Profiles of ARGs and their relationships with antibiotics, metals and environmental parameters in vertical sediment layers of three lakes in China.

Antibiotic resistance is a global health problem, and the role of antibiotics and metal pollution in antibiotic resistance in sediment biocenosis is limited. The occurrence and relationship between antibiotic resistance genes (ARGs), antibiotics, metals and environmental parameters were investigated in vertical layers of sediments in rural and urban lakes. Generally, the total concentrations of seven antibiotics were significantly higher in the rural lake (Lake Taihu = 96%) than in the urban lakes (Xuanwu = 0.3%, Wulongtan = 3%), while similar concentrations were observed for metals (Taihu (34%), Xuanwu (33%) and Wulongtan (33%)). The concentration of metals and antibiotics were mostly higher in the surface sediment layers than the deeper ones (for antibiotics; surface layers = 89%, deeper layer = 11%, for metals; surface = 65%, deep = 35%). The ARGs showed no significant difference between surface and deeper sediments (surface = 48%, deep = 52%, p < 0.05). The potential ecological risk index of Ni, Cu, Zn, Cr, Mn, As, Cd, and Pb contamination showed that Lake Taihu and Wulongtan had moderate ecological risks while Lake Xuanwu had a low ecological risk. Pearson coefficient and network analysis showed that direct and indirect relationship existed among antibiotics, metals, environmental parameters, and ARGs, and the relationship was linked by key environmental components. tetA, blaTEM, SDZ, TOC, OFL, Cd, OTC, NOR, Ni, sulA, AUR, TC, DOX and TN were the major factors that influence the distribution of resistance genes, forming a complex network mechanism of antibiotic resistance. Our study revealed that antibiotics and heavy metals are widely distributed in the surficial sediments and the proliferation of ARGs are influenced by some key environmental components.

Distribution and relationship between antimicrobial resistance genes and heavy metals in surface sediments of Taihu Lake, China.

Heavy metals, pharmaceuticals, and other wastes released into the environment can significantly influence environmental antibiotic resistance. We investigated the occurrence of 22 antimicrobial resistance genes (ARGs) and 10 heavy metal concentrations, and the relationship between ARGs and heavy metals in surface sediment from seven sites of Lake Taihu. The results showed significant correlations (p < 0.05) between sediment ARG levels, especially for tetracycline and sulfonamides (e.g., tet(A), tet(D), tet(E), tet(O), sul1, sul2 and int-1) and specific heavy metals (Fe, Mn, Cr, Cu, Zn, among others) in the Lake. In the surface sediments, heavy metals showed an interaction with resistance genes, but the strength of interaction was diminished with increasing depth. For most of the heavy metals, the concentration of elements in the top sediments was higher than that in other depths. Tetracycline resistance genes (tet(A), tet(B), tet(D), tet(E) and tet(O), ß-lactam resistance genes (SHV, TEM, CTX, OXA and OXY) and sulfonamide resistance genes (sulA, sul1, sul2, sul3 and int-1) were detected. They showed a trend which inferred a statistically significant increase followed by decreases in the relative abundance of these ARGs (normalized to 16S rRNA genes) with increasing depth. This study revealed that tet(A), tet(O), TEM, OXY, int-1, sul1 and sul3 were widespread in surface sediments with high abundance, indicating that these genes deserve more attention in future work.

Interactions between water quality and microbes in epiphytic biofilm and superficial sediment of lake in trophic agriculture area.

