Fluvial biofilms exposed to desiccation and pharmaceutical pollution: New insights using metabolomics

Pharmaceutical impacts on aerobic granular sludge morphology and potential implications for abiotic removal

The goal of this study was to investigate abiotic pharmaceutical removal and abiotic pharmaceutical effects on aerobic granular sludge morphology. For 80 days, a pharmaceutical mixture containing approximately 150 μg/L each of diclofenac, erythromycin, and gemfibrozil was fed to an aerobic granular sludge sequencing batch reactor and granule characteristics were compared with those from a control reactor. Aqueous and solid phase pharmaceutical concentrations were monitored and staining was used to assess changes in biofilm structures. Solid phase pharmaceutical concentrations were elevated over the first 12 days of dosing; however, they then dropped, indicative of desorption. The lipid content in pharmaceutical-exposed granules declined by approximately half over the dosing period, though the relative concentrations of other key biofilm components (proteins, alpha-, and beta-polysaccharides) did not change. Batch experiments were conducted to try to find an explanation for the desorption observed, but reduced solid phase pharmaceutical concentrations could not be linked with the presence of common wastewater constituents such as ammonia or phosphate. Sorption of all three compounds was modeled best by the Henry isotherm, indicating that, even at 150 μg/L, granules' sorption site coverage was incomplete. Altogether, this study demonstrates that simplified batch systems may not accurately represent the complex abiotic processes occurring in flow-through, biotic systems.

Effects of combining flow intermittency and exposure to emerging contaminants on the composition and metabolic response of streambed biofilm bacterial communities

Freshwater ecosystems are characterised by the co-occurrence of stressors that simultaneously affect the biota. Among these, flow intermittency and chemical pollution severely impair the diversity and functioning of streambed bacterial communities. Using an artificial streams mesocosm facility, this study examined how desiccation and pollution caused by emerging contaminants affect the composition of stream biofilm bacterial communities, their metabolic profiles, and interactions with their environment. Through an integrative analysis of the composition of biofilm communities, characterization of their metabolome and composition of the dissolved organic matter, we found strong genotype-to-phenotype interconnections. The strongest correlation was found between the composition and metabolism of the bacterial community, both of which were influenced by incubation time and desiccation. Unexpectedly, no effect of the emerging contaminants was observed, which was due to the low concentration of the emerging contaminants and the dominant impact of desiccation. However, biofilm bacterial communities modified the chemical composition of their environment under the effect of pollution. Considering the tentatively identified classes of metabolites, we hypothesised that the biofilm response to desiccation was mainly intracellular while the response to chemical pollution was extracellular. The present study demonstrates that metabolite and dissolved organic matter profiling may be effectively integrated with compositional analysis of stream biofilm communities to yield a more complete picture of changes in response to stressors.

Metabolomic and cultivation insights into the tolerance of the spacecraft-associated Acinetobacter toward Kleenol 30, a cleanroom floor detergent

Introduction

Stringent cleaning procedures during spacecraft assembly are critical to maintaining the integrity of life-detection missions. To ensure cleanliness, NASA spacecraft are assembled in cleanroom facilities, where floors are routinely cleansed with Kleenol 30 (K30), an alkaline detergent.

Methods

Through metabolomic and cultivation approaches, we show that cultures of spacecraft-associated Acinetobacter tolerate up to 1% v/v K30 and are fully inhibited at ≥2%; in comparison, NASA cleanrooms are cleansed with ~0.8-1.6% K30.

Results

For A. johnsonii 2P08AA (isolated from a cleanroom floor), cultivations with 0.1% v/v K30 yield (1) no changes in cell density at late-log phase, (2) modest decreases in growth rate (~17%), (3) negligible lag phase times, (4) limited changes in the intracellular metabolome, and (5) increases in extracellular sugar acids, monosaccharides, organic acids, and fatty acids. For A. radioresistens 50v1 (isolated from a spacecraft surface), cultivations yield (1) ~50% survivals, (2) no changes in growth rate, (3) ~70% decreases in the lag phase time, (4) differential changes in intracellular amino acids, compatible solutes, nucleotide-related metabolites, dicarboxylic acids, and saturated fatty acids, and (5) substantial yet differential impacts to extracellular sugar acids, monosaccharides, and organic acids.

