Enhancing Molecular Characterization of Dissolved Organic Matter by Integrative Direct Infusion and Liquid Chromatography Nontargeted Workflows.

Dissolved organic matter (DOM) in aquatic systems is a highly heterogeneous mixture of water-soluble organic compounds, acting as a major carbon reservoir driving biogeochemical cycles. Understanding DOM molecular composition is thus of vital interest for the health assessment of aquatic ecosystems, yet its characterization poses challenges due to its complex and dynamic chemical profile. Here, we performed a comprehensive chemical analysis of DOM from highly urbanized river and seawater sources and compared it to drinking water. Extensive analyses by nontargeted direct infusion (DI) and liquid chromatography (LC) high-resolution mass spectrometry (HRMS) through Orbitrap were integrated with novel computational workflows to allow molecular- and structural-level characterization of DOM. Across all water samples, over 7000 molecular formulas were calculated using both methods (∼4200 in DI and ∼3600 in LC). While the DI approach was limited to molecular formula calculation, the downstream data processing of MS2 spectral information combining library matching and in silico predictions enabled a comprehensive structural-level characterization of 16% of the molecular space detected by LC-HRMS across all water samples. Both analytical methods proved complementary, covering a broad chemical space that includes more highly polar compounds with DI and more less polar ones with LC. The innovative integration of diverse analytical techniques and computational workflow introduces a robust and largely available framework in the field, providing a widely applicable approach that significantly contributes to understanding the complex molecular composition of DOM.

From dysbiosis to neuropathologies: Toxic effects of glyphosate in zebrafish.

Glyphosate, a globally prevalent herbicide known for its selective inhibition of the shikimate pathway in plants, is now implicated in physiological effects on humans and animals, probably due to its impacts in their gut microbiomes which possess the shikimate pathway. In this study, we investigate the effects of environmentally relevant concentrations of glyphosate on the gut microbiota, neurotransmitter levels, and anxiety in zebrafish. Our findings demonstrate that glyphosate exposure leads to dysbiosis in the zebrafish gut, alterations in central and peripheral serotonin levels, increased dopamine levels in the brain, and notable changes in anxiety and social behavior. While the dysbiosis can be attributed to glyphosate's antimicrobial properties, the observed effects on neurotransmitter levels leading to the reported induction of oxidative stress in the brain indicate a novel and significant mode of action for glyphosate, namely the impairment of the microbiome-gut-axis. While further investigations are necessary to determine the relevance of this mechanism in humans, our findings shed light on the potential explanation for the contradictory reports on the safety of glyphosate for consumers.

Snow-Dependent Biogeochemical Cycling of Polycyclic Aromatic Hydrocarbons at Coastal Antarctica.

The temporal trend of polycyclic aromatic hydrocarbons (PAHs) in coastal waters with highly dynamic sources and sinks is largely unknown, especially for polar regions. Here, we show the concurrent measurements of 73 individual PAHs and environmental data, including the composition of the bacterial community, during three austral summers at coastal Livingston (2015 and 2018) and Deception (2017) islands (Antarctica). The Livingston 2015 campaign was characterized by a larger snow melting input of PAHs and nutrients. The assessment of PAH diagnostic ratios, such as parent to alkyl-PAHs or LMW to HMW PAHs, showed that there was a larger biodegradation during the Livingston 2015 campaign than in the Deception 2017 and Livingston 2018 campaigns. The biogeochemical cycling, including microbial degradation, was thus yearly dependent on snow-derived inputs of matter, including PAHs, consistent with the microbial community significantly different between the different campaigns. The bivariate correlations between bacterial taxa and PAH concentrations showed that a decrease in PAH concentrations was concurrent with the higher abundance of some bacterial taxa, specifically the order Pseudomonadales in the class Gammaproteobacteria, known facultative hydrocarbonoclastic bacteria previously reported in degradation studies of oil spills. The work shows the potential for elucidation of biogeochemical processes by intensive field-derived time series, even in the harsh and highly variable Antarctic environment.

Bacterial responses to background organic pollutants in the northeast subarctic Pacific Ocean.

