Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area

What happens to biomass burning-emitted particles in the ocean? A laboratory experimental approach based on their tracers

Wildfires, controlled burns, and biofuel combustion (biomass burning or BB) are major contributors to particulate matter in the atmosphere and thus have an impact on climate, human health, and ecosystems. Once emitted, the particulate matter derived from BB can be taken up by the oceans. However, the fate and impact of BB in the marine biological carbon pump, and carbon cycle are largely unknown. This work presents the first attempt to investigate the bioavailability of two BB tracers, levoglucosan and galactosan, in seawater inoculated with marine prokaryotes. Levoglucosan and galactosan were incubated with a marine bacterial inoculum and monitored for six weeks under controlled laboratory conditions. Along with the anhydrosugar concentrations, multiple chemical and biological parameters were monitored over time. The results indicate that levoglucosan and galactosan can be assimilated by marine prokaryotes as their concentrations decreased by 97 ± 4 % and 36 ± 21 % (n = 3) of their initial values. However, this decrease occurred only after a 9 and 15 days from the beginning of the experiment, respectively. The decrease in the levoglucosan and galactosan concentrations was accompanied by an increase in both heterotrophic prokaryotic production, and abundance. These results demonstrate that these anhydrosugars have the potential to be assimilated by heterotrophic prokaryotes and thus contribute to the microbial food web functioning. Under our experimental conditions, levoglucosan exhibited a bacterial growth efficiency of 17 ± 5 % (n = 3), suggesting that most of the levoglucosan is mineralized into CO2. Prokaryotic diversity analyses revealed the predominance of a few bacterial genera from the Roseobacter clade that were selected after the addition of the anhydrosugars. The presence of this widespread marine bacterial clade reflects its ability to process semilabile compounds (here levoglucosan and galactosan) originating from BB and contribute to the dissolved organic matter pool in surface seawaters.

Extreme hydrological regimes of a small urban river: impact on trace element partitioning, enrichment and fluxes

The input of trace elements from a small urban river (Las River, Toulon, France) located on the northern Mediterranean coast was studied during both base flow and flood events. A 2-year monitoring period of water flow and suspended particulate matter (SPM) showed a typical Mediterranean hydrological regime: a strong increase in water flow and SPM during short flood periods. During the flood event, an up to 2-fold increase in dissolved trace element (DTM) concentrations and particulate trace element content in SPM (PTM) was observed compared to the baseline discharge. The enrichment factor of elements in the SPM ranges from low or moderate for Co, Ni and Cr (1.0-4.7) to extremely high for Cd (157). However, the enrichment factors decrease from base flow to flood, indicating a dilution effect with a large yield of weathering particles with higher particle size. The most significant total trace element loading occurred during flood, ranging from 78% for As and Ni to 91% for Pb, while PTM loading during flood ranged from 35% for As to 77% for Pb. The specific dissolved fluxes during the flood are significantly higher for Pb, Cu and Zn than in the surrounding rivers, indicating specificity in the catchment (lithology). This study shows the importance of monitoring the transport of pollutants through small urban rivers and their potential impact on the coastal region, especially when they enter small and closed bays, as a receiving pool.

Microbial indicators along a metallic contamination gradient in tropical coastal sediments

The structure and diversity of microbial community inhabiting coastal sediments reflect the exposition to contaminants. Aiming to assess the changes in the microbiota from Sepetiba Bay (SB, Brazil) sediments, correlations between the 16S rRNA gene data (V4-V5 region), metal contamination factors (CF), and the ecological risk classification provided by the Quality Ratio (QR) index were considered. The results show that microbial diversity differs significantly between the less (SB external sector) and the most (SB internal sector) polluted sectors. Also, differences in the microbial community structure regarding the ecological risk classifications validated the QR index as a reliable tool to report the SB chronic contamination. Microbial indicator genera resistant to metals (Desulfatiglans, SEEP-SRB1, Spirochaeta 2, among others) presented mainly anaerobic metabolisms. These genera are related to the sulfate reducing and methanogenic metabolisms probably participating in the natural attenuation processes but also associated with greenhouse gas emissions. In contrast, microbial indicator genera sensitive to metals (Rubripirellula, Blastopirellula, Aquibacter, among others) presented mainly aerobic metabolisms. It is suggested that future works should investigate the metabolic functions to evaluate the influence of metallic contaminants on microbial community inhabiting SB sediment.

Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline

Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach's to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages' features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.

Cd transfers during marine sediment resuspension over short and long-term period: Associated risk for coastal water quality

Cadmium (Cd) is a highly toxic metal, regularly monitored uniformly for water quality across Europe, but scarcely for sediments. This study was designed to compare the kinetics of Cd remobilization and the amplitude of its transfers with different marine sediments. The results showed a highly reproducible transfer kinetics. Dissolved Cd was strongly and quickly removed from the dissolved phase (from 5 min up to 7 h). Then, the dissolved Cd concentration increased progressively to reach a maximal value after two weeks of mixing. The influence of the resuspension intensity representing light wind-induced resuspension up to dredging operations was observed after 2 weeks. The intensity of the sediment resuspension clearly impacted the amplitude of Cd remobilization, dissolved Cd ranging from a few ngL^-1 to few hundreds of ngL^-1, exceeding the maximal dissolved Cd concentration accepted by the European Union Water Framework Directive (WFD-2008/105 32/EC).