Discussion

These combined results suggest that (1) K30 manifests strain-dependent impacts on the intracellular metabolomes, cultivation kinetics, and survivals, (2) K30 influences extracellular trace element acquisition in both strains, and (3) K30 is better tolerated by the floor-associated strain. Hence, this work lends support towards the hypothesis that repeated cleansing during spacecraft assembly serve as selective pressures that promote tolerances towards the cleaning conditions.

Presence of pharmaceuticals and bacterial resistance genes in river epilithic biofilms exposed to intense agricultural and urban pressure

The continuous discharge of pharmaceutical compounds into the aquatic environment has raised concerns over the contamination of water resources. Urban activities and intensive animal breeding are important sources of contamination. The accumulation of antibiotics may lead to the transfer or alternatively maintain the presence of resistance genes in natural microbial communities existing in epilithic biofilms. The objective of this study was to evaluate the pharmaceutical contamination levels and the presence of resistance genes in biofilms from a South Brazilian watershed. The Guaporé watershed exhibits a high diversity of land use, including agricultural and urban areas with differing levels of anthropogenic pressure. Seventeen sites along the Guaporé watershed were monitored. Biofilm samples were collected in two seasons (winter and summer), and the pharmaceutical concentration and quantity of resistance genes were analyzed. All monitored sites were contaminated with pharmaceuticals. Agricultural activities contribute through transferring pharmaceuticals derived from the application of animal waste to agricultural fields. The most contaminated site (pharmaceuticals and bacterial resistance genes) was located in an urban area exposed to high pressure. Decreases in the contamination of biofilms were also observed, exemplifying processes of natural attenuation in the watershed. The quality of the biofilms sampled throughout the watershed served as a useful tool to understand and monitor environmental pollution.

Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern

Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (bla_KPC, bla_NDM, and bla_OXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with bla_KPC being the most detected (88 % of samples), followed by bla_NDM (64 %) and bla_OXA-48 (23 %). Fish gut samples showed higher concentrations of bla_KPC and bla_NDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of bla_NDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.

Community metabolomics provides insights into mechanisms of pollution-induced community tolerance of periphyton

Chemical pollution is a major concern for freshwater ecosystems, but the impact and mechanisms of chemical stressors on communities are barely understood. Pollution stress beyond natural homeostatic capacities can trigger succession of tolerant species within a community, enhancing the overall community tolerance. This process was operationalized in the Pollution-Induced Community Tolerance (PICT) concept and applied in many case studies, however, the molecular mechanisms of community tolerance and implications for ecological functions remain largely unexplored. Our study aimed to demonstrate that 1) community metabolomics can unravel potential mechanisms of PICT in periphyton and 2) induced tolerance helps to maintain primary production under re-occuring pollution. To this end, we grew periphyton for 5 weeks with and without the model herbicide diuron in microcosms, quantified PICT, and determined the related metabolic fingerprint of periphyton by GC-MS-based untargeted metabolomics. Further, we explored the autotrophic community based on pigment composition and functional parameters including photosynthesis and gross primary production. Chronic diuron exposure resulted in a shift in pigment composition, higher community tolerance and an individual metabolic fingerprint in the contaminated communities. Opposing responses of selected metabolites during a short-term exposure indicated differences in diuron pre-adaptation in the different communities. Metabolites (threonic acid and two sugar acid lactones) were found to be related to tolerance development, suggesting that ascorbate metabolism was induced in contaminated communities. Despite these compensating mechanism, contaminated communities were compromised in production-to-respiration ratio and biomass. A ranking of sensitivity thresholds of different biological endpoints revealed that metabolites were less sensitive than photosynthetic parameters, which reflects the mode-of-action of the herbicide. In conclusion, we could demonstrate that community metabolomics is able to unravel complex biochemical changes and allows mechanistic insights into community tolerance. Moreover, we were able to show that induced community tolerance was insufficient to safeguard functions like primary production.

