Spatial variation in bacterial biomass, community composition and driving factors across a eutrophic river

Response of microbial communities and biogeochemical cycling functions to sediment physicochemical properties and microplastic pollution under damming and water diversion projects

Understanding the interactions among flow-sediment, microorganisms, and biogeochemical cycles is crucial for comprehending the ecological response mechanisms of dams and water diversion. This study focused on the spatial patterns of carbon, nitrogen, phosphorus, and sulfur (CNPS) cycle functional genes in the water resource for the middle route of the South-to-North Water Diversion Project in China, specifically the Danjiangkou Reservoir (comprising the Han and Dan reservoirs). The investigation incorporated sediment physicochemical properties and microplastic pollution. Numerous microbial species were identified, revealing that microbial communities demonstrated sensitivity to changes in sedimentary mud content. The communities exhibited greater β diversity due to finer sediment particles in the Han Reservoir (HR), whereas in the Dan Reservoir (DR), despite having higher sediment nutrient content and MPs pollution, did not display this pattern. Regarding the composition and structure of microbial communities, the study highlighted that sediment N and P content had a more significant influence compared to particle size and MPs. The quantitative microbial element cycling (QMEC) results confirmed the presence of extensive chemolithotrophic microbes and strong nitrogen cycle activity stemming from long-term water storage and diversion operations. The denitrification intensity in the HR surpassed that of the DR. Notably, near the pre-dam area, biological nitrogen fixation, phosphorus removal, and sulfur reduction exhibited noticeable increases. Dam construction refined sediment, fostering the growth of different biogeochemical cycling bacteria and increasing the abundance of CNPS cycling genes. Furthermore, the presence of MPs exhibited a positive correlation with S cycling genes and a negative correlation with C and N cycling genes. These findings suggest that variations in flow-sediment dynamics and MPs pollution have significant impact the biogeochemical cycle of the reservoir.

Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere

BACKGROUND

The widespread nature of plastic pollution has given rise to wide scientific and social concern regarding the capacity of these materials to serve as vectors for pathogenic bacteria and reservoirs for Antimicrobial Resistance Genes (ARG). In- and ex-situ incubations were used to characterise the riverine plastisphere taxonomically and functionally in order to determine whether antibiotics within the water influenced the ARG profiles in these microbiomes and how these compared to those on natural surfaces such as wood and their planktonic counterparts.

RESULTS

We show that plastics support a taxonomically distinct microbiome containing potential pathogens and ARGs. While the plastisphere was similar to those biofilms that grew on wood, they were distinct from the surrounding water microbiome. Hence, whilst potential opportunistic pathogens (i.e. Pseudomonas aeruginosa, Acinetobacter and Aeromonas) and ARG subtypes (i.e. those that confer resistance to macrolides/lincosamides, rifamycin, sulfonamides, disinfecting agents and glycopeptides) were predominant in all surface-related microbiomes, especially on weathered plastics, a completely different set of potential pathogens (i.e. Escherichia, Salmonella, Klebsiella and Streptococcus) and ARGs (i.e. aminoglycosides, tetracycline, aminocoumarin, fluoroquinolones, nitroimidazole, oxazolidinone and fosfomycin) dominated in the planktonic compartment. Our genome-centric analysis allowed the assembly of 215 Metagenome Assembled Genomes (MAGs), linking ARGs and other virulence-related genes to their host. Interestingly, a MAG belonging to Escherichia -that clearly predominated in water- harboured more ARGs and virulence factors than any other MAG, emphasising the potential virulent nature of these pathogenic-related groups. Finally, ex-situ incubations using environmentally-relevant concentrations of antibiotics increased the prevalence of their corresponding ARGs, but different riverine compartments -including plastispheres- were affected differently by each antibiotic.

CONCLUSIONS

Our results provide insights into the capacity of the riverine plastisphere to harbour a distinct set of potentially pathogenic bacteria and function as a reservoir of ARGs. The environmental impact that plastics pose if they act as a reservoir for either pathogenic bacteria or ARGs is aggravated by the persistence of plastics in the environment due to their recalcitrance and buoyancy. Nevertheless, the high similarities with microbiomes growing on natural co-occurring materials and even more worrisome microbiome observed in the surrounding water highlights the urgent need to integrate the analysis of all environmental compartments when assessing risks and exposure to pathogens and ARGs in anthropogenically-impacted ecosystems. Video Abstract.

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts

In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.

Deposition kinetics of bacteriophage MS2 on Microcystis aeruginosa and kaolin surface

Waterborne virus contamination might easily adsorb on the organic or inorganic surface in the complex aquatic environment. A quartz crystal microbalance coupled with dissipation monitoring was used to investigate the effects of the ionic strength of monovalent cation and divalent cation and pH on the deposition kinetics of bacteriophage MS2 on silica surface coated with Microcystis aeruginosa or kaolin, which represents organic or inorganic particle, respectively. Derjaguin-Landau-Verwey-Overbeek theory was used to illustrate the deposition mechanisms of MS2. The increased concentration of Na⁺ significantly enhanced the deposition rates of MS2 on both coated silica surfaces due to the reduction of repulsive electrostatic interactions. However, the MS2 deposition rates decreased at higher ionic strength of Ca²⁺, which accounted for the steric and hydrophobic interactions. And the higher MS2 deposition rates on both surfaces occurred at pH 3. In addition, the deposition rates of MS2 on kaolin-coated silica surfaces were higher than on the Microcystis-coated surface under all studied conditions. Furthermore, the Derjaguin-Landau-Verwey-Overbeek theory could elucidate the deposition mechanism in Na⁺ solution, whereas the steric and hydrophobic interactions should be considered for the presence of high concentration of Ca²⁺.