Epiphytic and superficial sediment biofilm-dwelling microbial communities play a pivotal role in water quality regulation and biogeochemical cycling in shallow lakes. However, the interactions are far from clear between water physicochemical parameters and microbial community on aquatic plants and in surface sediments of lake in trophic agriculture area. This study employed Illumina sequencing, Partial Least Squares Path Modeling (PLS-PM), and physico-chemical analytical methods to explore the interactions between water quality and microbes (bacteria and eukaryotes) in three substrates of trophic shallow Lake Cyohoha North, Rwanda. The Lake Cyohoha was significantly polluted with total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), and ammonia nitrogen (NH3-N) in the wet season compared to the dry season. PLS-PM revealed a strong positive correlation (+0.9301) between land use types and physico-chemical variables in the rainy season. In three substrates of the trophic lake, Proteobacteria, Cyanobacteria, Firmicutes, and Actinobacteria were dominant phyla in the bacterial communities, and Rotifers, Platyhelminthes, Gastrotricha, and Ascomycota dominated in microeukaryotic communities. As revealed by null and neutral models, stochastic processes predominantly governed the assembly of bacterial and microeukaryotic communities in biofilms and surface sediments. Network analysis revealed that the microbial interconnections in Ceratophyllum demersum were more stable and complex compared to those in Eichhornia crassipes and sediments. Co-occurrence network analysis (|r| > 0.7, p < 0.05) revealed that there were complex interactions among physicochemical parameters and microbes in epiphytic and sediment biofilms, and many keystone microbes on three substrates played important role in nutrients removal, food web and microbial community stable. These findings emphasize that eutrophic water influence the structure, composition, and interactions of microbes in epiphytic and surface sediment biofilms, and provided new insights into the interconnections between water quality and microbial community in presentative substrates in tropical lacustrine ecosystems in agriculturally polluted areas. The study provides useful information for water quality protection and aquatic plants restoration for policy making and catchment management.

Effect of erythromycin on epiphytic bacterial communities and water quality in wetlands.

The occurrence of antibiotics such as erythromycin (ERY) under macrolide group, has long been acknowledged for negatively affecting ecosystems in freshwater environments. However, the effects of ERY on water quality and microbial communities in epiphytic biofilms are poorly understood. Here, Scanning Electron Microscopy (SEM), High-throughput sequencing, and physicochemical analytical methods were employed to unravel the impact of ERY on the water quality and bacterial morphology, biodiversity, composition, interaction, and ecological function in epiphytic biofilms attached to Vallisneria natans and artificial plants in mesocosmic wetlands. The study showed that ERY exposure significantly impaired the nutrient removal capacity (TN, TP, and COD) and altered the epiphytic bacterial morphology of V. natans and artificial plants. ERY did not affect the bacterial α-diversity. Notwithstanding ERY decreased the bacterial composition, but the relative abundance of Proteobacteria and Patescibacteria spiked by 62.2 % and 54 %, respectively, in V. natans, while Desulfobacteria and Chloroflexi increased by 8.9 % and 11.2 %, respectively, in artificial plants. Notably, ERY disturbed the food web structure and metabolic pathways such as carbohydrate metabolism, amino acid metabolism, energy metabolism, cofactor and vitamin metabolism, membrane transport, and signal transduction. This study revealed that ERY exposure disrupted the bacterial morphology, composition, interaction or food web structure, and metabolic functions in epiphytic biofilm. These data underlined that ERY negatively impacts epiphytic bacterial communities and nutrient removal in wetlands.

Exploring microbial diversity and ecological function of epiphytic and surface sediment biofilm communities in a shallow tropical lake.

Microbial communities in epiphytic biofilms and surface sediments play a vital role in the biogeochemical cycles of the major chemical elements in freshwater. However, little is known about the diversity, composition, and ecological functions of microbial communities in shallow tropical lakes dominated by aquatic macrophytes. In this study, epiphytic bacterial and eukaryotic biofilm communities on submerged and floating macrophytes and surface sediments were investigated in Lake Rumira, Rwanda in August and November 2019. High-throughput sequencing data revealed that members of the phyla, including Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, Chloroflexi, Bacteriodetes, Verrumicrobia, and Myxomycota, dominated bacterial communities, while the microeukaryotic communities were dominated by Unclassified (uncl) SAR(Stramenopiles, Alveolata, Rhizaria), Rotifers, Ascomycota, Gastrotricha, Platyhelminthes, Chloroplastida, and Arthropoda. Interestingly, the eukaryotic OTUs (operational taxonomic units) number and Shannon indices were significantly higher in sediments and epiphytic biofilms on Eicchornia crassipes than Ceratophyllum demersum (p < 0.05), while no differences were observed in bacterial OTUs number and Shannon values among substrates. Redundancy analysis (RDA) showed that water temperature, pH, dissolved oxygen (DO), total nitrogen (TN), and electrical conductivity (EC) were the most important abiotic factors closely related to the microbial community on C. demersum and E. crassipes. Furthermore, co-occurrence networks analysis (|r| > 0.7, p < 0.05) and functional prediction revealed more complex interactions among microbes on C. demersum than on E. crassipes and sediments, and those interactions include cross-feeding, parasitism, symbiosis, and predatism among organisms in biofilms. These results suggested that substrate-type and environmental factors were the strong driving forces of microbial diversity in epiphytic biofilms and surface sediments, thus shedding new insights into microbial community diversity in epiphytic biofilms and surface sediments and its ecological role in tropical lacustrine ecosystems.