Thousands of man-made synthetic chemicals are released to oceans and compose the anthropogenic dissolved organic carbon (ADOC). Little is known about the effects of this chronic pollution on marine microbiome activities. In this study, we measured the pollution level at three sites in the Northeast Subarctic Pacific Ocean (NESAP) and investigated how mixtures of three model families of ADOC at different environmentally relevant concentrations affected naturally occurring marine bacterioplankton communities' structure and metabolic functioning. The offshore northernmost site (North) had the lowest concentrations of hydrocarbons, as well as organophosphate ester plasticizers, contrasting with the two other continental shelf sites, the southern coastal site (South) being the most contaminated. At North, ADOC stimulated bacterial growth and promoted an increase in the contribution of some Gammaproteobacteria groups (e.g. Alteromonadales) to the 16 rRNA pool. These groups are described as fast responders after oil spills. In contrast, minor changes in South microbiome activities were observed. Gene expression profiles at Central showed the coexistence of ADOC degradation and stress-response strategies to cope with ADOC toxicities. These results show that marine microbial communities at three distinct domains in NESAP are influenced by background concentrations of ADOC, expanding previous assessments for polar and temperate waters.

Rain Amplification of Persistent Organic Pollutants.

Scavenging of gas- and aerosol-phase organic pollutants by rain is an efficient wet deposition mechanism of organic pollutants. However, whereas snow has been identified as a key amplification mechanism of fugacities in cold environments, rain has received less attention in terms of amplification of organic pollutants. In this work, we provide new measurements of concentrations of perfluoroalkyl substances (PFAS), organophosphate esters (OPEs), and polycyclic aromatic hydrocarbons (PAHs) in rain from Antarctica, showing high scavenging ratios. Furthermore, a meta-analysis of previously published concentrations in air and rain was performed, with 46 works covering different climatic regions and a wide range of chemical classes, including PFAS, OPEs, PAHs, polychlorinated biphenyls and organochlorine compounds, polybromodiphenyl ethers, and dioxins. The rain-aerosol (KRP) and rain-gas (KRG) partition constants averaged 105.5 and 104.1, respectively, but showed large variability. The high field-derived values of KRG are consistent with adsorption onto the raindrops as a scavenging mechanism, in addition to gas-water absorption. The amplification of fugacities by rain deposition was up to 3 orders of magnitude for all chemical classes and was comparable to that due to snow. The amplification of concentrations and fugacities by rain underscores its relevance, explaining the occurrence of organic pollutants in environments across different climatic regions.

Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon.

Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membrane-compromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.

Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters.

Thousands of semi-volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny-Ålesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.

Snow Amplification of Persistent Organic Pollutants at Coastal Antarctica.

Many legacy and emerging persistent organic pollutants (POPs) have been reported in polar regions, and act as sentinels of global pollution. Maritime Antarctica is recipient of abundant snow precipitation. Snow scavenges air pollutants, and after snow melting, it can induce an unquantified and poorly understood amplification of concentrations of POPs. Air, snow, the fugacity in soils and snow, seawater and plankton were sampled concurrently from late spring to late summer at Livingston Island (Antarctica). Polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) concentrations in snow and air were close to equilibrium. POPs in soils showed concentrations close to soil-air equilibrium or net volatilization depending on chemical volatility. Seawater-air fugacity ratios were highly correlated with the product of the snow-air partition coefficient and the Henry's law constant (KSA H'), a measure of snow amplification of fugacity. Therefore, coastal seawater mirrored the PCB congener profile and increased concentrations in snowmelt due to snowpack releasing POPs to seawater. The influence of snowpack and glacier inputs was further evidenced by the correlation between net volatilization fluxes of PCBs and seawater salinity. A meta-analysis of KSA, estimated as the ratio of POP concentrations in snow and air from previously reported simultaneous field measurements, showed that snow amplification is relevant for diverse families of POPs, independent of their volatility. We claim that the potential impact of atmospheric pollution on aquatic ecosystems has been under-predicted by only considering air-water partitioning, as snow amplification influences, and may even control, the POP occurrence in cold environments.

Pivotal Role of Snow Deposition and Melting Driving Fluxes of Polycyclic Aromatic Hydrocarbons at Coastal Livingston Island (Antarctica).

The atmosphere-land-ocean dynamics of semivolatile organic compounds in polar regions is poorly understood, also for the abundant and ubiquitous polycyclic aromatic hydrocarbons (PAHs). We report the concentrations and fluxes of PAHs in a polar coastal ecosystem (Livingston Island, Antarctica). From late spring (December 2014) to late summer (February 2015), we sampled air, snow, coastal seawater, plankton, and the fugacity in soils and snow. The concentrations of PAHs in seawater were low but increased during the austral summer. The PAH concentrations in snow were significantly higher than in coastal seawater. Soil-air fugacity ratios showed a net volatilization of PAH when soils were covered with lichens, and close to air-soil equilibrium for bare soils. Concentrations in surface snow were also close to equilibrium with atmospheric PAHs. Conversely, there was a net diffusive deposition of PAHs to coastal seawater during late spring, but a net volatilization from seawater during late summer. Volatilization fluxes were correlated with seawater temperature and salinity, consistent with a key role of snowmelt to the fluxes and dissolved phase concentrations during the austral summer. The comprehensive assessment provided here shows that the fugacity amplification in snow is transferred to soils and coastal seawater supporting PAH concentrations and fluxes.

