The problematic of microplastics pollution in the marine environment is tightly linked to their colonization by a wide diversity of microorganisms, the so-called plastisphere. The composition of the plastisphere relies on a complex combination of multiple factors including the surrounding environment, the time of incubation along with the polymer type, making it difficult to understand how the biofilm evolves during the microplastic lifetime over the oceans. To better define bacterial community assembly processes on plastics, we performed a 5 months spatio-temporal survey of the plastisphere in an oyster farming area in the Bay of Brest (France). We deployed three types of plastic pellets in two positions in the foreshore and in the water column. Plastic-associated biofilm composition in all these conditions was monitored using 16 S rRNA metabarcoding and compared to free-living and attached bacterial members of seawater. We observed that bacterial families associated to plastic pellets were significantly distinct from the ones found in seawater, with a significant prevalence of filamentous Cyanobacteria on plastics. No convergence towards a unique plastisphere was detected between polymers exposed in the intertidal and subtidal area, emphasizing the central role of the surrounding environment on constantly shaping the plastisphere community diversity. However, we could define a bulk of early-colonizers of marine biofilms such as Alteromonas, Pseudoalteromonas or Vibrio. These early-colonizers could reach high abundances in floating microplastics collected in field-sampling studies, suggesting the plastic-associated biofilms could remain at early development stages across large oceanic scales. Our study raises the hypothesis that most members of the plastisphere, including putative pathogens, could result of opportunistic colonization processes and unlikely long-term transport.

DNA metabarcoding can provide a high-throughput and rapid method for characterizing responses of communities to environmental stressors. However, within bulk samples, DNA metabarcoding hardly distinguishes live from the dead organisms. Here, both DNA and RNA metabarcoding were applied and compared in experimental freshwater mesocosms conducted for assessment of ecotoxicological responses of zooplankton communities to remediation treatment until 38 days post oil-spill. Furthermore, a novel indicator of normalized vitality (NV), sequence counts of RNA metabarcoding normalized by that of DNA metabarcoding, was developed for assessment of ecological responses. DNA and RNA metabarcoding detected similar taxa richness and rank of relative abundances. Both DNA and RNA metabarcoding demonstrated slight shifts in measured α-diversities in response to treatments. NV presented relatively greater magnitudes of differential responses of community compositions to treatments compared to DNA or RNA metabarcoding. NV declined from the start of the experiment (3 days pre-spill) to the end (38 days post-spill). NV also differed between Rotifer and Arthropoda, possibly due to differential life histories and sizes of organisms. NV could be a useful indicator for characterizing ecological responses to anthropogenic influence; however, the biology of target organisms and subsequent RNA production need to be considered.

Headwater streams are a hotspot of freshwater biodiversity, carrying indispensable resource pools of aquatic species. However, up to now, there remain many challenges to accurately and efficiently characterize the responses of this vulnerable ecosystem to human-induced changes. Here, we collected macroinvertebrate data from 12 different headwater streams in the Liao River of northeast China by DNA metabarcoding approach, to reveal biodiversity changes and ecological thresholds affected by human beings. Our data showed that the community composition and structure of headwater streams had unique and significant differences under human impacts, and 5-day biological oxygen demand (BOD₅) and ammonia nitrogen (NH₃–N) were the key variables explaining the variation in community structure. Although α diversity had a unimodal relationship with nutrients and organic loads, β diversity and its turnover component (species replacement) increased significantly. In addition, 22 and 33 indicative taxa were identified to have significant negative responses to BOD₅ and NH₃–N, respectively, and the change points derived from Threshold Indicator Taxa Analysis (TITAN) for the negative response of their frequency and abundance were BOD₅ >3.42 mg/L and NH₃–N >0.14 mg/L. Overall, this study reveals the biodiversity changes in headwater streams from the aspects of α and β diversity, and also determines the thresholds of BOD₅ and NH₃–N pollutants for one reach at one date from 12 headwater streams, suggesting the potential of DNA metabarcoding approach for threshold analyses in headwater streams.

