Genetic characterization of Salmonella and Shigella spp. isolates recovered from water and riverbed sediment of the Apies River, South Africa

Riverbed sediment is a vital component of river ecosystems and plays an important role in many geomorphological and ecological processes. However, when re-suspension occurs, pathogenic bacteria associated with sediment particles may be released into the water column, thus creating a health risk to those who use such water for drinking, household and recreational purposes. The aim of this study was to investigate the presence of bacterial pathogens Salmonella spp. and Shigella spp. in the Apies River and to ascertain whether there was any level of genetic relatedness between river water and riverbed sediment isolates of these pathogenic bacteria. A total of 124 water and sediment samples were collected from a site located on the Apies Rivers upstream of the Daspoort Wastewater Treatment Works, Pretoria, Gauteng, South Africa, between August and November 2014. In order to detect and identify the target bacteria, samples were analysed by culture-dependent and culture-independent techniques (quantitative real-time PCR). Genetic relatedness was established using Sanger sequencing of the invA gene of Salmonella spp. and ipaH of Shigella spp. Results of this study displayed the presence of the target bacteria both in the water and sediment of the river. The phylogenetic tree of Salmonella spp. revealed a ≥ 99% and 99% genetic relatedness between river water and riverbed sediment isolates for Salmonella spp. and Shigella spp., respectively. The degree of genetic relatedness between sediment and water pathogen isolates suggests that these organisms could possibly have a common origin and that there could be possible movement of microorganisms between the water column and the sediments.Keywords: Salmonella spp., Shigella spp., river water, riverbed sediment, genetic relatednes

Distribution patterns of bacterial communities and their potential link to variable viral lysis in temperate freshwater reservoirs

International audienceMan-made reservoirs which receive substantial inputs of terrestrial organic matter are characterized by physiologically diverse and distinct bacterial communities. Here we examined bacterial community structure using Illumina MiSeq sequencing of 16S rRNA genes and evaluated the potential role of viruses in influencing them in two productive freshwater reservoirs namely, Villerest and Grangent (Central France). Two dimensional nonmetric multidimensional scaling analyses indicated that bacterial communities in both reservoirs were structurally different in time and space, with Villerest harboring more diverse communities than Grangent reservoir. The bacterial communities in both reservoirs were dominated by hgcI clade (Actinobacteria) and Limnohabitans (Betaproteobacteria) which are known to have adaptive life strategies towards top-down mechanisms and resource utilization. In Villerest, thermal stratification of water column which resulted in temporary anoxia especially during summer promoted the occurrence of anoxygenic phototrophic and methanotrophic bacteria. Overall, low bacterial richness which was linked to viral lytic infection possibly suggests that a relatively small number of highly active bacterial populations sustained high bacterial activity and viral abundances. Weighted UniFrac analysis indicated that a minimum threshold viral infection and virus-to-bacteria ratio (serve as a proxy) of 10% and 10, respectively, is required to exert its impact on phylogenetic structure of bacterial community. Therefore depending on the levels of viral infection we suggest that viruses at times can prevail over other trophic or top-down factors in shaping and structuring bacterial communities in such man-made artificial freshwater systems

Taxonomical resolution and distribution of bacterioplankton along the vertical gradient reveals pronounced spatio-temporal patterns in contrasted temperate freshwater Lakes.

International audienc

Differential impact of lytic viruses on the taxonomical resolution of freshwater bacterioplankton community structure

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MOESM1 of Genetic relatedness of faecal coliforms and enterococci bacteria isolated from water and sediments of the Apies River, Gauteng, South Africa

Additional file 1. Additional material

Broiler chickens and early life programming: Microbiome transplant-induced cecal community dynamics and phenotypic effects.

The concept of successional trajectories describes how small differences in initial community composition can magnify through time and lead to significant differences in mature communities. For many animals, the types and sources of early-life exposures to microbes have been shown to have significant and long-lasting effects on the community structure and/or function of the microbiome. In modern commercial poultry production, chicks are reared as a single age cohort and do not directly encounter adult birds. This scenario is likely to initiate a trajectory of microbial community development that is significantly different than non-industrial settings where chicks are exposed to a much broader range of environmental and fecal inocula; however, the comparative effects of these two scenarios on microbiome development and function remain largely unknown. In this work, we performed serial transfers of cecal material through multiple generations of birds to first determine if serial transfers exploiting the ceca in vivo, rather than the external environment or artificial incubations, can produce a stable microbial community. Subsequently, we compared microbiome development between chicks receiving this passaged, i.e. host-selected, cecal material orally, versus an environmental inoculum, to test the hypothesis that the first exposure of newly hatched chicks to microbes determines early GI microbiome structure and may have longer-lasting effects on bird health and development. Cecal microbiome dynamics and bird weights were tracked for a two-week period, with half of the birds in each treatment group exposed to a pathogen challenge at 7 days of age. We report that: i) a relatively stable community was derived after a single passage of transplanted cecal material, ii) this cecal inoculum significantly but ephemerally altered community structure relative to the environmental inoculum and PBS controls, and iii) either microbiome transplant administered at day-of-hatch appeared to have some protective effects against pathogen challenge relative to uninoculated controls. Differentially abundant taxa identified across treatment types may inform future studies aimed at identifying strains associated with beneficial phenotypes