Impacts of nano-titanium dioxide toward Vallisneria natans and epiphytic microbes.

In this study, Vallisneria natans plants were exposed to 5 and 20 nm of titanium dioxide nanoparticles (TiO2 NPs) anatase and 600-1000 nm of bulk at 5 and 20 mg/L for 30 days. SEM images and EDX spectra revealed that epiphytic biofilms were more prone to TiO2 NPs adhesion than bare plant leaves. TiO2 NPs injured plant leaf cells, ruptured epiphytic diatoms membranes and increased the ratio of free-living microbes. The TN, NH4⁺-N and NO3--N concentrations significantly decreased, respectively, by 44.9%, 33.6%, and 23.6% compared to bulk treatments after 30 days due to macrophyte damage and a decline in diversity of epiphytic bacterial community and abundance of nitrogen cycle bacteria. TiO2 NPs size-dependent decrease in bacterial relative abundance was detected, including phylum Cyanobacteria, Planctomycetes, and Verrucomicrobia. Although TiO2 NPs increased eukaryotic diversity and abundance, abundances of Bacillariophyceae and Vampyrellidae classes and Gastrotricha and Phragmoplastophyta phylum decreased significantly under TiO2 NPs exposure compared to bulk and control. TiO2 NPs reduced intensities of interaction relationships among epiphytic microbial genera. This study shed new light on the potential effects of TiO2 NPs toxicity toward aquatic plants and epiphytic microbial communities and its impacts on nitrogen species removal in wetlands.

Ciprofloxacin increased abundance of antibiotic resistance genes and shaped microbial community in epiphytic biofilm on Vallisneria spiralis in mesocosmic wetland.

This study investigated the fate of ciprofloxacin (CIP) in wetlands dominated by Vallisneria spiralis. About 99% of CIP was degraded from overlaying water within 4 days of treatment but significantly inhibited the nutrient removal capacity (TN, TP, and COD) by causing a drastic reduction in microbial aggregation in epiphytic biofilm and bacterial biodiversity. CIP triggered resistance mechanisms among dominant bacteria phyla such as Proteobacteria, Actinobacteria, and Planctomycetes causing their increased relative abundance. Additionally, the relative abundances of eukaryotic microorganisms (including; Chloroplastida, Metazoa, and Rhizaria) and 13 ARGs subtypes (including; Efflux pump, Tetracycline, Multi-drug, Rifampin, Beta-lactam, Peptide, Trimethoprim) were significantly increased. While dominant metabolic pathways such as Carbohydrate, amino acid, energy and nucleotide metabolism were inhibited. This study revealed that V. spiralis has great sorption capacity for CIP than sediment and though CIP was effectively removed from the overlying water, it caused a prolonged effect on the epiphytic biofilm microbial communities.

The fate of tetracycline in vegetated mesocosmic wetlands and its impact on the water quality and epiphytic microbes.

The fate of antibiotics and their impact on antibiotic resistance genes (ARGs) and microbial communities are far from clear in wetlands. The fate and impact of tetracycline (TC) on the nutrient degradation of wetlands and epiphytic microbes were investigated. This study showed that after TC spiking, 99.7% of TC were removed from the surface water of wetlands containing Vallisneria spiralis within 4 days post-treatment. TC spiking impaired the nutrient removal capacity and disrupted epiphytic microbial community structure while enhancing the abundance of 11 ARGs subtypes, including tetracycline resistance genes, tetX, tetM, tetO, tetQ, tetS, and tet36. TC decreased bacterial biodiversity but amplified the relative abundance of Proteobacteria and Firmicutes by 4% and 61%, respectively, and increased eukaryotic diversity. 16 metabolic pathways including Carbohydrate, Energy, Amino acid, 'cofactor and vitamins' metabolisms were significantly (p < 0.01) increased in TC treatment. Phylogenetic, functional prediction analysis indicated that Flavobacterium was positively related with xenobiotics, cell motility, 'terpenoids and polyketides' metabolism but negatively related to nucleotide metabolism, while Rhodobacter showed a reverse trend but positively related with nucleotide and 'glycan biosynthesis' and metabolism. These data highlighted that TC has negative impacts on epiphytic microbial community and nutrients removal in wetlands.

