The importance of per-, poly-fluoroalkyl substances (PFASs) effects on riverine microbiomes is receiving increased recognition in the environmental sciences. However, few studies have explored how PFASs affect microbiomes across trophic levels, specifically through predator-prey interactions. This study examined the community profiles of planktonic archaea, bacteria, fungi, algae, protozoa, and metazoa in a semi-industrial and agricultural river alongside their interactions with 15 detected PFASs. As abiotic factors, PFASs affected community coalescence more than biogenic substances (p < 0.05). For biotic regulations, sub-communities in rare biospheres (including always rare taxa-ART and critically rare taxa-CRT) contributed to spatial community coalescence more than sub-communities in abundant biospheres (always abundant taxa-AAT and critically abundant taxa-CAT) (p < 0.05). Metazoa-bacteria (Modularity = 1.971) and protozoa-fungi (1.723) were determined to be the most stable predator-prey networks. Based on pathway models, short-chain PFBA (C4) was shown to weaken the trophic transfer efficiencies from heterotrophic bacteria (HB) to heterotrophic flagellates (HF) (p < 0.05). Long-chain PFTeDA (C14) promoted HB to amoeba (p < 0.05), which we postulate is the pathway for PFTeDA to enter the microbial food chain. Our preliminary results elucidated the influence of PFASs on planktonic microbial food webs and highlighted the need to consider protecting and remediating riverine ecosystems containing PFASs.

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.

The application of low ozone dosage to minimize the problems caused by filamentous foaming was evaluated in two bioreactors of an urban wastewater treatment plant. Filamentous and nitrifying bacteria, as well as protist and metazoa, were monitored throughout a one-year period by FISH and conventional microscopy to examine the effects of ozone application on these specific groups of microorganisms. Multivariate data analysis was used to determine if the ozone dosage was a key factor determining the low carbon and nitrogen removal efficiencies observed throughout the study period, as well as to evaluate its impact on the biological communities monitored. The results of this study suggested that ozonation did not significantly affect the COD removal efficiency, although it had a moderate effect on ammonia removal efficiency. Filamentous bacteria were the community most influenced by ozone (24.9% of the variance explained by ozone loading rate), whilst protist and metazoa were less affected (11.9% of the variance explained). Conversely, ozone loading rate was not a factor in determining the nitrifying bacterial community abundance and composition, although this environmental variable was correlated with ammonia removal efficiency. The results of this study suggest that different filamentous morphotypes were selectively affected by ozone.

Biotic indices for monitoring marine ecosystems are mostly based on the analysis of benthic macroinvertebrate communities. Due to their high sensitivity to pollution and fast response to environmental changes, bacterial assemblages could complement the information provided by benthic metazoan communities as indicators of human-induced impacts, but so far, this biological component has not been well explored for this purpose. Here we performed 16S rRNA gene amplicon sequencing to analyze the bacterial assemblage composition of 51 estuarine and coastal stations characterized by different environmental conditions and human-derived pressures. Using the relative abundance of putative indicator bacterial taxa, we developed a biotic index that is significantly correlated with a sediment quality index calculated on the basis of organic and inorganic compound concentrations. This new index based on bacterial assemblage composition can be a sensitive tool for providing a fast environmental assessment and allow a more comprehensive integrative ecosystem approach for environmental management.

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.

