The mechanisms behind nitrogen removal by the submersed macrophyte-biofilm complex in wetlands remain to be fully elucidated. This study investigated the role of Myriophyllum spicatum and the biofilm on their leaves in nitrogen removal in mesocosm experiments. ¹⁵N tracking showed that 61.9% and 30% of the ¹⁵N, respectively, was removed from the system and assimilated by the macrophyte-biofilm complex after loading with 5.4 mg L⁻¹¹⁵N labelled NH₄⁺ for 17 days. Nitrogen budget results showed that about 0.2%, 0.2% and 3.6% of the nitrogen were emitted as water-, HCl- and NaOH-soluble nitrogen-gas species, respectively. Bacteria (76.7–91.8%) were the predominant domain in all samples, followed by eukaryotes (8.0–23.0%), archaea and viruses. Network analyses showed that there were positive- and negative-correlative relationships among nitrogen-cycling genes and nitrifiers and denitrifiers. Our data highlight the important role of biofilm on submersed macrophytes for nitrogen removal.

Acid mine drainage (AMD),characterized by strong acidity and high metal concentrations, generates from the oxidative dissolution of metal sulfides, and acidophiles can accelerate the process significantly. Despite extensive research in microbial diversity and community composition, little is known about seasonal variations of microbial community structure (especially micro eukaryotes) in response to environmental conditions in AMD ecosystem. To this end, AMD samples were collected from Nanshan AMD lake, Anhui Province, China, over a full seasonal cycle from 2013 to 2014, and water chemistry and microbial composition were studied. pH of lake water was stable (∼3.0) across the sampling period, while the concentrations of ions varied dramatically. The highest metal concentrations in the lake were found for Mg and Al, not commonly found Fe. Unexpectedly, ultrahigh concentration of chlorophyll a was measured in the extremely acidic lake, reaching 226.43–280.95 μg/L in winter, even higher than those in most eutrophic freshwater lakes. Both prokaryotic and eukaryotic communities showed a strong seasonal variation. Among the prokaryotes, “Ferrovum”, a chemolithotrophic iron-oxidizing bacterium was predominant in most sampling seasons, although it was a minor member prior to September, 2012. Fe2+ was the initial geochemical factor that drove the variation of the prokaryotic community. The eukaryotic community was simple but varied more drastically than the prokaryotic community. Photoautotrophic algae (primary producers) formed a food web with protozoa or flagellate (top consumers) across all four seasons, and temperature appeared to be responsible for the observed seasonal variation. Ochromonas and Chlamydomonas (responsible for high algal bloom in winter) occurred in autumn/summer and winter/spring seasons, respectively, because of their distinct growth temperatures. The closest phylogenetic relationship between Chlamydomonas species in the lake and those in Arctic and Alpine suggested that the native Chlamydomonas species may have been both acidophilic and psychrophilic after a long acclimation time in this extreme environment.

Acid mine drainage (AMD) is generated by the bio-oxidation of sulfide minerals. To understand the AMD formation and evolution, it is necessary to determine the composition and variation of acidophilic community, and their role in AMD ecosystem. In this study, we compared seasonal variations of geochemistry and microbial composition of two adjacent AMD lakes with different formation histories in Anhui Province, China. Lake Paitu (PT) formed in 1970s near a mine dump and the pH was in the range of 3.01–3.16, with the lowest in spring and summer while the highest in winter. The main ions in PT were Al and SO₄²⁻, whereas Fe concentration was relatively low. The concentrations of these ions were the lowest in summer and the highest in winter. Lake Tafang (TF) formed in around 2013 in a pit was more acidic (pH 2.43–2.75), but the seasonal variation of pH was the same as PT. Compared with Lake PT, TF had higher Fe, lower Al and SO₄²⁻ concentrations, and showed no significant seasonal changes. Despite salient seasonal variations of prokaryotic composition in Lake PT, Ferrovum was the major iron-oxidizing bacterium in most seasons. Furthermore, Lake PT was also rich in heterotrophic bacteria (48.6 ± 15.9%). Both prokaryotic diversity and evenness of Lake TF were lower than PT, and chemolithotrophic iron-oxidizing bacteria (71.7 ± 25.4%) were dominant in almost all samples. Besides Ferrovum, more acid tolerant iron-oxidizer Leptospirillum and Acidithiobacillus were also abundant in Lake TF. Chlamydomonas was the major eukaryote in Lake PT and it flourished repeatedly at the end of December, causing an extremely high chlorophyll a concentration (587 μg/L) at one sampling site in 2016, which provided rich nutrients for heterotrophic bacteria. The main alga in Lake TF was Chrysonebula, but its concentration was low, apparently because of the strong acidity and dark red color of lake water.