The impacts of straw substrate on biofloc formation, bacterial community and nutrient removal in shrimp ponds.

This study explored biofloc technology for shrimp culture based on straw substrates with a size of 40 mu, 80 mu, and 120 mu. Straw substrates utilization stimulated shrimp growth compared to control. Treatment with 40 mu had the best ammonium (71.60%) and nitrite nitrogen (77.78%) removal rates generally. In all biofloc treatments, Proteobacteria (4.10-56.1%) was the most dominant phylum, followed by Bacteroidetes (2.44-38.21%), Planctomycetes (0.45-21.41%), and Verrucomicrobia (1.2-10.30%). Redundancy analysis showed that salinity was a significant factor closely related to the microbial community in biofloc. The environmental parameters (DO > pH > TN > NH4+-N > COD > Salinity > EC), nitrification, and denitrification genes (amoA > napA > nirK) were significant factors that interrelated with the bacterial genus in the network analysis. This study highlighted a novel technology of reusing agricultural waste that transformed inorganic nitrogen using nutrient recycling to control water quality in the culture system and produced microbial proteins that served as a natural nutritional supplement to enhance shrimp growth.

Epiphytic bacterial community shift drives the nutrient cycle during Potamogeton malaianus decomposition.

Epiphytic bacteria on submerged macrophytes play important roles in the nutrient cycle in freshwater ecosystems. However, little is known about the composition and role of epiphytic bacteria during the decomposition of submerged macrophytes. In this study, the alterations in epiphytic bacterial composition, abundances of nitrogen cycle-related genes and nutrient release were investigated in a 56-day decomposition process of Potamogeton malaianus. The total reduced biomass was positively related to the contents of carbon, nitrogen and phosphorus released from plant residues. Nutrient released from plant litter showed a positively effect on the concentrations of carbon, nitrogen and phosphorus in the overlying water (p < 0.01). The carbon, phosphorus and nitrogen decreased with decomposition process in both plant debris and overlying water. Humic acid-like substances were the main component of dissolved organic matter in the conditioning stage, whereas fulvic acid-like substances dominated in the fragmentation stage. Results from network analysis and canonical correspondence analysis showed dominant bacterial clades changed with decomposition process. Bacteroidetes was the most abundant phylum in the leaching stage and Spirochaetes, Chlorobi, and Bacteroidetes dominated in the conditioning stage, while Chlorobi dominated in the fragmentation stage. The highest abundance of cnorB and nosZ were detected in the leaching and fragmentation stage, respectively. Bacterial denitrification contributed to nitrogen removal and might be promoted by high ORP and DOC concentration. Our results indicate that epiphytic bacterial community shift drived the metabolism of nutrients C, N, and S during the decomposition of P. malaianus.

Responses of bacterial community structure and denitrifying bacteria in biofilm to submerged macrophytes and nitrate.

Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations. The biofilm cells were evenly distributed on artificial plants but appeared in microcolonies on the surfaces of submerged macrophytes. Proteobacteria was the most abundant phylum in all samples, accounting for 27.3-64.8% of the high-quality bacterial reads, followed by Chloroflexi (3.7-25.4%), Firmicutes (3.0-20.1%), Acidobacteria (2.7-15.7%), Actinobacteria (2.2-8.7%), Bacteroidetes (0.5-9.7%), and Verrucomicrobia (2.4-5.2%). Cluster analysis showed that bacterial community structure can be significantly different on macrophytes versus from those on artificial plants. Redundancy analysis showed that electrical conductivity and nitrate concentration were positively correlated with Shannon index and operational taxonomic unit (OTU) richness (log10 transformed) but somewhat negatively correlated with microbial density. The relative abundances of five denitrifying genes were positively correlated with nitrate concentration and electrical conductivity but negatively correlated with dissolved oxygen.