Could benthic biofilm analyses be used as a reliable proxy for freshwater environmental health?

Does exposure timing of macrolide antibiotics affect the development of river periphyton? Insights into the structure and function

Discharged sewage is the dominant source of urban river pollution. Macrolide antibiotics have emerged as prominent contaminants, which are frequently detected in sewage and rivers and pose a threat to aquatic microbial community. As a typical primary producer, periphyton is crucial for maintaining the biodiversity and functions of aquatic ecosystem. However, effects of antibiotic exposure time as well as the recovery process of periphyton remain undetermined. In the present study, five exposure scenarios of two typical macrolides, erythromycin (ERY) and roxithromycin (ROX) were investigated at 50 µg/L, dose to evaluate their potential detrimental effects on the structure and function of periphyton and the subsequent recovery process in 14 days. Results revealed that the composition of periphytic community returned to normal over the recovery period, except for a few sensitive species. The antibiotics-caused significant photodamage to photosystem II, leading to continuous inhibition of the photosynthetic capacity of periphyton. Furthermore, no significant difference in carbon metabolism capacity was observed after direct antibiotic exposure, while the amine carbon utilization capacity of periphyton remarkably increased during the recovery process. These results indicated that periphyton community was capable of coping with the periodic exposure of antibiotic pollutants and recovering on its own. However, the ecological functions of periphyton can be permanently disturbed due to macrolide exposure. Overall, this study sheds light on the influence of macrolide exposure on the development, structure and function of the periphytic microbial community in rivers.

Relationship between stream size, watershed land use, and pesticide concentrations in headwater streams

A quantitative multiresidue study of current-use pesticides in multiple matrices was undertaken with field sampling at 32 headwater streams near Lac Saint-Pierre in Québec, Canada. A total of 232 samples were collected in five campaigns of stream waters and streambed sediments from streams varying in size and watershed land use. Novel multiresidue analytical methods from previous work were successfully applied for the extraction of pesticide residues from sediments via pressurized liquid extraction (PLE) and quantitative analysis using ultra high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) with online sample preparation on a hydrophilic-lipophilic balance (HLB) column. Of the 31 target compounds, including 29 pesticides and two degradation products of atrazine, 29 compounds were detected at least once. Consistent with other studies, atrazine and metolachlor were the most widely-detected herbicides. Detections were generally higher in water than sediment samples and the influence of land use on pesticide concentrations was only detectable in water samples. Small streams with a high proportion of agricultural land use in their watershed were generally found to have the highest pesticide concentrations. Corn and soybean monoculture crops, specifically, were found to cause the greatest impact on pesticide concentration in headwater streams and correlated strongly with many of the most frequently detected pesticides. This study highlights the importance of performing multiresidue pesticide monitoring programs in headwater streams in order to capture the impacts of agricultural intensification on freshwater ecosystems.

Towards the fate of antibiotics and the development of related resistance genes in stream biofilms

Antibiotics are ubiquitously found in natural surface waters and cause great harm to aquatic organisms. Stream biofilm is a complex and active community composed of algae, bacteria, fungi and other microorganisms, which mainly adheres to solid substances such as rocks and sediments. The durability and diverse structural and metabolic characteristics of biofilms make them a representative of microbial life in aquatic micrecosystems and can reflect major ecosystem processes. Microorganisms and extracellular polymeric substances in biofilms can adsorb and actively accumulate antibiotics. Therefore, biofilms are excellent biological indicators for detecting antibiotic in polluted aquatic environments, but the biotransformation potential of stream biofilms for antibiotics has not been fully explored in the aquatic environment. The characteristics of stream biofilm, such as high abundance and activity of bacterial community, wide contact area with pollutants, etc., which increases the opportunity of biotransformation of antibiotics in biofilm and contribute to bioremediation to improve ecosystem health. Recent studies have demonstrated that both exposure to high and sub-minimum inhibitory concentrations of antibiotics may drive the development of antibiotic resistance genes (ARGs) in natural stream biofilms, which are susceptible to the effects of antibiotic residues, microbial communities and mobile genetic elements, etc. On the basis of peer-reviewed papers, this review explores the distribution behavior of antibiotics in stream biofilms and the contribution of biofilms to the acquisition and spread of antibiotic resistance. Considering that antibiotics and ARGs alter the structure and ecological functions of natural microbial communities and pose a threat to river organisms and human health, our research findings provide comprehensive insights into the migration, transformation, and bioavailability of antibiotics in biofilms.