Seawater copper content controls biofilm bioaccumulation and microbial community on microplastics

The adsorption of trace metals on microplastics (MPs) is affected by the presence of surficial biofilms but their interactions are poorly understood. Here, we present the influence of Cu levels in real seawater (Toulon Bay, NW Mediterranean Sea) on microbial communities and Cu content of the resulting biofilms grown during incubation experiments on high density polyethylene. Two sets of incubation experiments were run with seawater supplied with MPs, sampled in two sites with contrasting Cu levels: Pt12 (most contaminated site) and Pt41P (less contaminated site). For each incubation experiment, 5 treatments were considered differing in Cu concentrations, ranging between 30 and 400 nM and between 6 and 60 nM, for Pt12 and Pt41p, respectively. A control experiment (filtered at 0.2 μm) was run in parallel for each incubation experiment. We observed that, at the time scale of the incubation period, both prokaryotic and eukaryotic richness and diversity were higher in the biofilms formed from the most contaminated site. In addition, we showed that Cu levels are shaping biofilm communities, evidencing co-occurrence patterns between prokaryotes and eukaryotes with diatoms playing a central role. These differences in biofilm formation were reflected in the amount of bioaccumulated Cu per dry weight of MPs, exhibiting higher values in the most contaminated site. Within this site, the increase of Cu seawater content enhanced its bioaccumulation onto MPs until reaching saturation. This study strongly suggests a striking link between seawater copper content, biofilm community shaping and the resulting Cu bioaccumulation onto MPs.

Impact of anthropogenic organic matter on bacterial community distribution in the continental shelf sediments of southeastern Arabian Sea

The objective of this study was to understand the influence of anthropogenic organic matter on the spatial distribution microbial community in the continental shelf sediments of the Southeastern Arabian Sea (SEAS). The sediment samples were taken from the inner shelf (30 m depths) and outer shelf (100-200 m). The C:N_molar ratio of the sediment displayed a significant variation between the inner and outer shelf and a higher terrestrial organic input in the inner shelf. Microbial community composition also showed a significant variation between the inner and outer shelf (p ≤ 0.05). Proteobacteria was the dominant phylum in the outer shelf sediments (42.5%), whereas Desulfobacterota (21.9%) was the dominant phylum in the inner shelf. Complex terrestrial organic matter degrading bacteria dominated the inner shelf, whereas oligophilic microbial community and autochthonous organic matter utilizing bacteria dominated the outer shelf. Thus the source of organic matter controlled the microbial distribution in the SEAS.

Shedding light on the bacterial resistance to toxic UV filters: a comparative genomic study

UV filters are toxic to marine bacteria that dominate the marine biomass. Ecotoxicology often studies the organism response but rarely integrates the toxicity mechanisms at the molecular level. In this study, in silico comparative genomics between UV filters sensitive and resistant bacteria were conducted in order to unravel the genes responsible for a resistance phenotype. The genomes of two environmentally relevant Bacteroidetes and three Firmicutes species were compared through pairwise comparison. Larger genomes were carried by bacteria exhibiting a resistant phenotype, favoring their ability to adapt to environmental stresses. While the antitoxin and CRISPR systems were the only distinctive features in resistant Bacteroidetes, Firmicutes displayed multiple unique genes that could support the difference between sensitive and resistant phenotypes. Several genes involved in ROS response, vitamin biosynthesis, xenobiotic degradation, multidrug resistance, and lipophilic compound permeability were shown to be exclusive to resistant species. Our investigation contributes to a better understanding of UV filters resistance phenotypes, by identifying pivotal genes involved in key pathways.

Species-specific isotope tracking of mercury uptake and transformations by pico-nanoplankton in an eutrophic lake

The present study aims to explore the bioaccumulation and biotic transformations of inorganic (iHg) and monomethyl mercury (MMHg) by natural pico-nanoplankton community from eutrophic lake Soppen, Switzerland. Pico-nanoplankton encompass mainly bacterioplankton, mycoplankton and phytoplankton groups with size between 0.2 and 20 μm. Species-specific enriched isotope mixture of ¹⁹⁹iHg and ²⁰¹MMHg was used to explore the accumulation, the subcellular distribution and transformations occurring in natural pico-nanoplankton sampled at 2 different depths (6.6 m and 8.3 m). Cyanobacteria, diatoms, cryptophyta, green algae and heterotrophic microorganisms were identified as the major groups of pico-nanoplankton with diatoms prevailing at deeper samples. Results showed that pico-nanoplankton accumulated both iHg and MMHg preferentially in the cell membrane/organelles, despite observed losses. The ratios between the iHg and MMHg concentrations measured in the membrane/organelles and cytosol were comparable for iHg and MMHg. Pico-nanoplankton demethylate added ²⁰¹MMHg (~4 and 12% per day depending on cellular compartment), although the involved pathways are to further explore. Comparison of the concentrations of ²⁰¹iHg formed from ²⁰¹MMHg demethylation in whole system, medium and whole cells showed that 82% of the demethylation was biologically mediated by pico-nanoplankton. No significant methylation of iHg by pico-nanoplankton was observed. The accumulation of iHg and MMHg and the percentage of demethylated MMHg correlated positively with the relative abundance of diatoms and heterotrophic microorganisms in the pico-nanoplankton, the concentrations of TN, Mg²⁺, NO₃^-, NO₂^-, NH₄⁺ and negatively with the concentrations of DOC, K⁺, Na⁺, Ca²⁺, SO₄^2-. Taken together the results of the present field study confirm the role of pico-nanoplankton in Hg bioaccumulation and demethylation, however further research is needed to better understand the underlying mechanisms and interconnection between heterotrophic and autotrophic microorganisms.

