Aquatic Microbial Communities Research Articles

Elevated Fungicide and Nutrient Concentrations Change Structure but not Function of Aquatic Microbial Communities.

Leaf decomposition is a key process in stream ecosystems within forested catchments; it is driven by microbial communities, particularly fungi and bacteria. These microorganisms make nutrients and energy bound in leaves available for wider parts of the food web. Leaf-associated microorganisms are subjected to anthropogenic pressures, such as the increased exposure to nutrients and fungicides associated with land-use change. We assessed the sensitivity of leaf-associated microbial communities with differing exposure histories, namely, from pristine (P) streams, and streams impacted by wastewater (W) and agricultural run-off (vineyards; V). In the laboratory, microbial communities were exposed to elevated nutrient (NO3-N: 0.2-18.0 mg/L, PO4-P: 0.02-1.8 mg/L) and fungicide concentrations (sum concentration 0-300 µg/L) in a fully crossed 3 × 4 × 4-factorial design over 21 days. Leaf decomposition and exoenzyme activity were measured as functional endpoints, and fungal community composition and microbial abundance served as structural variables. Overall, leaf decomposition did not differ between fungicide treatments or exposure histories. Nonetheless, substantial changes in the fungal community composition were observed after exposure to environmentally relevant fungicide concentrations. Elevated nutrient concentrations assisted leaf decomposition, and the effect size depended on the exposure history. The observed changes in the fungal community composition support the principle of functional redundancy, with highly efficient decomposers maintaining leaf decomposition. Environ Toxicol Chem 2024;00:1-12. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Microbial hitchhikers on microplastics: The exchange of aquatic microbes across distinct aquatic habitats.

Microplastics (MPs) have the potential to modify aquatic microbial communities and distribute microorganisms, including pathogens. This poses a potential risk to aquatic life and human health. Despite this, the fate of 'hitchhiking' microbes on MPs that traverse different aquatic habitats remains largely unknown. To address this, we conducted a 50-day microcosm experiment, manipulating estuarine conditions to study the exchange of bacteria and microeukaryotes between river, sea and plastisphere using a long-read metabarcoding approach. Our findings revealed a significant increase in bacteria on the plastisphere, including Pseudomonas, Sphingomonas, Hyphomonas, Brevundimonas, Aquabacterium and Thalassolituus, all of which are known for their pollutant degradation capabilities, specifically polycyclic aromatic hydrocarbons. We also observed a strong association of plastic-degrading fungi (i.e., Cladosporium and Plectosphaerella) and early-diverging fungi (Cryptomycota, also known as Rozellomycota) with the plastisphere. Sea MPs were primarily colonised by fungi (70%), with a small proportion of river-transported microbes (1%-4%). The mere presence of MPs in seawater increased the relative abundance of planktonic fungi from 2% to 25%, suggesting significant exchanges between planktonic and plastisphere communities. Using microbial source tracking, we discovered that MPs only dispersed 3.5% and 5.5% of river bacterial and microeukaryotic communities into the sea, respectively. Hence, although MPs select and facilitate the dispersal of ecologically significant microorganisms, drastic compositional changes across distinct aquatic habitats are unlikely.

In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer

Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.

The relationship between water quality and the microbial virulome and resistome in urban streams in Brazil

Urban streams that receive untreated domestic and hospital waste can transmit infectious diseases and spread drug residues, including antimicrobials, which can then increase the selection of antimicrobial-resistant bacteria. Here, water samples were collected from three different urban streams in the state of São Paulo, Brazil, to relate their range of Water Quality Indices (WQIs) to the diversity and composition of aquatic microbial taxa, virulence genes (virulome), and antimicrobial resistance determinants (resistome), all assessed using untargeted metagenome sequencing. There was a predominance of phyla Proteobacteria, Actinobacteria, and Bacteroidetes in all samples, and Pseudomonas was the most abundant detected genus. Virulence genes associated with motility, adherence, and secretion systems were highly abundant and mainly associated with Pseudomonas aeruginosa. Furthermore, some opportunistic pathogenic genera had negative correlations with WQI. Many clinically relevant antimicrobial resistance genes (ARGs) and efflux pump-encoding genes that confer resistance to critically important antimicrobials were detected. The highest relative abundances of ARGs were β-lactams and macrolide-lincosamide-streptogramin. No statistically supported relationship was detected between the abundance of virulome/resistome and collection type/WQI. On the other hand, total solids were a weak predictor of gene abundance patterns. These results provide insights into various microbial outcomes given urban stream quality and point to its ecological complexity. In addition, this study suggests potential consequences for human health as mediated by aquatic microbial communities responding to typical urban outputs.