Sertraline is a widely used antidepressant that becomes an aquatic pollutant through metabolic excretion and improper disposal. Determining the impact of sertraline on benthic microbial ecosystems is important for the transformation of river biogenic elements. However, the molecular initiating event induced by sertraline is more readily observed at higher levels, such as the individual or population level of larger organisms, and the effect is not pronounced in benthic organisms, which are directly involved in nitrogen transformation. Therefore, this study used DNA metabarcoding to analyze the effect of sertraline on the microbial ecosystem and material cycles in river sediment through the lens of a microbial food web. The presence of sertraline in the river sediment enhanced the mineralization capacity of nitrogen and increased the accumulation of nitrate in the sediment. Sertraline affected the structure of the microbial food web by stimulating different successions of bacteria and eukaryotes. A structural equation model revealed that sertraline affected the microbial food web model through top-down forces (predation) by reducing the trophic transfer efficiency from metazoans to protozoans. This effect resulted in decreases in the trophic transfer efficiency from protozoans to bacteria and increases in nitrogen mineralization capacity. This was followed by a gradual increase in the nitrification reaction under the action of nitrifying bacteria, increasing the threat to the ecological health of rivers. The results show that sertraline affects the material cycle of river ecosystems and emphasizes that the assessment of the ecological risks of sertraline needs to be considered from the perspective of the material cycle of ecosystems.

DNA-derived measurements of biological composition have the potential to produce data covering all of life, and provide a tantalizing proposition for researchers and managers. We used metabarcoding to compare benthic eukaryote composition from five estuaries of varying condition. In contrast to traditional studies, we found biotic richness was greatest in the most disturbed estuary, with this being due to the large volume of extraneous material (i.e. run-off from aquaculture, agriculture and other catchment activities) being deposited in the system. In addition, we found strong correlations between composition and a number of environmental variables, including nutrients, pH and turbidity. A wide range of taxa responded to these environmental gradients, providing new insights into their sensitivities to natural and anthropogenic stressors. Metabarcoding has the capacity to bolster current monitoring techniques, enabling the decisions regarding ecological condition to be based on a more holistic view of biodiversity.

To understand the fate of plastic in oceans and the interaction with marine organisms, we investigated the incorporation of (bio)polymers and microplastics in selected benthic foraminiferal species by applying FTIR (Fourier Transform Infrared) microscopy. This experimental methodology has been applied to cultured benthic foraminifera Rosalina globularis, and to in situ foraminifera collected in a plastic remain found buried into superficial sediment in the Mediterranean seafloor, Rosalina bradyi, Textularia bocki and Cibicidoides lobatulus. In vitro foraminifera were treated with bis-(2-ethylhexyl) phthalate (DEHP) molecule to explore its internalization in the cytoplasm. Benthic foraminifera are marine microbial eukaryotes, sediment-dwelling, commonly short-lived and with reproductive cycles which play a central role in global biogeochemical cycles of inorganic and organic compounds. Despite the recent advances and investigations into the occurrence, distribution, and abundance of plastics, including microplastics, in marine environments, there remain relevant knowledge gaps, particularly on their effects on the benthic protists. No study, to our knowledge, has documented the molecular scale effect of plastics on foraminifera.Our analyses revealed three possible ways through which plastic-related molecules and plastic debris can enter a biogeochemical cycle and may affect the ecosystems: 1) foraminifera in situ can grow on plastic remains, namely C. lobatulus, R. bradyi and T. bocki, showing signals of oxidative stress and protein aggregation in comparison with R. globularis cultured in negative control; 2) DEHP can be incorporated in the cytoplasm of calcareous foraminifera, as observed in R. globularis; 3) microplastic debris, identified as epoxy resin, can be found in the cytoplasm and the agglutinated shell of T. bocki.We hypothesize that plastic waste and their associated additives may produce modifications related to the biomineralization process in foraminifera. This effect would be added to those induced by ocean acidification with negative consequences on the foraminiferal biogenic carbon (C) storage capacity.