Integration of spatio-temporal variations of surface metabolomes and epibacterial communities highlights the importance of copper stress as a major factor shaping host-microbiota interactions within a Mediterranean seaweed holobiont

BACKGROUND

Although considered as holobionts, macroalgae and their surface microbiota share intimate interactions that are still poorly understood. Little is known on the effect of environmental parameters on the close relationships between the host and its surface-associated microbiota, and even more in a context of coastal pollutions. Therefore, the main objective of this study was to decipher the impact of local environmental parameters, especially trace metal concentrations, on an algal holobiont dynamics using the Phaeophyta Taonia atomaria as a model. Through a multidisciplinary multi-omics approach combining metabarcoding and untargeted LC-MS-based metabolomics, the epibacterial communities and the surface metabolome of T. atomaria were monitored along a spatio-temporal gradient in the bay of Toulon (Northwestern Mediterranean coast) and its surrounding. Indeed, this geographical area displays a well-described trace metal gradient particularly relevant to investigate the effect of such pollutants on marine organisms.

RESULTS

Epibacterial communities of T. atomaria exhibited a high specificity whatever the five environmentally contrasted collecting sites investigated on the NW Mediterranean coast. By integrating metabarcoding and metabolomics analyses, the holobiont dynamics varied as a whole. During the occurrence period of T. atomaria, epibacterial densities and α-diversity increased while the relative proportion of core communities decreased. Pioneer bacterial colonizers constituted a large part of the specific and core taxa, and their decrease might be linked to biofilm maturation through time. Then, the temporal increase of the Roseobacter was proposed to result from the higher temperature conditions, but also the increased production of dimethylsulfoniopropionate (DMSP) at the algal surface which could constitute of the source of carbon and sulfur for the catabolism pathways of these taxa. Finally, as a major result of this study, copper concentration constituted a key factor shaping the holobiont system. Thus, the higher expression of carotenoids suggested an oxidative stress which might result from an adaptation of the algal surface metabolome to high copper levels. In turn, this change in the surface metabolome composition could result in the selection of particular epibacterial taxa.

CONCLUSION

We showed that associated epibacterial communities were highly specific to the algal host and that the holobiont dynamics varied as a whole. While temperature increase was confirmed to be one of the main parameters associated to Taonia dynamics, the originality of this study was highlighting copper-stress as a major driver of seaweed-epibacterial interactions. In a context of global change, this study brought new insights on the dynamics of a Mediterranean algal holobiont submitted to heavy anthropic pressures. Video abstract.

Assessment of potential variability of cadmium and copper trace metals using hindcast estimates

Trace metals are vital to primary productivity and play an essential role as main components in regulating oceanic biogeochemical cycles. Dissolved and particulate trace metals within the water column may vary due to primary production, temperature, and nutrient changes, factors that may also vary spatially and temporally. Furthermore, assessment of trace metals mainly relies on in situ observation, and so wide-area investigation of trace-metal concentration may be challenging and subject to technical constraints. A specific approach is therefore necessary that combines biogeochemical proxies, satellite data, and trace-metal linear correlation. This study aims to assess the potential spatio-temporal variability of sea surface cadmium (Cd) and copper (Cu) concentrations in Indonesian seas and surrounding areas. The correlations of Cd and Cu concentrations with primary production and nutrient data were used to convert hindcast satellite data into estimates of the metals' concentrations. The potential variability of trace metals can be determined by overlaying both data. Indonesia's Fisheries Management Areas (FMAs) were used for data clustering and analysis. The results show that Cd and Cu trace metals have similar distribution patterns throughout the year. However, dissolved Cu has a more diverse coverage area than dissolved Cd, including within the Halmahera, Seram, and Maluku Seas (FMAs 716 and 717), the Makassar Strait (FMA 717), and the Java-Sumatra upwelling area (FMA 573). Both Cd and Cu concentrations in the Java-Sumatra upwelling region follow the periodic upwelling pattern. Overall, both Cd and Cu show a declining trend in concentration from 2012 to 2019. It is estimated that dissolved Cd concentration declined from 1500-2000 pmol/kg in 2012 to 1000-1500 pmol/kg in 2019 for all locations. Dissolved Cu concentration decreased from 30-35 nmol/kg in 2012 to 25-30 nmol/kg in 2019. Estimated dissolved Cd and Cu follow the linear functions of silicate (SiO₄), nitrate (NO₃), and primary productivity. The fluctuation of anthropogenic activities and global warming are likely to indirectly impact the decline in metal concentrations by affecting nutrients and primary productivity.

