Bacterial community structure transformed after thermophilically composting human waste in Haiti

Abstract

Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98-99%), Lachnospiraceae (83-94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.

Fig 1. OTU relative richness calculated at each stage of a thermophilic composting process at two locations: Cap-Haitien and Port-au-Prince, Haiti.

a) average number of OTU per composting process stage, error bars indicate standard deviation; b) distribution of OTU within phyla containing at least five OTU (main dataset of 7531 OTU); c) distribution of OTU within phyla comprising the 1768 OTU defined as human gut associated for this dataset (present in at least half the Bucket samples). Number of samples included per location: Bucket (n = 12), Thermophilic (n = 9 in Cap-Haitian, n = 7 in Port-au-Prince), Curing (n = 3), and Bagged (n = 3).

Fig 2. Proportion of microbial community derived from untreated source material (Bucket) samples throughout the composting process.

Proportions were estimated by SourceTracker using binary OTU data from individual Bucket samples as the training (source) set and Thermophilic, Curing and Bagged samples as sinks. Source proportions in each Bucket sample were estimated using the leave-one-out validation procedure and averaged. Error bars are standard deviations around the mean.

Fig 3. Non-metric multidimensional scaling (NMDS) plots of Bray-Curtis similarity matrices based on standardized OTU intensities.

Number of samples at each stage at each location were: Bucket (12), Thermophilic compost (9), Curing (3), Bagged (3). a) Cap-Haitien, b) Port-au-Prince

Fig 4. Pie charts show a summary of bacterial orders containing OTU that changed the most in relative abundance (probe intensity scores) through the thermophilic composting process.

OTU for each location were included if they were within the top 100 OTU changing the most (for all pairwise comparisons within a location) and/or had at least a 10-fold change in average abundance across compost stages within each location. OTU within the orders could differ by location. Average intensity values were calculated for each OTU and percent contributions were summed at the order level for each stage and location. Named orders are those contributing at least 2% at any compost stage in either location. Following pie charts clockwise, names are listed in the legend from left to right.