Bromodeoxyuridine labelling and fluorescence-activated cell sorting of polyamine-transforming bacterioplankton in coastal seawater.

Polyamines (PAs) are a group of nitrogen-rich dissolved organic nitrogen (DON) compounds that are ubiquitously distributed in marine environments. To identify bacteria that are involved in PA transformations, coastal bacterioplankton microcosms were amended with a single PA model compound, i.e. putrescine (PUT) or spermidine (SPD), or with no addition as controls (CTRs). Bromodeoxyuridine (BrdU) was added to all the microcosms to label newly synthesized DNAs. Fluorescence-activated cell sorting (FACS) analysis indicated significant increases in numbers of total cells and cells with both high and low levels of BrdU incorporation in the PUT and SPD microcosms, but not in the CTRs. 16S rDNA pyrotag sequencing of FACS-sorted cells indicated that PUT- and SPD-transforming bacteria were composed similarly of a diverse group of taxa affiliated with Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria (especially Roseobacter of its alpha lineage). Broad taxonomic distribution of PA-transforming bacteria was also indicated by the abundance and distribution of PA transporter gene homologues in a survey of sequenced marine bacterial genomes. Our results suggest that PAs may be common DON substrates for marine bacterioplankton, in line with the hypothesis that bacterially mediated PA transformation accounts for an important proportion of marine DON flux.

Nitrogen-cycling genes in epilithic biofilms of oligotrophic high-altitude lakes (central Pyrenees, Spain).

Microbial biofilms in oligotrophic environments are the most reactive component of the ecosystem. In high-altitude lakes, exposed bedrock, boulders, gravel, and sand in contact with highly oxygenated water and where a very thin epilithic biofilm develops usually dominate the littoral zone. Traditionally, these surfaces have been considered unsuitable for denitrification, but recent investigations have shown higher biological diversity than expected, including diverse anaerobic microorganisms. In this study, we explored the presence of microbial N-cycling nirS and nirK (denitrification through the conversion of NO2(-) to NO), nifH (N2 fixation), anammox (anaerobic ammonium oxidation), and amoA (aerobic ammonia oxidation, both bacterial and archaeal) genes in epilithic biofilms of a set of high-altitude oligotrophic lakes in the Pyrenees. The concentrations of denitrifying genes determined by quantitative PCR were two orders of magnitude higher than those of ammonia-oxidizing genes. Both types of genes were significantly correlated, suggesting a potential tight coupling nitrification-denitrification in these biofilms that deserves further confirmation. The nifH gene was detected after nested PCR, and no signal was detected for the anammox-specific genes used. The taxonomic composition of denitrifying and nitrogen-fixing genes was further explored by cloning and sequencing. Interestingly, both microbial functional groups were richer and more genetically diverse than expected. The nirK gene, mostly related to Alphaproteobacteria (Bradyrhizobiaceae), dominated the denitrifying gene pool as expected for oxygen-exposed habitats, whereas Deltaproteobacteria (Geobacter like) and Cyanobacteria were the most abundant among nitrogen fixers. Overall, these results suggest an epilithic community more metabolically diverse than previously thought and with the potential to carry out an active role in the biogeochemical nitrogen cycling of high-altitude ecosystems. Measurements of activity rates should be however carried out to substantiate and further explore these findings.

Diel gene expression profiles of a phosphorus limited mountain lake using metatranscriptomics.

