title: Full-scale mesophilic biogas plants using manure as C-source: bacterial community shifts along the process cause changes in the abundance of resistance genes and mobile genetic elements.
abstract: The application of manure, typically harboring bacteria carrying resistance genes (RGs) and mobile genetic elements (MGEs), as co-substrate in biogas plants (BGPs) might be critical when digestates are used as fertilizers. In the present study, the relative abundance of RGs and MGEs in total community (TC-) DNA from manure, fermenters and digestate samples taken at eight full-scale BGPs co-fermenting manure were determined by real-time PCR. In addition, the bacterial community composition of all digestates as well as manure and fermenter material from one BGP (BGP3) was characterized by 454-pyrosequencing of 16S rRNA amplicons from TC-DNA. Compared to respective input manures, relative abundances determined for sul1, sul2, tet(M), tet(Q), intI1, qacEΔ1, korB and traN were significantly lower in fermenters, whereas relative abundances of tet(W) were often higher in fermenters. The bacterial communities in all digestates were dominated by Firmicutes and Bacteroidetes while Proteobacteria were low in abundance and no Enterobacteriaceae were detected. High-throughput sequencing revealed shifts in bacterial communities during treatment for BGP3. Although in comparison to manure, digestate bacteria had lower relative abundances of RGs and MGEs except for tet(W), mesophilic BGPs seem not to be effective for prevention of the spread of RGs and MGEs via digestates into arable soils.
authors.affiliation: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany Institute of Environmental and Sustainable Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
authors.forename: Birgit
authors.initials: B
authors.lastname: Wolters
authors.affiliation: College of Resources and Environmental Science, China Agricultural University, 100094 Beijing, China.
authors.forename: Guo-Chun
authors.initials: GC
authors.lastname: Ding
authors.affiliation: Institute of Environmental and Sustainable Chemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Kreuzig
authors.affiliation: Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany kornelia.smalla@jki.bund.de.
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
mesh_terms: D041963:Bacteroidetes / Q000235:genetics*; D056804:Biofuels; D019149:Bioreactors / Q000382:microbiology; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D005285:Fermentation; D005308:Fertilizers / Q000382:microbiology*; D000068536:Bacillota / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008372:Manure / Q000382:microbiology*; D064307:Microbiota / Q000235:genetics; D010957:Plasmids / Q000235:genetics; D020560:Proteobacteria / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D056804:Biofuels; D005308:Fertilizers; D008372:Manure; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA amplicon sequencing; bacterial community; biogas plants; integrons; plasmids; resistance genes