Genetic relatedness of faecal coliforms and enterococci bacteria isolated from water and sediments of the Apies River, Gauteng, South Africa

Concentration of faecal coliforms and Enterococcus spp. in water and sediments of Apies River demonstrates that the river receives high loads of external faecal pollution. This study also revealed significant differences in faecal coliforms and Enterococcus spp. loads between the Apies River sediment and water samples. These findings corroborate those of Abia et al. (2015b, c) who reported high E. coli levels in water and riverbed sediments of Apies River. The abundance of E. coli in Apies River sediments measured by membrane filtration in the present study were comparable to those of Colilert®-18 methods previously reported in riverbed sediments of the Apies River (Abia et al. 2015c). Walk et al. (2007) have also outlined the survival and growth of faecal bacteria in aquatic sediments and also pointed out that sediments may represent their secondary habitat after the intestinal tract of warm-blooded animals which serves as their primary habitat. Sediments can be “reservoirs” of metabolically active faecal indicator bacteria (Pianetti et al. 2004). This has also been confirmed by studies conducted in subtropical areas, where E. coli and enterococci displayed higher growth and survival rates in marine sediments than in the overlying seawater (Hartz et al. 2008). When bacteria enter the river, they may form flocs and settle in the bottom of rivers by adhering to sand, rocks, and other particulate matter where they can live and thrive for long periods of time (Craig et al. 2004). This causes the faecal coliforms and enterococci loads in the sediment to be higher than in the overlying water, except during heavy rainfall and runoff events when the load of bacteria in the water increases prior to settling out into the sediment (Orear and Dalman 2011).

Stumpf et al. (2010) examined the input of faecal coliforms during storm flow and base flow, and observed that during storm flow the bacterial load on average was 30–37 times greater than the base flow bacterial loads. Further, the sediment E. coli counts reached log₁₀ 2.89 CFU/100 mL, well above the EPA proposed safe limit of log₁₀ 2.37 CFU/100 mL, and hence sediment acted as a reservoir and source of faecal contamination to the overlying water (Stumpf et al. 2010). Similar results were seen in the Apies River study where sediment faecal coliform counts were as high as log₁₀ 7.61 CFU/100 mL. At this concentration and also taking into consideration re-suspension, the findings of this study suggest sediments in Apies River to be a major source of bacterial contamination during periods of low river flow. When sediment and water faecal coliform levels were compared, it was found that on average the bacterial concentration in the sediment was 1- to 3000-folds higher than in the overlying water. Sediments consistently had faecal coliform concentrations that ranged from 1 to 383 times greater than the adjacent water column (Orear and Dalman 2011). In our study, only 21.9% of all the water samples analysed were found to fall within the target water quality range (TWQR) as set out in the South African Water Quality Guidelines for Domestic Water Use (Volume 1) and for Recreational Water Use (Volume 2) (DWAF 1996). In terms of the national standards set by SANS 241 (SABS 2006) and the South African Water Quality Guidelines (Volume 1) (DWAF 1996), the limit for faecal coliforms is 0 CFU/100 mL for water that is meant for domestic use; any concentration ?500 CFU/100 mL in drinking water can lead to gastrointestinal (GI) illness. For recreational activities the minimum acceptable risk is 8.5% GI illness risk in terms of the microbiological indicators given in the South African Water Quality Guidelines (Volume 2) (DWAF 1996). The Skinner Spruit (SP) water and sediment close to the Daspoort WWTP recorded the highest levels of both faecal coliform and Enterococcus spp. According to the most recent South African Green Drop Progress Report (DWA 2012), this treatment plant with a microbiological compliance level of 87.3% has been treating the wastewater adequately, while the Skinner Spruit, a tributary of the Apies River, is reported to carry elevated microbial loads and thus negatively impacts the water quality of the effluent discharged by this WWTP. High counts were also observed after rainfall events, confirming the findings of Pandey et al. (2012) where a sudden increase in faecal coliform counts is mostly the result of both surface water run-off and re-suspension of the stream bottom sediment.

The enterococci levels found in water were 2–4 logs lower than those found in riverbed sediment. These counts were consistently higher than those of faecal coliforms during the entire sampling period in Fig. 2b. Ferguson et al. (2005) found enterococci to be present in all the samples taken for the study conducted. The geometric mean enterococci concentrations in sediment samples were also higher (log₁₀ 3.77 CFU/10 g) than the faecal coliform concentrations (log₁₀ 3.27 CFU/10 g). Their occurrence in both water and sediment may suggest a movement between these two environments.

Unlike in other studies, the number of faecal coliforms enumerated from the riverbed sediment samples did not correlate with those enumerated from the river water samples (Craig et al. 2004). A similar attempt to correlate E. coli densities in water and in sediment by Valiela et al. (1991), An et al. (2002) and Byappanahalli et al. (2006) was also not successful. This indicated that the faecal coliform densities in water did not relate with the densities in riverbed sediments, leaving the Enterococcus spp. to be more related faecal indicators of riverbed sediment. Many studies have proven the Enterococcus spp. standard to be the more sensitive compared to faecal coliforms for recreational purposes (Noble et al. 2003; Benedict and Neumann 2004; Neumann et al. 2006).

The faecal coliforms isolated exhibit a 98% nucleotide sequence homology which emphasises the positive correlation between faecal coliforms in river water and riverbed sediment, as also reported earlier (Grant et al. 2001; Boehm et al. 2002; Kim et al. 2004; Noble and Xu 2004). However, these results can also imply a common ancestry and thus likely derived from the same source. Using the phylogenetic tree, Njage and Buys (2015) reported the genetic similarity between commensal and pathogenic E. coli strains from lettuce and irrigation water, even at a distance of 246 km apart.

Unlike faecal coliforms, the phylogenetic tree of enterococci, shown in Fig. 4, revealed that Enterococcus faecalis was the predominant species found in all the river water and riverbed sediment samples, findings corroborating those of Ferguson et al. (2005). With a bootstrap value of 100%, this may suggest that Enterococcus spp. isolated from river water and riverbed sediment samples may be highly similar at the molecular level. Anderson et al. (1997) found that enterococci of marine sediment were suggestive of natural or environmental sources of contamination to overlying water.

Microbial loads of faecal coliforms and enterococci in Apies River revealed a river that is highly polluted with faecal contamination. There is thus a need to rehabilitate or restore this stream to its once pristine state. The correlation coefficient study revealed enterococci counts to be the better indicator than faecal coliforms in search of predicting the degree of contamination in the event of riverbed sediment re-suspension. The present study revealed a high prevalence of faecal indicator bacteria and provided evidence of the close genetic similarity between isolates from river water and riverbed sediment. A 98% homology among the nucleotide sequences between river water and riverbed sediment isolates indicated their close genetic similarity. There is therefore a need to incorporate sediment quality monitoring as an integral component of the nationwide routine surface water quality monitoring programmes. This study recommends future studies to be conducted on a multi-locus sequencing or whole genome sequencing techniques in order to emphasize or reject the finding of this study.