Benthic microbial diversity trends in response to heavy metals in an oxygen-deficient eutrophic bay of the Humboldt current system offshore the Atacama Desert

Mejillones Bay is a coastal ecosystem situated in an oxygen-deficient upwelling area impacted by mining activities in the coastal desert region of northern Chile, where conspicuous microbial life develops in the sediments. Herein, heavy metal (loid)s (HMs) such as Cu, Pb, As, Zn, Al, Fe, Cd, Mo, Ni and V as well as benthic microbial communities were studied using spectrometry and iTag-16 S rRNA sequencing. Samples were taken from two contrasting sedimentary localities in the Bay named Punta Rieles (PR) and Punta Chacaya (PC) within 10-50 m water-depth gradient. PR sediments were organic matter rich (21.1% of TOM at 50 m) and overlaid with low-oxygen waters (<0.06 ml O2/L bottom layer) compared with PC. In general, HMs like Al, Ni, Cd, As and Pb tended to increase in concentration with depth in PR, while the opposite pattern was observed in PC. In addition, PR presented a higher number of unique families (72) compared to PC (35). Among the top ten microbial families, Desulfobulbaceae (4.6% vs. 3.2%), Flavobacteriaceae (2.8% vs. 2.3%) and Anaerolineaceae (3.3% vs. 2.3%) dominated in PR, meanwhile Actinomarinales_Unclassified (8.1% vs. 4.2%) and Sandaracinaceae (4.4% vs. 2.0%) were more abundant in PC. Multivariate analyses confirmed that water depth-related variation was a good proxy for oxygen conditions and metal concentrations, explaining the structure of benthic microbial assemblages. Cd, Ni, As and Pb showed uniformly positive associations with communities that represented the keystone taxa in the co-occurrence network, including Anaerolineaceae, Thiotrichaceae, Desulfobulbaceae, Desulfarculaceae and Bacteroidales_unclassified communities. Collectively, these findings provide new insights for establishing the ecological interconnections of benthic microorganisms in response to metal contamination in a coastal upwelling environment.

Temperate and tropical coastal waters share relatively similar microbial biofilm communities while free-living or particle-attached communities are distinct

Free-living (FL) marine microbial communities differ from those attached to particles (PA). Likewise, biofilms (B) colonizing artificial surfaces, including plastics or ship hulls, hardly resemble their planktonic surroundings. However, few studies have examined the effect of the environment on these lifestyles and on the source of organisms colonizing marine surfaces. Using 16S rRNA gene metabarcoding, we identified specificities of marine prokaryotic community lifestyles (FL, PA or B) sampled in three coastal polluted locations with dissimilar environmental conditions: the North-Western Mediterranean Sea and the Atlantic and Indian Oceans. Biofilms developed over polyvinyl chloride (PVC) were found to be significantly different from FL or PA collected during the immersions. Alpha-diversity increased from FL to PA and to B, illustrating the integrative aspect of the latter, with little proportion of operational taxonomic units shared with the first two. Beta-diversity clustered first the lifestyles and then the sites. FL and PA were more affected by water quality, especially by trace metal contamination, whereas B were as sensitive to trace metals as to nutrients. Although biofilms should be supplied by the planktonic (ultra) rare biosphere, source tracking could only detect small contributions of FL or PA taxa to B communities.

Effect of Water Chemistry, Land Use Patterns, and Geographic Distances on the Spatial Distribution of Bacterioplankton Communities in an Anthropogenically Disturbed Riverine Ecosystem

The spatial distribution of bacterioplankton communities in rivers is driven by multiple environmental factors, including local and regional factors. Local environmental condition is associated with effect of river water chemistry (through species sorting); ecological process in region is associated with effects of land use and geography. Here, we investigated variation in bacterioplankton communities (free-living, between 0.22 and 5 μm) in an anthropogenically disturbed river using high-throughput DNA sequencing of community 16S rRNA genes in order to investigate the importance of water chemistry, land use patterns, and geographic distance. Among environmental factors, sulfate (SO₄ ^2-), manganese (Mn), and iron (Fe) concentrations were the water chemistry parameters that best explained bacterioplankton community variation. In addition, forest and freshwater areas were the land use patterns that best explained bacterioplankton community variation. Furthermore, cumulative dendritic distance was the geographic distance parameter that best explained bacterial community variation. Variation partitioning analysis revealed that water chemistry, land use patterns, and geographic distances strongly shaped bacterioplankton communities. In particular, the direct influence of land use was prominent, which alone contributed to the highest proportion of variation (26.2% in wet season communities and 36.5% in dry season communities). These results suggest that the mechanisms of species sorting and mass effects together control bacterioplankton communities, although mass effects exhibited higher contributions to community variation than species sorting. Given the importance of allochthonous bacteria input from various land use activities (i.e., mass effects), these results provide new insights into the environmental factors and determinant mechanisms that shape riverine ecosystem communities.