Metabolomics insight into the influence of environmental factors in responses of freshwater biofilms to the model herbicide diuron

Freshwater biofilms have been increasingly used during the last decade in ecotoxicology due to their ecological relevance to assess the effect(s) of environmental stress at the community level. Despite growing knowledge about the effect of various stressors on the structure and the function of these microbial communities, a strong research effort is still required to better understand their response to chemical stress and the influence of environmental stressors in this response. To tackle this challenge, untargeted metabolomics is an approach of choice because of its capacity to give an integrative picture of the exposure to multiple stress and associated effect as well as identifying the molecular pathways involved in these responses. In this context, the present study aimed to explore the use of an untargeted metabolomics approach to unravel at the molecular/biochemical level the response of the whole biofilm to chemical stress and the influence of various environmental factors in this response. To this end, archived high-resolution mass spectrometry data from previous experiments at our laboratory on the effect of the model photosynthesis inhibitor diuron on freshwater biofilm were investigated by using innovative solutions for OMICs data (e.g., DRomics) and more usual chemometric approaches (multivariate and univariate statistical analyses). The results showed a faster (1 min) and more sensitive response of the metabolome to diuron than usual functional descriptors, including photosynthesis. Also, the metabolomics response to diuron resulted from metabolites following various trends (increasing, decreasing, U/bell shape) along increasing concentration and time. This metabolomics response was influenced by the temperature, photoperiod, and flow. A focus on a plant-specific omega-3 (eicosapentaenoic acid) playing a key role in the trophic chain highlighted the potential relevance of metabolomics approach to establish the link between molecular alteration and ecosystem structure/functioning impairment but also how complex is the response and the influence of all the tested factors on this response at the metabolomics level. Altogether, our results underline that more fundamental researches are needed to decipher the metabolomics response of freshwater biofilm to chemical stress and its link with physiological, structural, and functional responses toward the unraveling of adverse outcome pathways (AOP) for key ecosystem functions (e.g., primary production).

The use of epilithic biofilms as bioaccumulators of pesticides and pharmaceuticals in aquatic environments

Biofilms are a consortium of communities of organisms that live in syntrophic relationships and present a higher organization level than that of individual cells. Biofilms dominate microbial life in streams and rivers, enable crucial ecosystem processes, contribute to global biogeochemical flows and represent the main active bacterial life form. Epilithic biofilms are the main biomass found in rivers; their exposure to contaminants can lead to changes in their structure and composition. The composition of these communities is influenced by physicochemical factors, temperature, light and prior exposure to pollutants, among other factors, and it can be used for water quality monitoring purposes. The heterogenous composition of biofilms enables them to accumulate compounds in an integrative manner. Moreover, the availability of several sorption sites and their likely saturation can contribute to bioaccumulation. In aquatic environments, biofilms are also susceptible to the acquisition of antibiotic resistance genes and participate in their dissemination. Anthropic pressure intensification processes continuously expose water resources and, consequently, biofilm communities to different contamination sources. Therefore, the use of biofilms to indicate environmental pollution is reinforced by the progress of studies on the subject. Biofilm communities' response to pollutants in aquatic environments can be mainly influenced by the presence of different organisms, which may change due to community development or age. The current research aims to review studies about biofilm contamination and highlight the importance of biofilm use to better evaluate and maintain the quality of water bodies.

Aquatic macroinvertebrates under stress: Bioaccumulation of emerging contaminants and metabolomics implications

The current knowledge on bioaccumulation of emerging contaminants (ECs) in aquatic invertebrates exposed to the realistic environmental concentrations is limited. Even less is known about the effects of chemical pollution exposure on the metabolome of aquatic invertebrates. We conducted an in situ translocation experiment with passive filter-feeding caddisfly larvae (Hydropsyche sp.) in an effluent-influenced river in order to i) unravel the bioaccumulation (and recovery) dynamics of ECs in aquatic invertebrates, and ii) test whether exposure to environmentally realistic concentrations of ECs will translate into metabolic profile changes in the insects. The experiment was carried out at two sites, upstream and downstream of the discharge of an urban wastewater treatment plant effluent. The translocated animals were collected at 2-week intervals for 46 days. Both pharmaceuticals and endocrine disrupting compounds (EDCs) were detected in water (62 and 7 compounds, respectively), whereas in Hydropsyche tissues 5 EDCs accumulated. Overall, specimens from the upstream site translocated to the impacted site reached higher ECs concentrations in their tissues, as a reflection of the contaminants' water concentrations. However, bioaccumulation was a temporary process susceptible to change under lower contaminant concentrations. Non-targeted metabolite profiling detected fine metabolic changes in translocated Hydropsyche larvae. Both translocations equally induced stress, but it was higher in animals translocated to the impacted site.

