Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge.
Two parallel anaerobic digestion lines were designed to match a "bovid-like" digestive structure. Each of the lines consisted of two continuous stirred tank reactors placed in series and separated by an acidic treatment step. The first line was inoculated with industrial inocula whereas the second was seeded with cow digestive tract contents. After 3 months of continuous sewage sludge feeding, samples were recovered for shotgun metaproteomic and DNA-based analysis. Strikingly, protein-inferred and 16S ribosomal DNA tags based taxonomic community profiles were not consistent. PCA however revealed a similar clustering pattern of the samples, suggesting that reproducible methodological and/or biological factors underlie this observation. The performances of the two digestion lines did not differ significantly and the cow-derived inocula did not establish in the reactors. A low throughput metagenomic dataset (3.4 × 10(6) reads, 1.1 Gb) was also generated for one of the samples. It allowed a substantial increase of the analysis depth (11 vs. 4% of spectral identification rate for the combined samples). Surprisingly, a high proportion of proteins from members of the "Candidatus Competibacter" group, a key microbial player usually found in activated sludge plants, was retrieved in our anaerobic digester samples. Data are available via ProteomeXchange with identifier PXD002420 (http://proteomecentral.proteomexchange.org/dataset/PXD002420).
Irstea, UR HBAN, Antony, France.
Ariane
A
Bize
Irstea, UR HBAN, Antony, France.
Laëtitia
L
Cardona
Irstea, UR HBAN, Antony, France.
Elie
E
Desmond-Le Quéméner
INRA, UR0050 Laboratoire de Biotechnologie de l'Environnement, Narbonne, France.
Audrey
A
Battimelli
Irstea, UR HBAN, Antony, France.
Nelly
N
Badalato
Irstea, UR HBAN, Antony, France.
Chrystelle
C
Bureau
Irstea, UR HBAN, Antony, France.
Céline
C
Madigou
INRA, UMR1319 MICALIS, PAPPSO, Jouy-en-Josas, France.
Didier
D
Chevret
INRA, UMR1319 MICALIS, PAPPSO, Jouy-en-Josas, France.
Alain
A
Guillot
INRA, UMR1319 MICALIS, PAPPSO, Jouy-en-Josas, France.
Véronique
V
Monnet
INRA, UR0050 Laboratoire de Biotechnologie de l'Environnement, Narbonne, France.
Jean-Jacques
JJ
Godon
Irstea, UR HBAN, Antony, France.
Théodore
T
Bouchez
D000693:Anaerobiosis / Q000235:genetics*; D032701:Biomimetics; D019149:Bioreactors; D019295:Computational Biology; D056186:Metagenomics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012722:Sewage / Q000382:microbiology*
D012336:RNA, Ribosomal, 16S; D012722:Sewage
Anaerobic digestion; Animal mimicry; Candidatus Competibacter; Cow digestive tracts; Microbiology; Two-stage system