Fluorescently labeled prey surrogates in combination with fluorescence‐activated cell sorting successfully discriminate actively feeding mixotrophs in a lake water sample

AbstractMixotrophic protists are capable of acting both as primary producers and primary consumers at the base of the aquatic food web, thus constituting key organisms in ecosystems where they are abundant. However, their identity, abundance, ecological dynamics, and biogeochemical impact in aquatic ecosystems remain understudied in comparison to classically demarcated autotrophs or heterotrophs. In this study, we make use of fluorescently labeled prey and fluorescence‐activated cell sorting to taxonomically identify actively‐feeding individual mixotrophic flagellates from lake water. Replicated experiments were carried out to assess the performance of three different fluorescently labeled prey types and a fluorescent dye targeting food vacuoles. In the experiments, water from an oligotrophic lake was exposed independently to each type of reporter and cells were individually sorted based on fluorescent signals for predation and chlorophyll a. A total of 927 individual single cells were successfully recovered, with all fluorescent reporters exhibiting high sensitivity for putative mixotrophic taxa: overall, 87% of the occurrences could be assigned to dictyochophytes, 9% to chrysophytes, and 3% to dinoflagellates. As a result, we were able to detect cryptic diversity within pedinellid algae and report a Prorocentrum‐like freshwater occurrence. We argue that this procedure can be a valuable tool to uncover relevant and unexpected active mixotrophic species in a wider range of aquatic environments, and could easily be coupled to other techniques to describe the finer details of the trophic status of aquatic microbial communities.

Something in the water: aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment and behaviour.

Microorganisms colonize the gastrointestinal tract of animals and establish symbiotic host-associated microbial communities that influence vertebrate physiology. More specifically, these gut microbial communities influence neurodevelopment through the microbiota-gut-brain (MGB) axis. We tested the hypothesis that larval amphibian neurodevelopment is affected by the aquatic microbial community present in their housing water. Newly hatched Northern Leopard Frog (Lithobates pipiens) tadpoles were raised in pond water that was unmanipulated (natural) or autoclaved. Tadpoles raised in autoclaved pond water had a gut microbiota with reduced bacterial diversity and altered community composition, had decreased behavioural responses to sensory stimuli, were larger in overall body mass, had relatively heavier brains and had altered brain shape when compared with tadpoles raised in natural pond water. Further, the diversity and composition of the gut microbiota were associated with tadpole behavioural responses and brain measurements. Our results suggest that aquatic microbial communities shape tadpole behaviour and brain development, providing strong support for the occurrence of the MGB axis in amphibians. Lastly, the dramatic role played by aquatic microbial communities on vertebrate neurodevelopment and behaviour should be considered in future wildlife conservation efforts.