The genetic basis of bacterial functionality in freshwater systems remains largely unexplored despite its relevance in biogeochemical cycles. In this study, we used metatranscriptomic sequencing to analyse day and night gene expression profiles of the bacterial planktonic assemblage from the phosphorus (P) limited Lake Llebreta (1620 m above sea level) in the Limnological Observatory of the Pyrenees (LOOP, Central Pyrenees). The goal of the study was to obtain clues about the ecological strategies of bacteria in a highly oligotrophic environment, particularly those related to processing P and energy capture. An average of 37 871 unique reads were obtained per treatment using 454 pyrosequencing of amplified messenger RNA (mRNA), of which ∼ 37% matched a protein function in BLASTx analysis against the NCBI RefSeq database. In general, an overabundance of transcripts for energy acquisition (e.g. photosynthesis, oxidative phosphorylation, proteorhodopsins and bacteriochlorophyll a) was observed in the day compared with the night. Several different forms of P were metabolized by the community, with the relative abundance of transcripts related to phosphonate and phosphate uptake pointing to a major role of organic P in controlling this ecosystem. Bacteroidetes and Betaproteobacteria were the most actively transcribing phyla in the community, but showed different strategies for supplemental sources of energy: Bacteroidetes appeared to rely on creating H+ gradients across the membrane by using proteorhodopsins during the day and pyrophosphatases at night, whereas Betaproteobacteria appeared to be oxidizing carbon monoxide (CO) that potentially was generated by photooxidation of dissolved organic matter. When these diel freshwater metatranscriptomes were compared with those from two pelagic marine systems, gene expression patterns distinguished freshwater versus marine samples but showed common differences between day and night transcriptomes related to energy production.

Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica.

Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h-1. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.

Inputs, amplification and sinks of perfluoroalkyl substances at coastal Antarctica.

The sources, biogeochemical controls and sinks of perfluoroalkyl substances, such as perfluoroalkyl acids (PFAAs), in polar coastal regions are largely unknown. These were evaluated by measuring a large multi-compartment dataset of PFAAs concentrations at coastal Livingston and Deception Islands (maritime Antarctica) during three austral summers. PFAAs were abundant in atmospheric-derived samples (aerosols, rain, snow), consistent with the importance of atmospheric deposition as an input of PFAAs to Antarctica. Such PFAAs deposition was unequivocally demonstrated by the occurrence of PFAAs in small Antarctic lakes. Several lines of evidence supported the relevant amplification of PFAAs concentrations in surface waters driven by snow scavenging of sea-spray aerosol-bound PFAAs followed by snow-melting. For example, vertical profiles showed higher PFAAs concentrations at lower-salinity surface seawaters, and PFAAs concentrations in snow were significantly higher than in seawater. The higher levels of PFAAs at Deception Island than at Livingston Island are consistent with the semi-enclosed nature of the bay. Concentrations of PFOS decreased from 2014 to 2018, consistent with observations in other oceans. The sink of PFAAs due to the biological pump, transfer to the food web, and losses due to sea-spray aerosols alone are unlikely to have driven the decrease in PFOS concentrations. An exploratory assessment of the potential sinks of PFAAs suggests that microbial degradation of perfluoroalkyl sulfonates should be a research priority for the evaluation of PFAAs persistence in the coming decade.

Impact of the antibiotic doxycycline on the D. magna reproduction, associated microbiome and antibiotic resistance genes in treated wastewater conditions.

Wastewater Treatment Plant (WWTP) effluents are important sources of antibiotics, antibiotic resistance genes (ARGs) and resistant bacteria that threaten aquatic biota and human heath. Antibiotic effects on host-associated microbiomes, spread of ARGs and the consequences for host health are still poorly described. This study investigated changes of the Daphnia magna associated microbiome exposed to the recalcitrant antibiotic doxycycline under artificial reconstituted lab water media (lab water) and treated wastewater media. D. magna individual juveniles were exposed for 10 days to treated wastewater with and without doxycycline, and similarly in lab water. We analysed 16 S rRNA gene sequences to assess changes in community structure, monitored Daphnia offspring production and quantified ARGs abundances by qPCR from both Daphnia and water (before and after the exposure). Results showed that doxycycline and media (lab water or wastewater) had a significant effect modulating Daphnia-associated microbiome composition and one of the most discriminant taxa was Enterococcus spp. Moreover, in lab water, doxycycline reduced the presence of Limnohabitans sp., which are dominant bacteria of the D. magna-associated microbiome and impaired Daphnia reproduction. Contrarily, treated wastewater increased diversity and richness of Daphnia-associated microbiome and promoted fecundity. In addition, the detected ARG genes in both lab water and treated wastewater medium included the qnrS1, sul1, and blaTEM, and the integron-related intI1 gene. The treated wastewater contained about 10 times more ARGs than lab water alone. Furthermore, there was an increase of sul1 in Daphnia cultured in treated wastewater compared to lab water. In addition, there were signs of a higher biodegradation of doxycycline by microbiomes of treated wastewater in comparison to lab water. Thus, results suggest that Daphnia-associated microbiomes are influenced by their environment, and that bacterial communities present in treated wastewater are better suited to cope with the effects of antibiotics.