Metabolome response to anthropogenic contamination on microalgae: a review

BACKGROUND

Microalgae play a key role in ecosystems and are widely used in ecological status assessment. Research focusing on such organisms is then well developed and essential. Anyway, approaches for a better comprehension of their metabolome's response towards anthropogenic stressors are only emerging.

AIM OF REVIEW

This review presents the biochemical responses of various microalgae species towards several contaminants including metals and chemicals as pesticides or industrial compounds. We aim to provide a comprehensive and up-to-date overview of analytical approaches deciphering anthropogenic contaminants impact on microalgae metabolome dynamics, in order to bring out relevant biochemical markers that could be used for risk assessment.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Studies to date on ecotoxicological metabolomics on microalgae are highly heterogeneous in both analytical techniques and resulting metabolite identification. There is a real need for studies using complementary approaches to determine biomarkers usable for ecological risk assessment.

Comprehensive study of sulfamethoxazole effects in marine mussels: Bioconcentration, enzymatic activities and metabolomics

Antibiotics accumulation in aquatic organisms may be of great concern from an ecological point of view but also from a human perspective, especially when they are accumulated in edible animals like marine mussels. In this work, mussels (Mytilus galloprovincialis) were exposed to sulfamethoxazole antibiotic (SMX) at 10 µg/L during 96 h, followed by 24 h of depuration. The experiment was carried out at summer and winter conditions. SMX showed a bioconcentration factor in mussel of 1.5 L/kg (dry weight) and 69% of the compound was eliminated from the organism in 24 h. The metabolomics approach revealed alterations in amino acids levels (aspartate, phenylalanine, valine and tryptophan) pinpointing disturbances in osmotic regulation and energy metabolism. Besides, the levels of some nucleotides (guanosine and inosine) and a carboxylic acid were also affected. However, SMX exposed mussels did not show any significant alteration in the enzymatic activities related to the xenobiotic metabolism and oxidative stress. Moreover, some of the changes observed in mussel's metabolites suggested alterations in mussel's organoleptic characteristics that can affect its quality as seafood commodity. Overall, our results showed that SMX exposure to marine mussels may have ecological implications by provoking sub-lethal effects to exposed organisms. Nevertheless, no risk for consumers derived from mussel ingestion is expected due to the low bioconcentration capacity of SMX and fast depuration in this seafood type.

Impact of fullerenes in the bioaccumulation and biotransformation of venlafaxine, diuron and triclosan in river biofilms

A huge variety of organic microcontaminants are presently detected in freshwater ecosystems, but there is still a lack of knowledge about their interactions, either with living organisms or with other contaminants. Actually, carbon nanomaterials like fullerenes (C₆₀) can act as carriers of organic microcontaminants, but their relevance in processes like bioaccumulation and biotransformation of organic microcontaminants by organisms is unknown. In this study, mesocosm experiments were used to assess the bioaccumulation and biotransformation of three organic microcontaminants (venlafaxine, diuron and triclosan) in river biofilms, and to understand how much the concomitant presence of C₆₀ at environmental relevant concentrations could impact these processes. Results indicated that venlafaxine exhibited the highest bioaccumulation (13% of the initial concentration of venlafaxine in water), while biotransformation was more evident for triclosan (5% of the initial concentration of triclosan in water). Furthermore, biotransformation products such as methyl-triclosan were also present in the biofilm, with levels up to 42% of the concentration of accumulated triclosan. The presence of C₆₀ did not involve relevant changes in the bioaccumulation and biotransformation of microcontaminants in biofilms, which showed similar patterns. Nevertheless, the study shows that a detailed evaluation of the partition of the organic microcontaminants and their transformation products in freshwater systems are important to better understand the impact of the co-existence of others microcontaminants, like carbon nanomaterials, in their possible routes of bioaccumulation and biotransformation.

