Research progress on microbiomes associated with animals in terrestrial and shallow-seawater habitats continually improves our understanding of symbiosis. Both bacteria and viruses (bacteriophages/phages) are the major components of the animal-associated microbiomes and are abundant, diverse, and functional. Bacteria-phage interactions are ecological important in animal holobionts and contribute to the maintenance of symbiosis. Animals in deep-sea ecosystems feature being symbiotic with chemosynthetic bacteria that serve essential biochemical and ecological functions, but their bacteriophages, which determine their fate, remain largely unknown. In this thesis, using metagenomic sequence-based analyses, we investigated a wide range of invertebrate-associated microbiomes to examine the p...[ Read more ]

Research progress on microbiomes associated with animals in terrestrial and shallow-seawater habitats continually improves our understanding of symbiosis. Both bacteria and viruses (bacteriophages/phages) are the major components of the animal-associated microbiomes and are abundant, diverse, and functional. Bacteria-phage interactions are ecological important in animal holobionts and contribute to the maintenance of symbiosis. Animals in deep-sea ecosystems feature being symbiotic with chemosynthetic bacteria that serve essential biochemical and ecological functions, but their bacteriophages, which determine their fate, remain largely unknown. In this thesis, using metagenomic sequence-based analyses, we investigated a wide range of invertebrate-associated microbiomes to examine the presence of phages and their interactions with bacterial symbionts colonizing hydrothermal vents or cold seeps in the deep ocean. In sponge holobionts, predominant sulfur-oxidizing bacteria belonging to the clade SUP05 and their putative phages belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae were unveiled. Phage sequences containing metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation horizontally transferred from the SUP05 bacteria implies a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment. In a deep-sea vent snail, we detected four Caudovirales phage genome bins having infected two endosymbionts (sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB)). To defend against the attack, SOB and MOB employed CRISPR–Cas systems to target phage DNA, and other potential defense systems to form multiple lines for anti-viral defense. To counter host defense, phages used antirestriction mechanisms and expressed methyltransferase genes that potentially counterbalance host restriction activity. We also provided insights into the interaction at a community-to-community level by investigating 80 metagenomes from 13 invertebrate species. Accordingly, we hypothesize that phage-bacteria interplay can play key roles in establishing and maintaining invertebrate-bacteria symbioses in deep-sea environments.