Community analysis of high- and low-nucleic acid-containing bacteria in NW Mediterranean coastal waters using 16S rDNA pyrosequencing.

The ecological significance of the marine bacterial populations distinguishable by flow cytometry on the basis of the fluorescence (FL) of their nucleic acid (NA) content and proxies of cell size (such as side scatter, SSC) remains largely unknown. Some studies have suggested that cells with high NA (HNA) content and high SSC (HS) represent the active members of the community, while the low NA (LNA) cells are inactive members of the same phylogenetic groups. But group-specific activity measurements and phylogenetic assignment after cell sorting have suggested this is not be the case, particularly in open-ocean communities. To test the extent to which the different NA subgroups are similar, and consequently the extent to which they likely have similar ecological and biogeochemical roles in the environment, we analysed the phylogenetic composition of three populations after cell sorting [high NA-high SC (HNA-HS), high NA-low SC (HNA-LS), low NA (LNA)] by 454 pyrosequencing in two contrasting periods of the year in NW Mediterranean coastal waters (BBMO, Blanes Bay Microbial Observatory) where these three populations have recurrent seasonal patterns. Statistical analyses showed that summer and winter samples were significantly different and, importantly, the sorted populations within a sample were composed of different taxa. The majority of taxa were associated with one NA fraction only, and the degree of overlap (i.e. OTUs present simultaneously in 2 fractions) between HNA and LNA and between summer and winter communities was very small. Rhodobacterales, SAR116 and Bacteroidetes contributed primarily to the HNA fraction, whereas other groups such as SAR11 and SAR86 contributed largely to the LNA fractions. Gammaproteobacteria other than SAR86 showed less preference for one particular NA fraction. An increase in diversity was observed from the LNA to the HNA-HS fraction for both sample dates. Our results suggest that, in Blanes Bay, flow cytometric signatures of natural communities track their phylogenetic composition.

Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica.

As much as 400 Tg of carbon from airborne semivolatile aromatic hydrocarbons is deposited to the oceans every year, the largest identified source of anthropogenic organic carbon to the ocean. Microbial degradation is a key sink of these pollutants in surface waters, but has received little attention in polar environments. We have challenged Antarctic microbial communities from the sea-surface microlayer (SML) and the subsurface layer (SSL) with polycyclic aromatic hydrocarbons (PAHs) at environmentally relevant concentrations. PAH degradation rates and the microbial responses at both taxonomical and functional levels were assessed. Evidence for faster removal rates was observed in the SML, with rates 2.6-fold higher than in the SSL. In the SML, the highest removal rates were observed for the more hydrophobic and particle-bound PAHs. After 24 h of PAHs exposure, particle-associated bacteria in the SML showed the highest number of significant changes in their composition. These included significant enrichments of several hydrocarbonoclastic bacteria, especially the fast-growing genera Pseudoalteromonas, which increased their relative abundances by eightfold. Simultaneous metatranscriptomic analysis showed that the free-living fraction of SML was the most active fraction, especially for members of the order Alteromonadales, which includes Pseudoalteromonas. Their key role in PAHs biodegradation in polar environments should be elucidated in further studies. This study highlights the relevant role of bacterial populations inhabiting the sea-surface microlayer, especially the particle-associated habitat, as relevant bioreactors for the removal of aromatic hydrocarbons in the oceans.

Microbial metabolic routes in metagenome assembled genomes are mirrored by the mass balance of polycyclic aromatic hydrocarbons in a high altitude lake.

Semivolatile organic pollutants have potential for long range atmospheric transport and can thus reach pristine remote lakes by atmospheric deposition. Polycyclic aromatic hydrocarbons (PAHs) are among the most abundant and toxic semivolatile pollutants affecting lakes, however, the main factors controlling their fate are still poorly known. Here we show two contrasting lines of evidence for the importance of microbial degradation on the environmental fate of PAHs in a high altitude deep lake. The first evidence is given by an assessment of the metagenomes from surface and deep waters from Lake Redon (Pyrenees Mountains), which shows the occurrence of the initial ring hydroxylating dioxygenases as well as other PAH degrading genes from the complete metabolic route of PAH degradation. The second line of evidence is by the application of an environmental fate model for PAHs to Lake Redon under two contrasting scenarios considering the inclusion or not of degradation. When degradation is included in the model, PAH concentrations in the sediment are predicted within a factor of two of those measured in Lake Redon. Finally, the extent of the degradation sink is quantified and compared to other cycling PAH fluxes in the lake.

Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters.

Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations - "key" in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change.