Life in an unsuspected antibiotics world: River biofilms

Waterborne bacteria that naturally live in biofilms are continuously exposed to pharmaceutical residues, regularly released into the freshwater environment. At the source level, the discharge of antibiotics into rivers has already been repeatedly linked to the development of antimicrobial resistance. But what about biofilms away from the discharge point? Two rivers, with sites subject to dispersed contamination of medium intensity, were studied as typical representatives of high- and middle-income countries. The biofilms developed on rocks indigenous to rivers are perfectly representative of environmental exposure. Our results show that away from the hotspots, the amount of antibiotics in the biofilms studied favours the maintenance and enrichment of existing resistant strains as well as the selection of new resistant mutants, and these favourable conditions remain over a period of time. Thus, in this type of river, the environmental risk of selection pressure is not only present downstream of urbanized areas but is also possible upstream and far downstream of wastewater treatment plant discharges. Despite this, correlation analysis found no strong positive correlation between antibiotic concentrations and the abundance of measured integrons and their corresponding resistance genes. Nevertheless, this work highlights the need to consider the risks of antibiotics beyond hotspots as well.

Impact of exposure to arsenic on the bacterial microbiota associated with river biofilms in the Pampas region

Freshwater contamination by arsenic (As) is a worldwide problem. It may be found in Pampean streams of Argentina at concentrations higher than those recommended by international organizations and stipulated by national regulations. Exposure to high As concentrations causes serious consequences to both human health and the environment. The general objective of this work was to evaluate the effect of As on the biofilm microbiota structure from Naveira stream, Luján, Province of Buenos Aires (Coordinates: 34º34'02″ S 59º03'51″ W). The biofilm collected was cultivated in glass aquaria at different As III concentrations (0, 0.2 and 20 mg / L), inside incubation chambers under controlled conditions (16 h light: 8 h dark and 24 ± 1 °C) and constant aeration for 31 d, with partial water renewal every 9 d. We amplified the hypervariable regions V3 and V4 of the bacterial 16S rRNA gene from biofilm bacterial community samples to determine the diversity and abundance of the different taxa. The taxonomic composition of each sample, the alpha diversity of each treatment and the main metabolic pathways were analyzed. Principal Component Analysis of the present phyla and a Linear Discriminant Analysis of the metabolic pathways was also performed. Significant changes were observed in relation to the taxonomic composition of the bacterial community after exposure to the metalloid. However, this effect was not observed at the low concentration used (0.2 mg / L), which is the one that corresponds to ecologically relevant levels. The significantly affected phyla were Verrucomicrobiota, Acidobacteriota, Patescibacteria, Hydrogenedentes and WPS-2. The relative abundances of the Verrucomicrobiota, WPS-2 and Patescibacteria groups were notably decreased in the treatment with high As, while the Acidobacteria group was increased in both treatments with As. The stream samples showed greater bacterial diversity than those grown in the laboratory without As. Finally, it was possible to characterize the metabolic profile of the biofilm developed under natural conditions in the leaves of the aquatic plant Elodea canadensis in the Naveira stream. In addition, results showed that biosynthesis-related pathways were more abundant at the high As concentration treatment (20 mg / L).

Occurrence and accumulation of pharmaceutical products in water and biota of urban lowland rivers

We evaluated the distribution of eleven groups of pharmaceutically active compounds (PhACs) in surface waters and biota of different trophic levels, in five sites of two lowland urban rivers in Argentine. Twenty-nine out of 39 PhACs and two metabolites were detected in at least one water sample (2-9622 ng/L), eleven detected in biofilms (1-179 ng/g d.w_.) and eight in the macrophyte Lemna gibba (4-112 ng/g d.w). The two more polluted sites had a similar distribution of the main groups of compounds. In surface waters, the largest concentrations were for the analgesic acetaminophen (9622 ng/L), the antibiotic sulfamethoxazole (326 ng/L), the antihypertensive valsartan (963 ng/L), the β-blocking agent atenolol (427 ng/L), the diuretic hydrochlorothiazide (445 ng/L) and the psychiatric drug carbamazepine (99 ng/L). The antibiotic ciprofloxacin exhibited the highest concentration in the biofilm (179 ng/g d.w_.) and in the macrophyte L. gibba (112 ng/g d.w_.) Several compounds were detected in the water but not in the biota (e.g., codeine and bezafibrate), and others (e.g., azithromycin and citalopram) were found in the biota but not in the surface water. Significant bioaccumulation factors (>1000 L/kg d.w.) were obtained for venlafaxine and ciprofloxacin in biofilm. Our results show that PhACs may accumulate in several biological compartments. Within an environmental compartment, similar PhACs profile and concentrations were found in different sites receiving urban pollution. Among different compartments, biofilms may be the most suitable biota matrix to monitor the immediate reception of PhACs in the biota. Our results indicate that the presence of PhACs in urban rivers and their accumulation in the biota could be incorporated as symptoms of the urban stream syndrome.