Enhancing robustness of halophilic aerobic granule sludge by granular activated carbon at decreasing temperature

High salinity seriously inhibits the growth and metabolism of microorganisms, resulting in poor settleability, excessive biomass loss and low treatment efficiency of biological wastewater treatment systems. The development of halophilic aerobic granular sludge (HAGS) is a feasible strategy for addressing this challenge. However, there are problems with the granulation of HAGS and the stability of granules at decreasing temperatures. In this study, granular activated carbon (GAC) with a large specific surface area and good biocompatibility was used to enhance the robustness of HAGS. The results showed that the addition of GAC shortened the granulation time from 60 d (control system) to 35 d (GAC-addition system). The proteins contents of extracellular polymeric substances (EPS) in the GAC-addition system was significantly higher (p < 0.05) than that in the control system during granulation. Satisfactory NH₄⁺-N and chemical oxygen demand (COD) removal efficiencies reached more than 96% in both systems at 18-26 °C. When the operating temperature was lower than 15 °C, the GAC-addition system exhibited better NH₄⁺-N removal performance (>80%) than the control system (<60%). Moreover, the abundance of almost all nitrogen metabolism-related genes in the GAC-addition system was higher than that in the control system. During the granulation process, the enrichment of functional microorganisms, including family Flavobacteriaceae, Rhodobacteraceae, and Cryomorphaceae, may promote the production of EPS by significantly upregulating (p < 0.05) the metabolic pathway "Signaling Molecules and Interaction" in the GAC-addition system. The overexpression of the nitrogen assimilation gene glnA in heterotrophic bacteria (Halomonas and Marinobacterium) may promote the conversion of inorganic nitrogen to extracellular proteins to adapt to the decreased operational temperature. Our findings confirm that GAC addition is a simple but effective strategy to accelerate granulation and enhance the robustness of HAGS in saline wastewater treatment.

Microbiome and antibiotic resistance profiling in submarine effluent-receiving coastal waters in Croatia

Wastewater treatment plant (WWTP) effluents are pointed as hotspots for the introduction of both commensal and pathogenic bacteria as well as their antibiotic resistance genes (ARGs) in receiving water bodies. For the first time, the effect of partially treated submarine effluents was explored at the bottom and surface of the water column to provide a comprehensive overview of the structure of the microbiome and associated AR, and to assess environmental factors leading to their alteration. Seawater samples were collected over a 5-month period from submarine outfalls in central Adriatic Sea, Croatia. 16S rRNA amplicon sequencing was used to establish taxonomic and resistome profiles of the bacterial communities. The community differences observed between the two discharge areas, especially in the abundance of Proteobacteria and Firmicutes, could be due to the origin of wastewaters treated in WWTPs and the limiting environmental conditions such as temperature and nutrients. PICRUSt2 analysis inferred the total content of ARGs in the studied microbiomes and showed the highest abundance of resistance genes encoding multidrug efflux pumps, such as MexAB-OprM, AcrEF-TolC and MdtEF-TolC, followed by the modified peptidoglycan precursors, transporter genes encoding tetracycline, macrolide and phenicol resistance, and the bla operon conferring β-lactam resistance. A number of pathogenic genera introduced by effluents, including Acinetobacter, Arcobacter, Bacteroides, Escherichia-Shigella, Klebsiella, Pseudomonas, and Salmonella, were predicted to account for the majority of efflux pump-driven multidrug resistance, while Acinetobacter, Salmonella, Bacteroides and Pseudomonas were also shown to be the predominant carriers of non-efflux ARGs conferring resistance to most of nine antibiotic classes. Taken together, we evidenced the negative impact of submarine discharges of treated effluents via alteration of physico-chemical characteristics of the water column and enrichment of bacterial community with nonindigenous taxa carrying an arsenal of ARGs, which could contribute to the further propagation of the AR in the natural environment.

Patterns of Structural and Functional Bacterioplankton Metacommunity along a River under Anthropogenic Pressure

Bacteria, an integral part of aquatic ecosystems, are responsible for the circulation of matter and flow of energy. Since bacterioplankton rapidly responds to any natural and human-induced disturbances in the environment, it can serve as a bioindicator of these changes. Knowing factors that shape the microbial community structure may help the sustainable management of the water environment. However, the identification of environmental signals affecting the structure and function of bacterioplankton is still a challenge. The study analyses the impact of environmental variables on basic microbial parameters, which determines the effectiveness of ecological processes in rivers. Measurements of bacterioplankton abundance (BA) and extracellular enzyme activity (EEA) were based on fluorescent markers. The bacterial community structure was determined by 16S rRNA gene amplicon sequencing (Illumina). The results indicate spatial variation in bacterioplankton abundance. Temporal variation was not significant. Lipase and aminopeptidase had the highest level of activity. EEA was not correlated with bacterial abundance but was significantly correlated with temperature. Moreover, differences in lipase, α-glucosidase and β-glucosidase activity levels between spring and summer were noted. At the same time, the location of sampling site had a significant influence on aminopeptidase activity. The taxonomic analysis of bacterioplankton communities in the Brda River indicated that, although different numbers of OTUs were recorded in the studied river sections, bacterioplankton biodiversity did not change significantly along the river with distance downstream. Anthropogenically modified river sections were characterized by the dominance of Flavobacterium (Bacterioidetes) and hgcl clade (Actinobacteria) taxa, known for their ability to produce extracellular enzymes. PCoA analysis revealed that the sites located in the lower river course (urban area) had the most similar bacterial community structure (β-diversity). The study provides new insight into the changes in microbial communities along the river and emphasizes the potential impact of anthropogenization on these processes.