Ballast water is a major vector of invasion by protozoans and metazoans. Bacterial invasion is less-well understood. We surveyed the bacterial diversity of ballast water from 26 container ships arriving at the Yangshan Deepwater Port, Shanghai, China during 2015–2016. We characterized the ballast microbiome using high-throughput sequencing (HTS) based on V4-V5 region of 16S rRNA genes. We simultaneously monitored physicochemical parameters of the ballast water, including temperature, pH, dissolved oxygen (DO), salinity, turbidity, total suspended solid (TSS), particulate organic carbon (POC), NO₂, NH₄, PO₄. Proteobacteria was the dominant phylum, comprising more than 50% of the OTUs of almost all vessels, followed by Bacteroidetes (12.08%), Actinobacteria (4.86%) Planctomycetes (3.24%) and Cyanobacteria (1.95%). The relative abundance of Cyanobacteria differed among vessels. It was negatively correlated with temperature, NO₃, pH, TSS, PO₄, and turbidity and positively correlated with NH₄, POC. The genus Synechococcus was the most common Cyanobacteria in our results. Escherichia coli were relatively rare; they are indicator-species of D-2 standards published by the IMO. The relative abundance of the genus Vibrio ranged from 0.003% to 24.88% among different vessels. Our results showed that HTS was able to profile the bacterial communities in ballast-waters, even when the approach was restricted by technical and other obstacles.

Global movement of nonindigenous species, within ballast water tanks across natural barriers, threatens coastal and estuarine ecosystem biodiversity. In 2012, the Port of Houston ranked 10th largest in the world and 2nd in the US (waterborne tonnage). Ballast water was collected from 13 vessels to genetically examine the eukaryotic microorganism diversity being discharged into the Port of Houston, Texas (USA). Vessels took ballast water onboard in North Atlantic Ocean between the Port of Malabo, Africa and Port of New Orleans, Louisiana, (USA). Twenty genera of Protists, Fungi and Animalia were identified from at least 10 phyla. Dinoflagellates were the most diverse and dominant identified (Alexandrium, Exuviaella, Gyrodinium, Heterocapsa, Karlodinium, Pfiesteria and Scrippsiella). We are reporting the first detection of Picobiliphytes, Apusozoa (Amastigomonas) and Sarcinomyces within ballast water. This study supports that global commerce by shipping contributes to long-distance transportation of eukaryotic microorganisms, increasing propagule pressure and invasion supply on ecosystems.

We investigated changes in protozoa and metazoa community in relation to process parameters in activated sludge from four wastewater treatment plants (WWTPs) throughout the period of 1 year. Principal component analysis (PCA) showed that activated sludge from investigated treatment plants had different dominating species representatives and community composition mainly depends on individual features of the treatment plants. Redundancy analysis (RDA) showed that the temperature in bioreactors was the most relevant factor explaining changes in the microorganism community, whereas reduction rate of chemical oxygen demand (COD), biological oxygen demand (BOD₅), suspended solids (SS), and total nitrogen (TN) did not sufficiently explain the variation in protozoa and metazoan community composition. The results indicate that in stable working WWTP it is difficult to find a pronounced link between activated sludge species composition, process parameters, and plant configuration. Applied multivariate analysis can be a valuable tool for the exploration of the relations between community composition and WWTP process parameters.

Activated sludge systems are prone to be affected by foaming occurrences causing the sludge to rise in the reactor and affecting the wastewater treatment plant (WWTP) performance. Nonetheless, there is currently a knowledge gap hindering the development of foaming events prediction tools that may be fulfilled by the quantitative monitoring of AS systems biota and sludge characteristics. As such, the present study focuses on the assessment of foaming events in full-scale WWTPs, by quantitative protozoa, metazoa, filamentous bacteria, and sludge characteristics analysis, further used to enlighten the inner relationships between these parameters. In the current study, a conventional activated sludge system (CAS) and an oxidation ditch (OD) were surveyed throughout a period of 2 and 3 months, respectively, regarding their biota and sludge characteristics. The biota community was monitored by microscopic observation, and a new filamentous bacteria index was developed to quantify their occurrence. Sludge characteristics (aggregated and filamentous biomass contents and aggregate size) were determined by quantitative image analysis (QIA). The obtained data was then processed by principal components analysis (PCA), cross-correlation analysis, and decision trees to assess the foaming occurrences, and enlighten the inner relationships. It was found that such events were best assessed by the combined use of the relative abundance of testate amoeba and nocardioform filamentous index, presenting a 92.9 % success rate for overall foaming events, and 87.5 and 100 %, respectively, for persistent and mild events.