The potential impacts of mining activities on tropical coastal ecosystems are poorly understood. In particular, limited information is available on the effects of metals on scleractinian corals which are foundation species that form vital structural habitats supporting other biota. This study investigated the effects of dissolved nickel and copper on the coral Acropora muricata and its associated microbiota. Corals collected from the Great Barrier Reef were exposed to dissolved nickel (45, 90, 470, 900 and 9050 μg Ni/L) or copper (4, 11, 32 and 65 μg Cu/L) in flow through chambers at the National Sea Simulator, Townsville, Qld, Australia. After a 96-h exposure DNA metabarcoding (16S rDNA and 18S rDNA) was undertaken on all samples to detect changes in the structure of the coral microbiome. The controls remained healthy throughout the study period. After 36 h, bleaching was only observed in corals exposed to 32 and 65 μg Cu/L and very high nickel concentrations (9050 μg Ni/L). At 96 h, significant discolouration of corals was only observed in 470 and 900 μg Ni/L treatments, the highest concentrations tested. While high concentrations of nickel caused bleaching, no changes in the composition of their microbiome communities were observed. In contrast, exposure to copper not only resulted in bleaching, but altered the composition of both the eukaryote and bacterial communities of the coral's microbiomes. Our findings showed that these effects were only evident at relatively high concentrations of nickel and copper, reflecting concentrations observed only in extremely polluted environments. Elevated metal concentrations have the capacity to alter the microbiomes which are inherently linked to coral health.

Standardized ecosystem-based monitoring surveys are critical for providing information on marine ecosystem health. Environmental DNA/RNA (eDNA/eRNA) metabarcoding may facilitate such surveys by quickly and effectively characterizing multi-trophic levels. In this study, we assessed the suitability of eDNA/eRNA metabarcoding to evaluate changes in benthic assemblages of bacteria, Foraminifera and other eukaryotes along transects at three offshore oil and gas (O&G) drilling and production sites, and compared these to morphologically characterized macro-faunal assemblages. Bacterial communities were the most responsive to O&G activities, followed by Foraminifera, and macro-fauna (the latter assessed by morphology). The molecular approach enabled detection of hydrocarbon degrading taxa such as the bacteria Alcanivorax and Microbulbifer at petroleum impacted stations. Most identified indicator taxa, notably among macro-fauna, were highly specific to site conditions. Based on our results we suggest that eDNA/eRNA metabarcoding can be used as a stand-alone method for biodiversity assessment or as a complement to morphology-based monitoring approaches.

Euplotes crassus, a single-celled eukaryote, is directly affected by environmental contaminants. Here, exponentially cultured E. crassus were exposed to cadmium, copper, lead, and zinc and then the reactive oxygen species (ROS) and total glutathione (GSH) levels were measured. Subsequently, the transcriptional modulation of glutathione peroxidase (GPx) and glutathione reductase (GR) were estimated by quantitative RT-PCR. After an 8-h exposure, significantly higher increases in the relative ROS and total GSH levels were observed in exposed group, compared to the controls. Real-time PCR data revealed that the expression levels of GPx and GR mRNA were sensitively modulated within 8h of exposure to all heavy metals. These findings suggest that these genes may be involved in cellular defense mechanisms by modulating their gene expression against heavy metal-induced oxidative stress. Thus, they may be useful as potential molecular biomarkers to assess sediment environments for contaminants.

Coral reef ecosystems in the Persian Gulf are frequently exposed to crude oil spills. We investigated benthic bacterial and eukaryote community structures at such coral reef sites subjected to different degrees of polycyclic aromatic hydrocarbon (PAH) pollution using environmental DNA (eDNA) metabarcoding. Both bacterial and eukaryote communities responded with pronounced shifts to crude oil pollution and distinguished control sites, moderately and heavily impacted sites with significant confidentiality. The observed community patterns were predominantly driven by Alphaproteobacteria and metazoans. Among these, we identified individual genera that were previously linked to oil spill stress, but also taxa, for which a link to hydrocarbon still remains to be established. Considering the lack of an early-warning system for the environmental status of coral reef ecosystems exposed to frequent crude-oil spills, our results encourage further research towards the development of an eDNA-based biomonitoring tool that exploits benthic bacterial and eukaryote communities as bioindicators.