Quantification of the covariation of lake microbiomes and environmental variables using a machine learning-based framework

It is known that microorganisms are essential for the functioning of ecosystems, but the extent to which microorganisms respond to different environmental variables in their natural habitats is not clear. In the current study, we present a methodological framework to quantify the covariation of the microbial community of a habitat and environmental variables of this habitat. It is built on theoretical considerations of systems ecology, makes use of state-of-the-art machine learning techniques and can be used to identify bioindicators. We apply the framework to a data set containing operational taxonomic units (OTUs) as well as more than twenty physicochemical and geographic variables measured in a large-scale survey of European lakes. While a large part of variation (up to 61%) in many environmental variables can be explained by microbial community composition, some variables do not show significant covariation with the microbial lake community. Moreover, we have identified OTUs that act as "multitask" bioindicators, i.e., that are indicative for multiple environmental variables, and thus could be candidates for lake water monitoring schemes. Our results represent, for the first time, a quantification of the covariation of the lake microbiome and a wide array of environmental variables for lake ecosystems. Building on the results and methodology presented here, it will be possible to identify microbial taxa and processes that are essential for functioning and stability of lake ecosystems.

Quantification of Microplastics in North-Western Mediterranean Harbors: Seasonality and Biofilm-Related Metallic Contaminants

The Mediterranean Sea is one of the most impacted basins in terms of microplastics pollution. Land-based activities are the major sources of plastic litter to the ocean, with harbors probably representing significant hotspots. In the framework of the SPlasH! project (Stop alle Plastiche in H2O, Interreg Marittimo project), microplastics were sampled in three north-western Mediterranean harbors during summer and winter. In this study, the areal concentrations of microplastics ranged from 5576 to 379,965 items·km−2. A decreasing gradient was observed from the inner to the outer zones of the studied harbors, pointing out these enclosed systems as hotspots regarding microplastic pollution. During summer, the areal concentrations of microplastics were higher than in winter, which could be explained by an enhancement of port activities leading to MPs production. The investigation of microplastics size classes distribution in the surface waters revealed that microplastics within the size range between 300 µm and 500 µm were the least represented. In this study, we assessed trace metal (Pb, Fe, Cu, V, Cd and As) bioaccumulation by the biofilm which developed on the surface of microplastics. The results highlighted that concentrations within the biofilm were higher than those in the surrounding waters. This result strongly suggested trace metal bioaccumulation on microplastics through biofilm formation. When trace metal concentrations were normalized over the corresponding surface of microplastics and macroplastics, higher values were obtained for microplastics, evidencing their enhanced capacities to bioaccumulate contaminants when compared to macroplastics.

Trace Metal Contamination Impacts Predicted Functions More Than Structure of Marine Prokaryotic Biofilm Communities in an Anthropized Coastal Area

Trace metal (TM) contamination in marine coastal areas is a worldwide threat for aquatic communities. However, little is known about the influence of a multi-chemical contamination on both marine biofilm communities' structure and functioning. To determine how TM contamination potentially impacted microbial biofilms' structure and their functions, polycarbonate (PC) plates were immerged in both surface and bottom of the seawater column, at five sites, along strong TM contamination gradients, in Toulon Bay. The PC plates were incubated during 4 weeks to enable colonization by biofilm-forming microorganisms on artificial surfaces. Biofilms from the PC plates, as well as surrounding seawaters, were collected and analyzed by 16S rRNA amplicon gene sequencing to describe prokaryotic community diversity, structure and functions, and to determine the relationships between bacterioplankton and biofilm communities. Our results showed that prokaryotic biofilm structure was not significantly affected by the measured environmental variables, while the functional profiles of biofilms were significantly impacted by Cu, Mn, Zn, and salinity. Biofilms from the contaminated sites were dominated by tolerant taxa to contaminants and specialized hydrocarbon-degrading microorganisms. Functions related to major xenobiotics biodegradation and metabolism, such as methane metabolism, degradation of aromatic compounds, and benzoate degradation, as well as functions involved in quorum sensing signaling, extracellular polymeric substances (EPS) matrix, and biofilm formation were significantly over-represented in the contaminated site relative to the uncontaminated one. Taken together, our results suggest that biofilms may be able to survive to strong multi-chemical contamination because of the presence of tolerant taxa in biofilms, as well as the functional responses of biofilm communities. Moreover, biofilm communities exhibited significant variations of structure and functional profiles along the seawater column, potentially explained by the contribution of taxa from surrounding sediments. Finally, we found that both structure and functions were significantly distinct between the biofilm and bacterioplankton, highlighting major differences between the both lifestyles, and the divergence of their responses facing to a multi-chemical contamination.