Anaerobic dihydrogen consumption of nutrient-limited aquifer sediment microbial communities examined by stable isotope analysis

ABSTRACT The biogeochemical consequences of dihydrogen (H2) underground storage in porous aquifers are poorly understood. Here, the effects of nutrient limitations on anaerobic H2 oxidation of an aquifer microbial community in sediment microcosms were determined in order to evaluate possible responses to high H2 partial pressures. Hydrogen isotope analyses of H2 yielded isotope depletion in all biotic setups indicating microbial H2 consumption. Carbon isotope analyses of carbon dioxide (CO2) showed isotope enrichment in all H2-supplemented biotic setups indicating H2-dependent consumption of CO2 by methanogens or homoacetogens. Homoacetogenesis was indicated by the detection of acetate and formate. Consumption of CO2 and H2 varied along the differently nutrient-amended setups, as did the onset of methane production. Plotting carbon against hydrogen isotope signatures of CH4 indicated that CH4 was produced hydrogenotrophically and fermentatively. The putative hydrogenotrophic Methanobacterium sp. was the dominant methanogen. Most abundant phylotypes belonged to typical ferric iron reducers, indicating that besides CO2, Fe(III) was an important electron acceptor. In summary, our study provides evidence for the adaptability of subsurface microbial communities under different nutrient-deficient conditions to elevated H2 partial pressures.

Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity

BackgroundThe visual organ plays a crucial role in sensing environmental information. However, its mucosal surfaces are constantly exposed to selective pressures from aquatic or airborne pathogens and microbial communities. Although few studies have characterized the conjunctival-associated lymphoid tissue (CALT) in the ocular mucosa (OM) of birds and mammals, little is known regarding the evolutionary origins and functions of immune defense and microbiota homeostasis of the OM in the early vertebrates.ResultsOur study characterized the structure of the OM microbial ecosystem in rainbow trout (Oncorhynchus mykiss) and confirmed for the first time the presence of a diffuse mucosal-associated lymphoid tissue (MALT) in fish OM. Moreover, the microbial communities residing on the ocular mucosal surface contribute to shaping its immune environment. Interestingly, following IHNV infection, we observed robust immune responses, significant tissue damage, and microbial dysbiosis in the trout OM, particularly in the fornix conjunctiva (FC), which is characterized by the increase of pathobionts and a reduction of beneficial taxa in the relative abundance in OM. Critically, we identified a significant correlation between viral-induced immune responses and microbiome homeostasis in the OM, underscoring its key role in mucosal immunity and microbiota homeostasis.ConclusionsOur findings suggest that immune defense and microbiota homeostasis in OM occurred concurrently in early vertebrate species, shedding light on the coevolution between microbiota and mucosal immunity.1WNPLmNTzstteMxSNP_LzTVideo

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances.

Understanding the communities' responses to disturbances is a prerequisite to predicting ecosystem dynamics and, thus, highly relevant considering global change. Microbial communities play key roles in numerous ecosystem functions and services, and the large diversity, rapid growth, and phenotypic plasticity of microorganisms are thought to allow high resistance and resilience. While potential metabolic costs associated with adaptations to fluctuating environments have been debated, little evidence supports trade-offs between resource availability, resistance, and resilience. Here, we experimentally assessed the compositional and functional responses of an aquatic microbial model community to disturbances and systematically manipulated resource availability. Our results demonstrate that the capacity to tolerate environmental fluctuations is constrained by resource availability and reflected in the selection of genomic traits.

Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides.

High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affectedby physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.

Rainfall-induced changes in aquatic microbial communities and stability of dissolved organic matter: Insight from a Fen river analysis