Cross-regional scale pollution of freshwater biofilms unveiled by antibiotic resistance genes

A comprehensive global profile of the distribution of ARGs in freshwater biofilms is lacking. We utilized metagenomic approaches to reveal the diversity, abundance, transferability and hosts of ARGs in 96 freshwater biofilm samples from 38 sampling sites across four countries. The abundant ARGs were associated with bacitracin, multidrug, polymyxin macrolide-lincosamide-streptogramin (MLS) aminoglycoside, β-lactam, chloramphenicol, sulfonamide and tetracycline resistance, consistent with the spectrum of antibiotics commonly used in human or veterinary medicine. As expected, the resistome in freshwater biofilm habitats was significantly influenced by geographical location and human footprint. Based on the co-occurrence pattern revealed by network analysis, mdtC, kdpE, and emrB were proposed as ARG indicators in freshwater biofilms that can be used to evaluate the abundance of 46 other co-occurring ARG subtypes quantitatively. Metagenomic assembly analysis revealed that the identified ARGs were hosted by more than 46 bacterial phyla, including various pathogens, which greatly expands the knowledge of resistome diversity in freshwater biofilms. Our study points to the central roles of biofilms in harbouring ARGs. The results could enhance understanding the distribution of ARGs in freshwater habitats, thereby strengthening the global environmental risk assessment and management of ARGs.

Benthic Biofilm Bacterial Communities and Their Linkage with Water-Soluble Organic Matter in Effluent Receivers

Benthic biofilms are pioneering microbial aggregates responding to effluent discharge from wastewater treatment plants (WWTPs). However, knowledge of the characteristics and linkage of bacterial communities and water-soluble organic matter (WSOM) of benthic biofilms in effluent-receiving rivers remains unknown. Here, we investigated the quality of WSOM and the evolution of bacterial communities in benthic biofilm to evaluate the ecological impacts of effluent discharge on a representative receiving water. Tryptophan-like proteins showed an increased proportion in biofilms collected from the discharge area and downstream from the WWTP, especially in summer. Biofilm WSOM showed weak humic character and strong autochthonous components, and species turnover was proven to be the main factor governing biofilm bacteria community diversity patterns. The bacterial community alpha diversity, interspecies interaction, biological index, and humification index were signally altered in the biofilms from the discharge area, while the values were more similar in biofilms collected upstream and downstream from the WWTP, indicating that both biofilm bacterial communities and WSOM characters have resilience capacities. Although effluent discharge simplified the network pattern of the biofilm bacterial community, its metabolic functional abundance was basically stable. The functional abundance of carbohydrate metabolism and amino acid metabolism in the discharge area increased, and the key modules in the non-random co-occurrence network also verified the important ecological role of carbon metabolism in the effluent-receiving river. The study sheds light on how benthic biofilms respond to effluent discharge from both ecological and material points of view, providing new insights on the feasibility of utilizing benthic biofilms as robust indicators reflecting river ecological health.

Active Microbiome Structure and Functional Analyses of Freshwater Benthic Biofilm Samples Influenced by RNA Extraction Methods

Advances in high-throughput sequencing technologies have enabled extensive studies of freshwater biofilms and significant breakthroughs in biofilm meta-omics. To date, however, no standardized protocols have been developed for the effective isolation of RNA from freshwater benthic biofilms. In this study, we compared column-based kit RNA extraction with five RNAzol-based extractions, differentiated by various protocol modifications. The RNA products were then evaluated to determine their integrity, purity and yield and were subjected to meta-transcriptomic sequencing and analysis. Significant discrepancies in the relative abundance of active communities and structures of eukaryotic, bacterial, archaebacterial, and viral communities were observed as direct outcomes of the tested RNA extraction methods. The column isolation-based group was characterized by the highest relative abundance of Archaea and Eukaryota, while the organic isolation-based groups commonly had the highest relative abundances of Prokaryota (bacteria). Kit extraction methods provided the best outcomes in terms of high-quality RNA yield and integrity. However, these methods were deemed questionable for studies of active bacterial communities and may contribute a significant degree of bias to the interpretation of downstream meta-transcriptomic analyses.