Exploring the impacts of heavy metals on spatial variations of sediment-associated bacterial communities

One of the fundamental objectives in modern ecology is to decipher how bacterial communities in natural environment respond to anthropogenic activities. In recent times consequences of marine pollution, especially with heavy metals (HMs) have received increasing attention. However, insights into the response of bacterial communities to HMs in coastal sediments of India remain scarce. Here, we analyzed HMs content in three areas, along the southern coastal region of India. Based on the calculated pollution indices viz., enrichment factor (EF), contamination factor (CF), geo-accumulation index (Igeo) and sediment quality guidelines (SQGs), the studied areas were classified as uncontaminated, moderately contaminated and significantly contaminated. To explore the response of bacterial community to HMs, sediment-associated microbiota was investigated using high-throughput 16S rRNA gene amplicon sequencing. The obtained metataxonomic results revealed that bacterial diversity and community composition varied considerably in significantly contaminated area than moderately contaminated and uncontaminated areas. Proportion of bacterial classes was higher for Gammaproteobacteria, Betaproteobacteria and Actinobacteria, but lower for Alphaproteobacteria and Flavobacteriia in significantly contaminated area. Also, samples of significantly contaminated area were dominated by well-documented metal-resistant bacterial genera such as Ralstonia and Arthrobacter. Canonical correspondence analysis (CCA) showed that spatial variability of bacterial community composition was strongly correlated with HMs content such as Chromium, Cadmium and Nickel. Further analysis using PICRUSt programme indicated that the predictive functional profile also varied considerably in significantly contaminated area. By linking HMs with bacterial compositional variations, the present study highlights the likely influence of HMs in shaping sedimentary microbiota of coastal regions.

Metal resistance genes enrichment in marine biofilm communities selected by biocide-containing surfaces in temperate and tropical coastal environments

Microorganisms able to form biofilms in marine ecosystems are selected depending on immersed surfaces and environmental conditions. Cell attachment directly on toxic surfaces like antifouling coatings suggests a selection of tolerant (or resistant) organisms with characteristics conferring adaptive advantages. We investigated if environment would drive metal resistance gene abundance in biofilms on artificial surfaces. Biofilms were sampled from three surfaces (a PVC reference and two antifouling coatings) deployed in three coastal waters with dissimilar characteristics: The Mediterranean Sea (Toulon) and Atlantic (Lorient) and Indian (Reunion) Oceans. The two coatings differed in metals composition, either Cu thiocyanate and Zn pyrithione (A3) or Cu2O (Hy). Metal resistance genes (MRG) specific to copper (cusA, copA, cueO) or other metals (czcA and pbrT) were monitored with qPCR in parallel to the microbial community using 16S rRNA gene metabarcoding. A lower α-diversity on A3 or Hy than on PVC was observed independent on the site. Weighted Unifrac suggested segregation of communities primarily by surface, with lower site effect. Metacoder log2 fold change ratio and LeFSe discrimination suggested Marinobacter to be specific of Hy and Altererythrobacter, Erythrobacter and Sphingorhabdus of A3. Likewise, the relative abundance of MRG (MRG/bacterial 16S rRNA) varied between surfaces and sites. A3 presented the greatest relative abundances for cusA, cueO and czcA. The latter could only be amplified from A3 communities, except at Toulon. Hy surface presented the highest relative abundance for copA, specifically at Lorient. These relative abundances were correlated with LeFSe discriminant taxa. Dasania correlated positively with all MRG except cueO. Marinobacter found in greater abundance in Hy biofilm communities correlated with the highest abundances of copA and Roseovarius with czcA. These results prove the selection of specific communities with abilities to tolerate metallic biocides forming biofilms over antifouling surfaces, and the secondary but significant influence of local environmental factors.

Impacts of copper and lead exposure on prokaryotic communities from contaminated contrasted coastal seawaters: the influence of previous metal exposure

Our understanding of environmental factors controlling prokaryotic community is largely hampered by the large environmental variability across spatial scales (e.g. trace metal contamination, nutrient enrichment and physicochemical variations) and the broad diversity of bacterial pre-exposure to environmental factors. In this article, we investigated the specific influence of copper (Cu) and lead (Pb) on prokaryotic communities from the uncontaminated site, using mesocosm experiments. In addition, we studied how pre-exposure (i.e. life history) affects communities, with reference to previous metal exposure on the response of three prokaryotic communities to similar Cu exposition. This study showed a stronger influence of Cu contamination than Pb contamination on prokaryotic diversity and structure. We identified 12 and 34 bacterial families and genera, respectively, contributing to the significant differences observed in community structure between control and spiked conditions. Taken altogether, our results point toward a combination of direct negative responses to Cu contamination and indirect responses mediated by interaction with phytoplankton. These identified responses were largely conditioned by the previous exposure of community to contaminants.

