Although antibacterial silver nanoparticles (AgNPs) are increasingly released into the environment and are very toxic to aquatic organisms, their effects on bacteria-based holobionts have been rarely studied. Here, we investigate the interactions between gut microbiota and zooplankton, Daphnia magna, under AgNP exposure through bioimaging, metatranscriptomic and gut microbiota translational techniques. The results demonstrated that the toxic symptoms of zooplankton were mediated by the gut microbiota at low concentrations of AgNPs, and the level of toxicity was influenced by the exposure time. At high AgNP concentrations, the mortality of zooplankton was due to the combined effects of the extinct gut microbiota and the accumulated toxicity. Exposure to AgNPs caused down-regulation of genes encoding proteasome, ATP synthesis, fatty acid biosynthesis, and β-oxidation in the host, with a shorter body length and decreased digestion and reproduction ability. These perturbations were relieved possibly through microbial sulfidation of Ag⁺, via the aggregation of nanoparticles and possibly the recovered synthesis of short-chain fatty acids (SFAs). The reduced fluorescence of AgNPs and the symptomatic palliation observed in the AgNP-tolerant microbiota inoculated D. magna further confirmed the detoxifying role of gut microbiota. Overall, our findings provide fundamental knowledge about the effects of AgNPs on bacteria-based holobionts.

Toxic differences between antibacterial silver (either ionic Ag⁺ and nanoparticle – AgNPs) were related to the microbial metabolism of enriched organic matter in the gut.

The shift between photoautotrophic and phagotrophic strategies in mixoplankton significantly impacts the planktonic food webs and biogeochemical cycling. Considering the projected global warming, studying how temperature impacts this shift is crucial. Here, we combined the transcriptome of in-lab cultures (mixotrophic dinoflagellate Lepidodinium sp.) and the metatranscriptome dataset of the global ocean to investigate the mechanisms underlying the shift of trophic strategies and its relationship with increasing temperatures. Our results showed that phagocytosis-related pathways, including focal adhesion, regulation of actin cytoskeleton, and oxidative phosphorylation, were significantly stimulated in Lepidodinium sp. when cryptophyte prey were added. We further compared the expression profiles of photosynthesis and phagocytosis genes in Lepidodinium sp. in the global sunlit ocean. Our results indicated that Lepidodinium sp. became more phagotrophic with increasing temperatures when the ambient chlorophyll concentration was >0.3 mg.m⁻³ (~20.58% of the ocean surface) but became more photoautotrophic with increasing temperatures when the chlorophyll concentration was between 0.2 and 0.3 mg.m⁻³ (~11.47% of the ocean surface). Overall, we emphasized the crucial role of phagocytosis in phago-mixotrophy and suggested that the expression profile of phagocytosis genes can be a molecular marker to target the phagotrophic activity of mixoplankton in situ.

The deep-sea ecosystem, a less-contaminated reservoir of antibiotic resistance genes (ARGs), has evolved antibiotic resistance for microbes to survive and utilize scarce resources. Research on the diversity and distribution of these genes in deep-sea environments is limited. Our metagenomics study employed short-read-based (SRB) and assembled-contig-based (ACB) methods to identify ARGs in deep-sea waters and sediments and assess their potential pathogenicity. SRB prediction was found to be more effective for studying the abundance and diversity of these genes, while combining both methods better illustrated the relationship of ARGs with the hosts. Deep-sea waters (DSW) and trenches had the highest diversity of ARGs, including β-lactams, multidrug resistance genes, and rifamycins. Mobile genetic elements, such as IncQ and RP4 plasmids, were also identified. The ratio of nonsynonymous to synonymous substitutions (pN/pS) values of these genes suggest different evolutionary strategies in response to deep-sea conditions and possible human impacts. These resistome profiles provide valuable insights into their natural origins as well as the ecological and evolutionary implications of antibiotic resistance in deep-sea ecosystems. The exploration of the global distribution of ARGs in diverse deep-sea environments is a novel approach that will assist in understanding their potential reservoirs and evolutionary mechanisms. Therefore, employing a comprehensive approach to studying ARGs is particularly necessary. Unique microbial life in deep-sea ecosystems, especially in deep-sea cold seeps sediments (DSCSS), deep-sea waters (DSW), and trench waters (TW), could be a valuable source of new antibiotics and resistance discovery.