Distribution of antibiotics in water, sediments and biofilm in an urban river (Córdoba, Argentina, LA)

In this study, we evaluated the distribution of up to forty-three antibiotics and 4 metabolites residues in different environmental compartments of an urban river receiving both diffuse and point sources of pollution. This is the first study to assess the fate of different antibiotic families in water, biofilms and sediments simultaneously under a real urban river scenario. Solid phase extraction, bead-beating disruption and pressurized liquid extraction were applied for sample preparation of water, biofilm and sediment respectively, followed by the quantification of target antibiotics by UPLC-ESI-MS/MS. Twelve antibiotics belonging to eight chemical families were detected in Suquía River samples (67% positive samples). Sites downstream the WWTP discharge were the most polluted ones. Concentrations of positive samples ranged 0.003-0.29 µg L^-1 in water (max. cephalexin), 2-652 µg kg^-1_d.w. in biofilm (max. ciprofloxacin) and 2-34 µg kg^-1_d.w. in sediment (max. ofloxacin). Fluoroquinolones, macrolides and trimethoprim were the most frequently detected antibiotics in the three compartments. However cephalexin was the prevalent antibiotic in water. Antibiotics exhibited preference for their accumulation from water into biofilms rather than in sediments (bioaccumulation factors > 1,000 L kg^-1_d.w. in biofilms, while pseudo-partition coefficients in sediments < 1,000 L kg^-1_d.w.). Downstream the WWTP there was an association of antibiotics levels in biofilms with ash-free dry weight, opposite to chlorophyll-a (indicative of heterotrophic communities). Cephalexin and clarithromycin in river water were found to pose high risk for the aquatic ecosystem, while ciprofloxacin presented high risk for development of antimicrobial resistance. This study contributes to the understanding of the fate and distribution of antibiotic pollution in urban rivers, reveals biofilm accumulation as an important environmental fate, and calls for attention to government authorities to manage identified highly risk antibiotics.

The role of organic matrices in the fate of hydrophobic pesticides: An outdoor stream mesocosm study

To assess potential aquatic pesticide risks, environmental monitoring strategies often focus on water and sediment. However, knowledge gaps with regard to the pollution status of organic matrices important for the structure and functioning of aquatic ecosystems do exist. The present study assessed the dissipation of the triazole fungicide tebuconazole (TEB; K_OW = 5.01 × 10³) and the pyrethroid insecticide etofenprox (ETO; K_OW = 7.94 × 10⁶) as model hydrophobic pesticide compounds among aquatic plants, vertical layers of allochthonous leaf litter, and detritus within flow-through outdoor stream mesocosms. During a 3-h pesticide exposure and a subsequent 24-h post-exposure period, retention was higher for ETO (max concentration: Myriophyllum spicatum > Elodea nuttallii > Ranunculus fluitans > Potamogeton perfoliatus ≫ leaf litter > detritus) and depended amongst other factors on surface area, while in the water compartment the pesticides reached concentration levels < LOQ 2 h after exposure. Desorption was observed for both pesticides in plants, and for TEB in detritus, while in leaves the ETO levels even increased over time, suggesting leaf litter to be a suitable additional sampling matrix for transient hydrophobic pesticide peaks, yet also a potential source of contamination for invertebrate shredders. The upper layer of leaf material contained higher ETO levels than those situated further in the sediment, which implies short-term positive effects for species inhabiting the deeper leaf layers, yet again pinpoints to a potential pesticide exposure pathway via organic matter in aquatic systems.

A statistical approach for modelling the physical process of bacterial attachment to abiotic surfaces

A statistical approach using a polynomial linear model in combination with a probability distribution model was developed to mathematically represent the process of bacterial attachment and study its mechanism. The linear deterministic model was built based on data from experiments investigating bacterial and substratum surface physico-chemical factors as predictors of attachment. The prediction results were applied to a normal-approximated binomial distribution model to probabilistically predict attachment. The experimental protocol used mixtures of Streptococcus salivarius and Escherichia coli, and mixtures of porous poly(butyl methacrylate-co-ethyl dimethacrylate) and aluminum sec-butoxide coatings, at varying ratios, to allow bacterial attachment to substratum surfaces across a range of physico-chemical properties (including the surface hydrophobicity of bacterial cells and the substratum, the surface charge of the cells and the substratum, the substratum surface roughness and cell size). The model was tested using data from independent experiments. The model indicated that hydrophobic interaction was the most important predictor while reciprocal interactions existed between some of the factors. More importantly, the model established a range for each factor within which the resultant attachment is unpredictable. This model, however, considers bacterial cells as colloidal particles and accounts only for the essential physico-chemical attributes of the bacterial cells and substratum surfaces. It is therefore limited by a lack of consideration of biological and environmental factors. This makes the model applicable only to specific environments and potentially provides a direction to future modelling for different environments.