Although considerable research progress on the effects of anthropogenic disturbance in the deep sea has been made in recent years, our understanding of these impacts at community level remains limited. Here, we studied deep-sea assemblages of Sicily (Mediterranean Sea) subject to different intensities of benthic trawling using environmental DNA (eDNA) metabarcoding and taxonomic identification of meiofauna communities. Firstly, eDNA metabarcoding data did not detect trawling impacts using alpha diversity whereas meiofauna data detected a significant effect of trawling. Secondly, both eDNA and meiofauna data detected significantly different communities across distinct levels of trawling intensity when we examined beta diversity. Taxonomic assignment of the eDNA data revealed that Bryozoa was present only at untrawled sites, highlighting their vulnerability to trawling. Our results provide evidence for community-wide impacts of trawling, with different trawling intensities leading to distinct deep-sea communities. Finally, we highlight the need for further studies to unravel understudied deep-sea biodiversity.

Seafloor pollution by benthic litter is an emerging phenomenon, although debris colonization by biota remains largely unexplored. We characterized the litter of the continental slope (~400–600 m) of the Gulf of Naples (Mediterranean) and investigated its fouling biota through integrative taxonomic approaches. Plastic pieces (82 %) with land-based origin (96 %) and limited sizes (10–20 cm) were the items most commonly encountered, suggesting a transfer to deep waters through floating and sinking. The majority of the items were not fouled, and the debris hosted an impoverished biota, leading to hypothesize that benthic litter supports wide communities only in shallow waters. Higher colonization rates were observed for gastropod and cephalopod eggs with no preference for materials and sizes, suggesting that even small pieces of soft plastic provide a spawning habitat for molluscs and affect species' connectivity in the deep-sea ecosystem. Holistic approaches are necessary to evaluate interactions between litter and biota.

Coral reef ecosystems in the Persian Gulf are frequently exposed to crude oil spills. We investigated benthic bacterial and eukaryote community structures at such coral reef sites subjected to different degrees of polycyclic aromatic hydrocarbon (PAH) pollution using environmental DNA (eDNA) metabarcoding. Both bacterial and eukaryote communities responded with pronounced shifts to crude oil pollution and distinguished control sites, moderately and heavily impacted sites with significant confidentiality. The observed community patterns were predominantly driven by Alphaproteobacteria and metazoans. Among these, we identified individual genera that were previously linked to oil spill stress, but also taxa, for which a link to hydrocarbon still remains to be established. Considering the lack of an early-warning system for the environmental status of coral reef ecosystems exposed to frequent crude-oil spills, our results encourage further research towards the development of an eDNA-based biomonitoring tool that exploits benthic bacterial and eukaryote communities as bioindicators.

Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon – one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.

The cyanobacteria management in water bodies requires a deep knowledge of the community composition. Considering the reliable and thorough information provided by the polyphasic approach in cyanobacteria taxonomy, here we assess the cyanobacterial community structure of the Cheffia reservoir from Algeria. Cyanobacteria were identified on the basis of morphological traits and next-generation sequencing (NGS); toxins-related genes were localized in addition to the identification of toxins; temperature and nutrient level of water samples were also determined. The polyphasic approach was essential for cyanobacteria investigation; 28 genera were identified through 16S rRNA metabarcoding with the dominance of taxa from Microcystis (34.2%), Aphanizomenon (20.1%), and Planktothrix (20.0%), and morphological analysis revealed the association in this water body of five species within the genus Microcystis: M. aeruginosa, M. novacekii, M. panniformis, M. ichthyoblabe, and M. flos-aquae. The presence of mcyE genotypes was detected; moreover, HPLC–PDA and LC–ESI–MS/MS revealed the production of microcystin-LR. Results obtained in our study are very important since this ecosystem is used for water supply and irrigation; as a consequence, a good water management plan is essential.

This prospective study was aimed to explore the bacterial diversity of marine mucilage developed in the Marmara Sea and the North Aegean Sea by metabarcoding. For this purpose, mucilage samples were collected from five different sampling locations, and the bacterial community structure was analyzed by 16S rRNA gene amplicon sequencing. The results highlighted a diverse bacterial community dominated by Proteobacteria and Bacteroidetes species. A negative and significant correlation between pH level and Campylobacterales, Clostridiales, and Vibronales abundances was detected, while a strong positive correlation was determined between total phosphorus (TP) and Campylobacterales. Results revealed that the bacterial community in the mucilage samples was predominated by particle-attached species preferring high-nutrient concentrations. This is the first study evaluating the bacterial diversity in a mucilage outbreak using a metabarcoding approach. Its results may contribute to this growing area of research and provide a database for further studies.