Diatom responses to sewage inputs and hydrological alteration in Mediterranean streams

We analyzed the conjoint effects of sewage inputs and hydrological alteration on the occurrence of teratological forms and on the assemblage composition of stream benthic diatoms. The study was performed in 11 Mediterranean streams which received treated or untreated urban sewage (Impact sites, I), whose composition and morphological anomalies were compared to upstream unaffected (Control, C) sites. The impact sites had high concentrations of ammonium, phosphorus, and pharmaceutical compounds (antibiotics, analgesics, and anti-inflammatories), particularly in those receiving untreated sewage. Impact sites had a higher proportion of teratological forms as well as a prevalence of diatom taxa tolerant to pollution. The differences in the diatom assemblage composition between the paired C and I sites were the largest in the impacted sites that received untreated sewage inputs as well as in the systems with lower dilution capacity. In these sites, the diatom assemblage was composed by a few pollution-tolerant species. Mediterranean river systems facing hydrological stress are highly sensitive to chemical contamination, leading to the homogenization of their diatom assemblages.

Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kützing

Metals are a recognised threat to aquatic organisms but the impact of metals such as copper (Cu) on benthic freshwater diatoms is poorly understood, even if diatoms are commonly used as water quality indicators. Our study aimed to elucidate the cellular targets of Cu toxicity and the mechanisms cells resort to counteract toxicity and to increase tolerance to Cu. A concerted approach analysing the biochemical, physiological and metabolome alterations in diatom cells was conducted by exposing the freshwater diatom Tabellaria flocculosa to 0, 0.3, 6 and 10μgCu/L. Cu was already toxic to T. flocculosa at concentrations common in environments and which are not usually considered to be contaminated (0.3μgCu/L). Under Cu impact, the metabolome of T. flocculosa changed significantly, especially at high concentrations (6 and 10μgCu/L). Cu toxicity was counteracted by increasing extracellular immobilization (EPS, frustulins), antioxidant (SOD, CAT) and detoxifying (GSTs) enzymes activity and low molecular weight antioxidants (GSH). These mechanisms were fuelled by higher energy production (increased ETS activity). At the highest Cu concentration (10μg/L), these processes were specially enhanced in an attempt to restrain the oxidative stress generated by high intracellular Cu concentrations. However, these mechanisms were not able to fully protect cells, and damage in membranes and proteins increased. Moreover, the decrease of hydroxylamine and unsaturated fatty acids and the increase of saturated fatty acids, 2-palmitoylglycerol, glycerol and diterpenoid compounds should be tested as new specific markers of Cu toxicity in future studies. This information can support the prediction of diatom behaviour in different Cu contamination levels, including highly impacted environments, such as mining scenarios, and may assist in environmental risk assessment policies and restoration programs.

Effects of water warming and acidification on bioconcentration, metabolization and depuration of pharmaceuticals and endocrine disrupting compounds in marine mussels (Mytilus galloprovincialis)

Warming and acidification are expected impacts of climate change to the marine environment. Besides, organisms that live in coastal areas, such as bivalves, can also be exposed to anthropogenic pollutants like pharmaceuticals (PhACs) and endocrine disrupting compounds (EDCs). In this study, the effects of warming and acidification on the bioconcentration, metabolization and depuration of five PhACs (sotalol, sulfamethoxazole, venlafaxine, carbamazepine and citalopram) and two EDCs (methylparaben and triclosan) were investigated in the mussel species (Mytilus galloprovincialis), under controlled conditions. Mussels were exposed to warming and acidification, as well as to the mixture of contaminants up to 15.7 μg L^-1 during 20 days; followed by 20 days of depuration. All contaminants bioconcentrated in mussels with levels ranging from 1.8 μg kg^-1 dry weight (dw) for methylparaben to 12889.4 μg kg^-1 dw for citalopram. Warming increased the bioconcentration factor (BCF) of sulfamethoxazole and sotalol, whereas acidification increased the BCF of sulfamethoxazole, sotalol and methylparaben. In contrast, acidification decreased triclosan levels, while both stressors decreased venlafaxine and citalopram BCFs. Warming and acidification facilitated the elimination of some of the tested compounds (i.e. sotalol from 50% in control to 60% and 68% of elimination in acidification and warming respectively). However, acidification decreased mussels' capacity to metabolize contaminants (i.e. venlafaxine). This work provides a first insight in the understanding of aquatic organisms' response to emerging contaminants pollution under warming and acidification scenarios.