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Coral reefs are under increasing threat, and the loss of reef‐associated fishes providing valuable ecosystem services is accelerating. The monitoring of such rapid changes has become a challenge for ecologists and ecosystems managers using traditional approaches like scuba divers performing underwater visual censuses (UVC) or diver operated video recording (DOV). However, the use of small, low‐cost robots could help tackle the challenge of such monitoring, provided that they perform at least as well as diver‐based methods. To address this question, tropical fish assemblages from 13 fringing reefs around Mayotte Island (Indian Ocean) were monitored along 50 m‐long transects using stereo videos recorded by a semi‐autonomous underwater vehicle (SAUV) and by a scuba diver (Diver Operated stereo Video system, DOV). Differences between the methods were tested for complementary fish assemblage metrics (species richness, total biomass, total density, Shannon diversity and Pielou evenness) and for the number and size of nine targeted species. SAUV recorded on average 35% higher biomass than DOV which in turn recorded on average 12% higher species richness. Biomass differences were found to be due to SAUV monitoring larger fishes than DOV, a potential marker of human‐related fish avoidance behaviour. This study demonstrates that SAUV provides accurate metrics of coral reef fish biodiversity compared to diver‐based procedures. Given their ability to conduct video transects at high frequency, 100 m depth range and at a moderate cost, SAUV is a promising tool for monitoring fish assemblages in coral reef ecosystems. New tools are needed in light of exosystemic global change monitoring, therefore we tested the possibility to use robots to perform coral reef fishes monitoring surveys. Thirteen fringing reefs around Mayotte Island (Indian Ocean) were surveyed along 50 m‐long transects using stereo videos recorded by a semi‐autonomous underwater vehicle (SAUV) and by the standard approach using a scuba‐diver operated stereo video system (DOV). SAUV recorded on average 35% higher biomass than DOV which recorded on average 12% higher species richness. The biomass differences were found to be due to SAUV monitoring larger fishes than DOV, a potential marker of human‐related fish wariness.

Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia , in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.