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Background  Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium  Bacillus anthracis . The dormant  B. anthracis  spores become vegetative after ingestion by grazing mammals. After killing the host,  B. anthracis  cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra ( Equus quagga ) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored  B. anthracis  throughout the period using cultivation, qPCR and shotgun metagenomic sequencing.    Results  The combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow  B. anthracis  population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the  B. cereus  group, despite their high sequence similarity. Vegetative  B. anthracis  abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g.  Frankiales  and  Rhizobiales  species) becomes temporarily dominated by the orders  Bacillales  and  Pseudomonadales,  known to contain plant growth-promoting species.    Conclusion  Our work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future  B. anthracis  transmission events at carcass sites may be indirectly facilitated by the recruitment of plant-beneficial bacteria.    Electronic supplementary material  The online version of this article (10.1186/s12866-017-1111-6) contains supplementary material, which is available to authorized users.

Temporal dynamics in microbial soil communities at anthrax carcass sites