Detection, occurrence, and fate of emerging contaminants in agricultural environments (2020)

A review of 79 papers published in 2019 is presented. The topics ranged from detailed descriptions of analytical methods, to fate and occurrence studies, to ecological effects and sampling techniques for a wide variety of emerging contaminants likely to occur in agricultural environments. New methods and studies on veterinary pharmaceuticals, antibiotics, anthelmintics, and engineered nanomaterials in agricultural environments continue to expand our knowledge base on the occurrence and potential impacts of these compounds. This review is divided into the following sections: Introduction, Analytical Methods, Antibiotics in Agroecosystems, Pharmaceutical Fate and Occurrence, Anthelmintics and Engineered Nanomaterials. PRACTITIONER POINTS: New research describes innovative new techniques for emerging contaminant detection in agricultural settings Newer classes of contaminants include human and veterinary pharmaceuticals Research in nanomaterials show that these also occur in agricultural environments and will likely be topics of future work.

Biomass addition alters community assembly in ultrafiltration membrane biofilms

Freshwater biofilms assemble from a pool of rare water column genotypes. Random density fluctuations and temporal species turnover of functionally equivalent potential colonizers result in compositional variability of newly formed biofilm communities. We hypothesized that stronger environmental filtering as induced by enhanced substrate levels might reduce the impact of a locally variable pool of colonizers and instead select for more universal habitat specialists. Our model were heterotrophic biofilms that form on membranes during gravity-driven ultrafiltration of lake water. In four separate experiments, biomass of the cyanobacterium Microcystis was added to the feed water of one set of treatments (BM) and the resulting biofilm communities were compared to unamended controls (CTRL). Biomass addition led to a significant shift of community assembly processes: Replicate BM biofilms were more similar to each other than by chance in 3 of 4 experiments, whereas the opposite was the case for CTRL communities. Moreover, BM communities were more stochastically assembled across experiments from a common 'regional' pool of biofilm colonizers, whereas the composition of CTRL communities was mainly determined by experiment-specific 'local' genotypes. Interestingly, community assembly processes were also related to both, physiology (aerobic vs. anaerobic lifestyle) and the phylogenetic affiliation of biofilm bacteria.

Biofilms Provide New Insight into Pesticide Occurrence in Streams and Links to Aquatic Ecological Communities

Streambed sediment is commonly analyzed to assess occurrence of hydrophobic pesticides and risks to aquatic communities. However, stream biofilms also have the potential to accumulate pesticides and may be consumed by aquatic organisms. To better characterize risks to aquatic life, the U.S. Geological Survey Regional Stream Quality Assessment measured 93 current-use and 3 legacy pesticides in bed sediment and biofilm from 54 small streams in California across a range of land-use settings. On average, 4 times as many current-use pesticides were detected in biofilm at a site (median of 2) as in sediment (median of 0.5). Of 31 current-use pesticides detected, 20 were detected more frequently in biofilm than in sediment and 10 with equal frequency. Pyrethroids as a class were the most potentially toxic to benthic invertebrates, and of the 9 pyrethroids detected, 7 occurred more frequently in biofilm than sediment. We constructed general additive models to investigate relations between pesticides and 6 metrics of benthic community structure. Pesticides in biofilm improved fit in 4 of the 6 models, and pesticides in sediment improved fit in 2. The results indicate that the sampling of stream biofilms can complement bed-sediment sampling by identification of more current-use pesticides present and better estimation of ecological risks.

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system

BACKGROUND

Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across steep gradients of water temperature and salinity.

RESULTS

Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. To better characterise the indigenous skin community, we excluded bacteria that were equally abundant in the skin samples and in the water samples, from our analysis of the skin samples. With this in mind, we found alpha diversity of the skin communities to be stable across sites, but higher in benthic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water community contamination from the fish skin communities. Finally, we found that human-induced eutrophication promotes dysbiosis of the fish skin community, with signatures relating to fish health.

CONCLUSIONS

Consideration of the background water microbiome when studying fish skin microbiomes, across varying fish species and water properties, exposes patterns otherwise undetected and highlight among-fish-species differences. We suggest that sporadic nutrient pollution events, otherwise undetected, drive fish skin communities to dysbiosis. This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring. Video abstract.