Microbial communities are pivotal in aquatic ecosystems, as they affect water quality, energy dynamics, nutrient cycling, and hydrological stability. This study explored the effects of rainfall on hydrological and photosynthetic parameters, microbial composition, and functional gene profiles in the Fen River. Our results demonstrated that rainfall-induced decreases in stream temperature, dissolved oxygen, pH, total phosphorus, chemical oxygen demand, and dissolved organic carbon concentrations. In contrast, rainfall increased total dissolved solids, salinity, and ammonia-nitrogen concentrations. A detailed microbial community structure analysis revealed that Cyanobacteria was the dominant microbial taxon in the Fen River, accounting for approximately 75% and 25% of the microalgal and bacterial communities, respectively. The abundance of Chlorophyta and Bacillariophyta increased by 47.66% and 29.92%, respectively, whereas the relative abundance of Bacteroidetes decreased by 37.55% under rainfall conditions. Stochastic processes predominantly affected the assembly of the bacterial community on rainy days. Functional gene analysis revealed variations in bacterial functions between sunny (Sun) and rainy (Rain) conditions, particularly in genes associated with the carbon cycle. The 3-oxoacyl-[acyl-carrier-protein] reductase gene was more abundant in the Fen River bacterial community. Particular genes involved in metabolism and environmental information processing, including the acetyl-CoA C-acetyltransferase (atoB), enoyl-CoA hydratase (paaF), and branched-chain amino acid transport system gene (livK), which are integral to environmental information processing, were more abundant in Sun than the Rain conditions. In contrast, the phosphate transport system gene, the galactose metabolic gene, and the pyruvate metabolic gene were more abundant in Rain. The excitation-emission matrix analysis with parallel factor analysis identified four fluorescence components (C1–C4) in the river, which were predominantly protein- (C1) and humic-like (C2–C4) substances. Rainfall affected organic matter production and transport, leading to changes in the degradation and stability of dissolved organic matter. Overall, this study offers insight into how rainfall affects aquatic ecosystems.

Surfactants: hygiene’s first line of defence against pollution

Surfactants are a diverse group of compounds that are widely used in a range of industrial, commercial and household applications. They are amphiphilic molecules that contain both hydrophilic and hydrophobic groups, which allow them to interact with both water and oil. Surfactants have a number of important properties, including the ability to reduce surface tension, emulsify liquids and solubilise hydrophobic compounds. These properties make them valuable in a range of applications, including detergents (hygiene products), cosmetics, pharmaceuticals and agricultural products. However, the widespread use of surfactants has also raised concerns about their environmental impacts. This review provides an overview of the properties and applications of surfactants, as well as their environmental impacts, the different types of surfactants and their properties and uses in different applications and the current understanding of the environmental fate and impacts of surfactants, including their interactions with aquatic organisms, microbial communities and natural ecosystems. Finally, ths study discusses strategies for minimising the environmental impacts of surfactants, including the development of biodegradable and environmentally friendly surfactants.

Differences in biodiversity and assembly mechanisms between planktonic and benthic diatom communities in riverine ecosystems: A case study in the Ashi river

Diatoms are an indispensable component of river ecosystem biodiversity and play an important role in aquatic ecosystems. The community assembly mechanism of diatoms has always been a central issue in the study of aquatic ecology. In recent years, many measures have been implemented in the Ashi River Basin (ASRB) to promote social and economic development, such as bridge construction, river bottom sand mining, agricultural irrigation, and urban expansion. However, there are few studies on the effects of these activities on the mechanism of diatom community assembly. First, we found that the α- and β-diversity of planktonic diatoms was higher in the normal season, while the α- and β-diversity of benthic diatoms was higher in the dry season, and the α- and β-diversity of both planktonic and benthic diatoms was reduced in the wet season. Second, the community structures of planktonic and benthic diatoms were significantly different in different hydrological periods, and the differences between planktonic diatoms communities were more evident than those between benthic diatom communities. Third, distance-decay analysis indicated that the distribution of the two types of diatom communities in the ASRB was influenced by both dispersal limitation and environmental selection. Finally, variance partitioning analysis revealed that dispersal limitation was the dominant driving factor for the spatial and temporal differentiation of planktonic and benthic diatoms. Our study reveals the important role of dispersal limitation in the community assembly of planktonic and benthic diatoms in rivers under different hydrological conditions. This study provides new insights for further understanding the relative importance of niche theory and neutral theory to aquatic microbial community assembly. Our research provides key information for analysing the structure of aquatic ecosystems and basic data for designing biodiversity conservation strategies in China's cold watersheds.

