Dynamics of a pig slurry microbial community during slurry anaerobic storage and management

The microbial community of a pig slurry was monitored on a farm for 6 months using both molecular and cultural approaches. Sampling was carried out at all the different stages of effluent handling, from the rearing building up to slurry spreading. Total DNA of each sample was extracted and analyzed by PCR-SSCP using primers targeting the 16S ribosomal RNA genes from the archaeal and bacterial domains but also the Eubacterium and Clostridium, the Bacillus-Streptococcus-Lactobacillus and the Bacteroides-Prevotella groups. Comparison of the SSCP profiles showed a rapid modification of the dominant bacterial community during the first 2 weeks of anaerobic storage and its relative stability thereafter. Several bacterial populations, identified as closely related to uncultured Clostridium and Porphyromonas and to Lactobacillus and Streptococcus cultured species commonly isolated from pig feces, remained present and dominant from the rearing building up to the time of spreading. Numeration of fecal indicators (Enterococci and Escherichia coli) performed in parallel using cultural methods revealed the same trends. On the other hand, the archaeal community adapted slowly during pig slurry storage and increased its diversity. A shift was observed between two hydrogenotrophic methanogenic Methanobrevibacter populations from the storage pit up into the pond. Microorganisms present in pig slurry at the time of spreading could no longer be detected in soil thereafter, either by molecular or cultural technique, probably because of the detection limit inherent in both techniques. La communauté microbienne d'un liser de porc a été suivi à la ferme pendant 6 mois en utilisant des approches moléculaires et culturales. Des prélèvements ont été réalisés à toutes les étapes de la gestion de l'effluent, du bâtiment d'élevage jusqu'a l'épandage. L'ADN total de chaque échantillon a été extrait et analysée par PCR-SSCP en utilisant des amorces ciblant les gènes ribosomaux de l'ARN 16S pour les domaines archaea et bactéries mais également pour les groupes bactériens Eubacterium-Clostridium, Bacillus-Streptococcus-Lactobacillus et pour le groupe Bacteroides-Prevotella. La comparaison des profils SSCP a montré une modification rapide de la communauté bactérienne dominante pendant les 2 premières semaines du stockage anaérobie ensuite cette communauté se stabilise. Plusieurs populations bactériennes, identifiées comme étant proches des Clostridium non cultivés, des Porphyromonas, des L