Long-term monitoring emphasizes impacts of the dredging on dissolved Cu and Pb contamination along with ultraplankton distribution and structure in Toulon Bay (NW Mediterranean Sea, France)

A long-term monitoring during dredging and non-dredging periods was performed. Total and dissolved Cu and Pb concentrations, DGT-labile Pb, ultraphytoplankton abundance and structure were monitored at four sites: dredging site, dumping site (inside/outside of a geotextile bag) and reference site. During the reference period (non-dredging), an increasing contamination in Pb, Cu and a progressive shift from Synechococcus to photosynthetic picoeukaryotes dominance was observed from reference to dumping site. Pb concentrations were significantly higher during dredging period, pointing out sediment resuspension as Pb major source of contamination. Unlike Pb, Cu concentrations were not statistically different during the two periods. Dredging period did not impact on ultraphytoplankton abundance and structure but influence heterotrophic prokaryotes abundance. Sediment resuspension is therefore a major driver of chemical and biological qualities in Toulon Bay. Furthermore, although the geotextile bag reduces particulate transport of the dredged sediment, the transport in the dissolved phase remains a major problem.

Toxicity of UV filters on marine bacteria: Combined effects with damaging solar radiation

Organic UV filters are of emerging concern due to their occurrence and persistence in coastal ecosystems. Because marine bacteria are crucial in the major biogeochemical cycles, there is an urgent need to understand to what extent these microorganisms are affected by those chemicals. This study deciphers the impact of five common sunscreen UV filters on twenty-seven marine bacteria, combining both photobiology and toxicity analysis on environmentally relevant species. Seven bacteria were sensitive to different organic UV filters at 1000 μg L^-1, including octinoxate and oxybenzone. This is the first report demonstrating inhibition of bacterial growth from 100 μg L^-1. None of the UV filters showed any toxicity at 1000 μg L^-1 on stationary phase cells, demonstrating that physiological state was found to be a key parameter in the bacterial response to UV-filters. Indeed, non-growing bacteria were resistant to UV filters whereas growing cells exhibited UV filter dependent sensitivity. Octinoxate was the most toxic chemical at 1000 μg L^-1 on growing cells. Interestingly, photobiology experiments revealed that the toxicity of octinoxate and homosalate decreased after light exposure while the other compounds were not affected. In terms of environmental risk characterization, our results revealed that the increasing use of sun blockers could have detrimental impacts on bacterioplanktonic communities in coastal areas. Our findings contribute to a better understanding of the impact of the most common UV filters on bacterial species and corroborate the importance to consider environmental parameters such as solar radiation in ecotoxicology studies.

Impacts of Anthropogenic Pollutants on Benthic Prokaryotic Communities in Mediterranean Touristic Ports

Ports and marinas are central nodes in transport network and play a strategic role in coastal development. They receive pollution from land-based sources, marine traffic and port infrastructures on one side and constitute a potential pollution source for the adjacent coastal areas on the other. The aim of the present study was to evaluate the effects of organic and inorganic co-contamination on the prokaryotic communities in sediments from three Mediterranean ports. The structure and composition of the bacterial and archaeal communities were assessed by targeted metagenomic analysis of the 16S rRNA gene, and the links of prokaryotic communities with environmental and pollution variables were investigated. The harbors presented pronounced site-specificity in the environmental properties and pollution status. Consistently, the structure of archaeal and bacterial communities in surface sediments exhibited a strong spatial variation among the three investigated ports. On the contrary, a wide overlap in composition of prokaryotic assemblages among sites was found, but local variation in the community composition and loss of prokaryotic diversity was highlighted in a heavily impacted port sector near a shipyard. We provided evidences that organic matter, metals and PAHs as well as temperature and salinity play a strong role in structuring benthic bacterial communities significantly contributing to the understanding of their responses to anthropogenic perturbations in marine coastal areas. Among metals, copper was recognized as strongly associated with the observed changes in bacterial assemblages. Overall, this study provides the first assessment of the effects exerted by multiple organic and inorganic contaminations on benthic prokaryotes in ports over a large spatial scale and designates bacterial community as a candidate tool for the monitoring of the sediment quality status in harbors.

A Multi-Omics Analysis Suggests Links Between the Differentiated Surface Metabolome and Epiphytic Microbiota Along the Thallus of a Mediterranean Seaweed Holobiont

Marine macroalgae constitute an important living resource in marine ecosystems and complex ecological interactions occur at their surfaces with microbial communities. In this context, the present study aimed to investigate how the surface metabolome of the algal holobiont Taonia atomaria could drive epiphytic microbiota variations at the thallus scale. First, a clear discrimination was observed between algal surface, planktonic and rocky prokaryotic communities. These data strengthened the hypothesis of an active role of the algal host in the selection of epiphytic communities. Moreover, significant higher epibacterial density and α-diversity were found at the basal algal parts compared to the apical ones, suggesting a maturation gradient of the community along the thallus. In parallel, a multiplatform mass spectrometry-based metabolomics study, using molecular networking to annotate relevant metabolites, highlighted a clear chemical differentiation at the algal surface along the thallus with similar clustering as for microbial communities. In that respect, higher amounts of sesquiterpenes, phosphatidylcholines (PCs), and diacylglycerylhydroxymethyl-N,N,N-trimethyl-β-alanines (DGTAs) were observed at the apical regions while dimethylsulfoniopropionate (DMSP) and carotenoids were predominantly found at the basal parts of the thalli. A weighted UniFrac distance-based redundancy analysis linking the metabolomics and metabarcoding datasets indicated that these surface compounds, presumably of algal origin, may drive the zonal variability of the epibacterial communities. As only few studies were focused on microbiota and metabolome variation along a single algal thallus, these results improved our understanding about seaweed holobionts. Through this multi-omics approach at the thallus scale, we suggested a plausible scenario where the chemical production at the surface of T. atomaria, mainly induced by the algal physiology, could explain the specificity and the variations of the surface microbiota along the thallus.

