Viral Communities Contribute More to the Lysis of Antibiotic-Resistant Bacteria than the Transduction of Antibiotic Resistance Genes in Anaerobic Digestion Revealed by Metagenomics

Ecological role of
the viral community on the fate of
antibiotic
resistance genes (ARGs) (reduction vs proliferation) remains unclear
in anaerobic digestion (AD). Metagenomics revealed a dominance of
Siphoviridae and Podoviridae among 13,895 identified viral operational
taxonomic units (vOTUs) within AD, and only 21 of the vOTUs carried
ARGs, which only accounted for 0.57 ± 0.43% of AD antibiotic
resistome. Conversely, ARGs locating on plasmids and integrative and
conjugative elements accounted for above 61.0%, indicating a substantial
potential for conjugation in driving horizontal gene transfer of ARGs
within AD. Virus–host prediction based on CRISPR spacer, tRNA,
and homology matches indicated that most viruses (80.2%) could not
infect across genera. Among 480 high-quality metagenome assembly genomes,
95 carried ARGs and were considered as putative antibiotic-resistant
bacteria (pARB). Furthermore, lytic phages of 66 pARBs were identified
and devoid of ARGs, and virus/host abundance ratios with an average
value of 71.7 indicated extensive viral activity and lysis. The infectivity
of lytic phage was also elucidated through laboratory experiments
concerning changes of the phage-to-host ratio, pH, and temperature.
Although metagenomic evidence for dissemination of ARGs by phage transduction
was found, the higher proportion of lytic phages infecting pARBs suggested
that the viral community played a greater role in reducing ARB numbers
than spreading ARGs in AD.