of the unit: the top, the middle and the bottom layer. A metagenomic approach was then applied to characterise the viral and bacterial composition of the vermicomposting system.

Results and discussion

A high abundance and diversity of bacteria were identified. Proteobacteria was the largest phyla in the compost (mainly Alpha-, Gamma- and Betaproteobacteria), constituting almost 65% of the bacterial reads in the data sets. DNA samples from several possible pathogenic bacteria, such as Salmonella spp., Escherichia coli, Enterobacter spp., Enterococcus spp. and Clostridium spp, were detected in the vermicompost, suggesting that there might still be harmful bacteria in the vermicast. Phages constituted the main viral group; apart from phages, mainly insect viruses were identified. The only animal or human virus identified was kobuvirus. In summary, metagenomic analysis was shown to be an efficient technology to characterise the microbial composition of vermicast. The data from this study contribute to a better understanding of the microbes present in this kind of composting system and can help determine measures necessary for safe manure handling.

Persistence of Escherichia coli in batch and continuous vermicomposting systems

Vermicomposting is a biooxidation process in which epigeicearthworms act in synergy with microbial populations to degrade organic matter. Vermicomposting does not go through a thermophilic stage as required by North American legislations for pathogen eradication. We examined the survival of a Green Fluorescent Protein (GFP) labeled Escherichia coli MG1655 as a model for the survival of pathogenic bacteria in both small-scale batch and medium-scale continuously-operated systems to discern the influence of the earthworm Eisenia fetida, nutrient content and the indigenous vermicompost microbial community on pathogen abundance. In batch systems, the microbial community had the greatest influence on the rapid decline of E. coli populations, and the effect of earthworms was only visible in microbially-impoverishedvermicomposts. No significant earthworm density-dependent relationship was observed on E. coli survival under continuous operation. E. coli numbers decreased below the US EPA compost sanitation guidelines of 10(3)Colony Forming Units (CFU)/g (dry weight) within 18-21days for both the small-scale batch and medium-scale continuous systems, but it took up to 51days without earthworms and with an impoverished microbial community to reach the legal limit. Nutrient replenishment (i.e. organic carbon) provided by continuous feed input did not appear to extend E. coli survival. In fact, longer survival of E. coli was noticed in treatments where less total and labile sugars were available, suggesting that sugars may support potentially antagonist bacteria in the vermicompost. Total N, pH and humidity did not appear to affect E. coli survival. Several opportunistic human pathogens may be found in vermicompost, and their populations are likely kept in check by antagonists.

Hygienic quality of faeces treated in urine diverting vermicomposting toilets

On-site sanitation solutions have gained much interest in recent years. One such solution is the urine diverting vermicomposting toilet (UDVT). This study evaluated the hygienic quality of the composted material in six UDVTs in operation in France. Samples were taken from three sampling positions in each toilet, with increasing distance from the fresh material. The concentration of Salmonella spp., Enterococcus spp., thermotolarent coliforms and coliphages were analysed and plotted against a number of variables. The variables found to have the greatest impact was the pH (for Enterococcus spp. and thermotolarent coliforms (TTC)) and time since last maintenance (coliphages). The pH was found to correlate with the material maturity. The current practise of maintenance can cause recontamination of the stabilised material and increase the risk of regrowth of pathogenic microorganisms. A modification in the maintenance procedure, in which a fourth maturation point is introduced, would eliminate this risk. UDVTs were found to be a good on-site sanitation option as the maintenance requirement is small and the system effectively reduced odour and concentration of pathogen and indicator organisms in human waste while keeping the accumulation of material down to a minimum. If the vermicompost is to be used for crops consumed raw, an additional sanitisation step is recommended.