Kinetic processes of copper and lead remobilization during sediment resuspension of marine polluted sediments

Contaminated sediments could act as a source of contamination to the surrounding environments by several processes (e.g., diffusive flux, sediment resuspension). This study aimed at highlighting the mechanisms of copper and lead mobilization from resuspended particles to the aqueous phase using laboratory experiments and a kinetic model. Three sediments, differed by their compositions and metal partition from Toulon Bay (SE France) were used. In addition, three solid/liquid ratios (0.1, 1 and 10 g L^-1) allowed simulating at best natural and anthropogenic scenarios (e.g., storm, nautical traffic, dredging). We monitored metal concentrations, physicochemical parameters (pH, Eh, [O₂]) and organic matter concentration along with their optical properties. Experimental results showed successive reactions over short and long terms (hour and day scale, respectively) that controlled Cu and Pb exchanges between particles and the aqueous phase over 4 weeks. The quick Cu removal was attributed to the implications of newly formed oxides while the long-term Cu release in the dissolved fraction from the more refractory solid pool is more likely related to organic complexation. In fact, we observed a transformation of the dissolved organic matter: an increase in molecular weight and in humic fluorescence properties. However, the Pb removal toward the end of the experiment could be explained by a migration toward the exchangeable sites of higher energy, which could correspond to the particulate organic matter or a combination with organic-coating carrier phases. Both kinetic rate and system response times (τ_i) were coherent despite the variability of parameters intrinsic to sediments (e.g., sediment composition and initial metal repartition) but also extrinsic parameters (solid/liquid ratios). Such a coherence would imply the universality of the obtained constants to be used in a more predictive approach to assess the potential of metal mobility using metal repartition in contaminated sediments when combined with hydrological and sedimentological models.

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale

The southern Gulf of Mexico (sGoM) is highly susceptible to receiving environmental impacts due to the recent increase in oil-related activities. In this study, we assessed the changes in the bacterioplankton community structure caused by a simulated oil spill at mesocosms scale. The 16S rRNA gene sequencing analysis indicated that the initial bacterial community was mainly represented by Gamma-proteobacteria, Alpha-proteobacteria, Flavobacteriia, and Cyanobacteria. The hydrocarbon degradation activity, measured as the number of culturable hydrocarbonoclastic bacteria (CHB) and by the copy number of the alkB gene, was relatively low at the beginning of the experiment. However, after four days, the hydrocarbonoclastic activity reached its maximum values and was accompanied by increases in the relative abundance of the well-known hydrocarbonoclastic Alteromonas. At the end of the experiment, the diversity was restored to similar values as those observed in the initial time, although the community structure and composition were clearly different, where Marivita, Pseudohongiella, and Oleibacter were detected to have differential abundances on days eight–14. These changes were related with total nitrogen (p value = 0.030 and r² = 0.22) and polycyclic aromatic hydrocarbons (p value = 0.048 and r² = 0.25), according to PERMANOVA. The results of this study contribute to the understanding of the potential response of the bacterioplankton from sGoM to crude oil spills.

Shear Stress as a Major Driver of Marine Biofilm Communities in the NW Mediterranean Sea

While marine biofilms depend on environmental conditions and substrate, little is known about the influence of hydrodynamic forces. We tested different immersion modes (dynamic, cyclic and static) in Toulon Bay (north-western Mediterranean Sea; NWMS). The static mode was also compared between Toulon and Banyuls Bays. In addition, different artificial surfaces designed to hamper cell attachment (self-polishing coating: SPC; and fouling-release coating: FRC) were compared to inert plastic. Prokaryotic community composition was affected by immersion mode, surface characteristics and site. Rhodobacteriaceae and Flavobacteriaceae dominated the biofilm community structure, with distinct genera according to surface type or immersion mode. Cell density increased with time, greatly limited by hydrodynamic forces, and supposed to delay biofilm maturation. After 1 year, a significant impact of shear stress on the taxonomic structure of the prokaryotic community developed on each surface type was observed. When surfaces contained no biocides, roughness and wettability shaped prokaryotic community structure, which was not enhanced by shear stress. Conversely, the biocidal effect of SPC surfaces, already major in static immersion mode, was amplified by the 15 knots speed. The biofilm community on SPC was 60% dissimilar to the biofilm on the other surfaces and was distinctly colonized by Sphingomonadaceae ((Alter)Erythrobacter). At Banyuls, prokaryotic community structures were more similar between the four surfaces tested than at Toulon, due possibly to a masking effect of environmental constraints, especially hydrodynamic, which was greater than in Toulon. Finally, predicted functions such as cell adhesion confirmed some of the hypotheses drawn regarding biofilm formation over the artificial surfaces tested here.