A major forthcoming sanitary issue concerns the apparition and spreading of drug-resistant microorganisms, potentially threatening millions of humans. In low-income countries, polluted urban runoff and open sewage channels are major sources of microbes. These microbes join natural microbial communities in aquatic ecosystems already impacted by various chemicals, including antibiotics. These composite microbial communities must adapt to survive in such hostile conditions, sometimes promoting the selection of antibiotic-resistant microbial strains by gene transfer. The low probability of exchanges between planktonic microorganisms within the water column may be significantly improved if their contact was facilitated by particular meeting places. This could be specifically the case within biofilms that develop on the surface of the myriads of floating macroplastics increasingly polluting urban tropical surface waters. Moreover, as uncultivable bacterial strains could be involved, analyses of the microbial communities in their whole have to be performed. This means that new-omic technologies must be routinely implemented in low- and middle-income countries to detect the appearance of resistance genes in microbial ecosystems, especially when considering the new ‘plastic context.’ We summarize the related current knowledge in this short review paper to anticipate new strategies for monitoring and surveying microbial communities.

Mediterranean coastal lagoons are particularly vulnerable to increasing direct anthropogenic threats and climate change. Understanding their potential responses to global and local changes is essential to develop management strategies adapted to these ecosystems. Salinity is a fundamental structuring factor for phytoplankton communities; however, its role under climate change is understudied. We hypothesized that salinity variations imposed by climate change and/or management actions could disturb Mediterranean lagoons’ phytoplankton communities. To test our hypothesis, we performed two 5-day microcosm experiments in which natural phytoplankton assemblages from the Santa Giulia lagoon (Corsica Island) were subjected to three increasing (53–63–73) and decreasing (33–26–20) levels of salinity, to mimic strong evaporation and flash flooding, respectively. Results indicate that over-salinization inhibited growth and modified the assemblages’ composition. Freshening, on the contrary, showed feeble effects, mainly boosting microphytoplankton abundance and depleting diversity at lowest salinity. In both experiments and under freshening in particular, initially rare species emerged, while photosynthetic activity was degraded by salinity increase only. We demonstrated that phytoplankton communities’ structure and metabolism are strongly altered by the predicted implications of climate change. Such impacts have to be considered for future management of coastal lagoons (control of sea exchanges and watershed fluxes). This work constitutes a priority step towards the proactive adapted management and conservation of such as-yet-neglected ecosystems in the context of climate change.