A perspective on how glyphosate and 2,4-D in wetlands may impact climate change

An increase in herbicide use is occurring due to a growing population and herbicide-resistant crops in agriculture, which has resulted in more herbicide tolerant target species. Glyphosate and 2,4-Dichlorophenoxyacetic acid (2,4-D) are two of the most commonly used herbicides worldwide and are more recently being used in combination in pre-mixed commercial formulas. Subsequently, herbicide contamination of wetlands will increase exposure of microorganisms to multiple chemical stressors. Methane is a potent greenhouse gas naturally emitted from wetlands, but herbicides may disrupt biogeochemical processes leading to an unbalanced methane cycle. We review the impacts of these herbicides on aquatic microbial communities from glyphosate-derived nutrient enrichment and 2,4-D inhibition of methane oxidation, and examine how these altered metabolic processes may lead to increased methane production in wetlands. The response of wetland ecosystems to herbicide contamination will vary across regions, in part due to the complexity of microbial communities, however, this perspective gives a glimpse into the potential global implications of continuing herbicide use on wetlands and demonstrates the importance for research on ecosystem-level co-stressors.

Conserved cobalamin acquisition protein 1 is essential for vitamin B12 uptake in both Chlamydomonas and Phaeodactylum.

Microalgae play an essential role in global net primary productivity and global biogeochemical cycling. Despite their phototrophic lifestyle, over half of algal species depend for growth on acquiring an external supply of the corrinoid vitamin B12 (cobalamin), a micronutrient produced only by a subset of prokaryotic organisms. Previous studies have identified protein components involved in vitamin B12 uptake in bacterial species and humans. However, little is known about its uptake in algae. Here, we demonstrate the essential role of a protein, cobalamin acquisition protein 1 (CBA1), in B12 uptake in Phaeodactylum tricornutum using CRISPR-Cas9 to generate targeted knockouts and in Chlamydomonas reinhardtii by insertional mutagenesis. In both cases, CBA1 knockout lines could not take up exogenous vitamin B12. Complementation of the C. reinhardtii mutants with the wild-type CBA1 gene restored B12 uptake, and regulation of CBA1 expression via a riboswitch element enabled control of the phenotype. When visualized by confocal microscopy, a YFP-fusion with C. reinhardtii CBA1 showed association with membranes. Bioinformatics analysis found that CBA1-like sequences are present in all major eukaryotic phyla. In algal taxa, the majority that encoded CBA1 also had genes for B12-dependent enzymes, suggesting CBA1 plays a conserved role. Our results thus provide insight into the molecular basis of algal B12 acquisition, a process that likely underpins many interactions in aquatic microbial communities.

Micro-pressure promotes endogenous phosphorus release in a deep reservoir by favouring microbial phosphate mineralisation and solubilisation coupled with sulphate reduction

Deep reservoirs vary in their hydrostatic pressure owing to artificial water level control. The potential migration of phosphorus (P) in reservoir sediments raises the risk of harmful algal blooms. To ascertain the mechanisms of endogenous P release in reservoirs, we characterised aquatic microbial communities associated with coupled iron (Fe), P and sulphur (S) cycling at the sediment–water interface. The responses of microbial communities to hydrostatic pressures of 0.2–0.7 mega pascals (MPa; that is, micro-pressures) were investigated through a 30-day simulation experiment. Our findings unravelled a potential mechanism that micro-pressure enhanced the solubilisation of Fe/aluminium (Al)-bound P caused by microbially-driven sulphate reduction, leading to endogenous P release in the deep reservoir. Although the vertical distribution of labile Fe was not affected by pressure changes, we did observe Fe resupply at sediment depths of 2–5 cm. Metagenomic analysis revealed increased abundances of functional genes for P mineralisation (phoD, phoA), P solubilisation (pqqC, ppx-gppA) and sulphate reduction (cysD, cysC) in sediments subjected to micro-pressure, which contrasted with the pattern of S oxidation gene (soxB). There was a tight connection between P and S cycling-related microbial communities, based on significant positive correlations between labile element (P and S) concentrations and functional gene (phoD, cysD) abundances. This provided strong support that Fe–P–S coupling processes were governed by micro-pressure through modulation of P and S cycling-related microbial functions. Key taxa involved in P and S cycling (for example, Bradyrhizobium, Methyloceanibacter) positively responded to micro-pressure and as such, indirectly drove P release from sediments by facilitating P mineralisation and solubilisation coupled with sulphate reduction.

Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans

Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) than roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiome in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.

Twenty Years of Research in Ecosystem Functions in Aquatic Microbial Ecotoxicology.

One of the major threats to freshwater biodiversity is water pollution including excessive loads of nutrients, pesticides, industrial chemicals, and/or emerging contaminants. The widespread use of organic pesticides for agricultural and nonagricultural (industry, gardening, etc.) purposes has resulted in the presence of their residues in various environments, including surface waters. However, the contribution of pesticides to the deterioration of freshwater ecosystems (i.e., biodiversity decline and ecosystem functions impairment) remains uncertain. Once in the aquatic environment, pesticides and their metabolites can interact with microbial communities, causing undesirable effects. The existing legislation on ecological quality assessment of water bodies in Europe is based on water chemical quality and biological indicator species (Water Framework Directive, Pesticides Directive), while biological functions are not yet included in monitoring programs. In the present literature review, we analyze 20 years (2000-2020) of research on ecological functions provided by microorganisms in aquatic ecosystems. We describe the set of ecosystem functions investigated in these studies and the range of endpoints used to establish causal relationships between pesticide exposure and microbial responses. We focus on studies addressing the effects of pesticides at environmentally realistic concentrations and at the microbial community level to inform the ecological relevance of the ecotoxicological assessment. Our literature review highlights that most studies were performed using benthic freshwater organisms and that autotrophic and heterotrophic communities are most often studied separately, usually testing the pesticides that target the main microbial component (i.e., herbicides for autotrophs and fungicides for heterotrophs). Overall, most studies demonstrate deleterious impacts on the functions studied, but our review points to the following shortcomings: (1) the nonsystematic analysis of microbial functions supporting aquatic ecosystems functioning, (2) the study of ecosystem functions (i.e., nutrient cycling) via proxies (i.e., potential extracellular enzymatic activity measurements) which are sometimes disconnected from the current ecosystem functions, and (3) the lack of consideration of chronic exposures to assess the impact of, adaptations to, or recovery of aquatic microbial communities from pesticides. Environ Toxicol Chem 2023;00:1-22. © 2023 SETAC.

Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms

The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and ~7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell−1 /~127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (102– 108 copies cell−1) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (105 – 107 cell−1) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20–22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0–102 copies cell−1, was significantly related to PSTs (ng cell−1), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.

Effect of chlorpyrifos on freshwater microbial community and metabolic capacity of zebrafish

Chlorpyrifos is a widely used organophosphorus insecticide because of its high efficiency and overall effectiveness, and it is commonly detected in aquatic ecosystems. However, at present, the impact of chlorpyrifos on the aquatic micro-ecological environment is still poorly understood. Here, we established aquatic microcosm systems treated with 0.2 and 2.0 µg/L chlorpyrifos, and employed omics biotechnology, including metagenomics and 16S rRNA gene sequencing, to investigate the effect of chlorpyrifos on the composition and functional potential of the aquatic and zebrafish intestinal microbiomes after 7 d and 14 d chlorpyrifos treatment. After 14 d chlorpyrifos treatment, the aquatic microbial community was adversely affected in terms of its composition, structure, and stability, while its diversity showed only a slight impact. Most functions, especially capacities for environmental information processing and metabolism, were destroyed by chlorpyrifos treatment for 14 d. We observed that chlorpyrifos increased the number of risky antibiotic resistance genes and aggravated the growth of human pathogens. Although no clear effects on the structure of the zebrafish intestinal microbial community were observed, chlorpyrifos treatment did alter the metabolic capacity of the zebrafish. Our study highlights the ecological risk of chlorpyrifos to the aquatic environment and provides a theoretical basis for the rational use of pesticides in agricultural production.