The emergence of resistance genes is a global phenomenon that poses a significant threat to both animals and humans. Lakes are important reservoirs of genes that confer resistant to antibiotics and metals. In this study, we investigated the distribution and diversity of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the sediment of Daihai Lake using high-throughput sequencing and metagenomic analysis. The results indicated that all sampling sites had similar bacterial community structures, with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes being the most abundant. A total of 16 ARG types containing 111 ARG subtypes were deposited in the sediment. Among the resistance genes to bacitracin, multidrug, macrolide-lincosamide-streptogramin (MLS), tetracycline, beta-lactam, and sulfonamide were the dominant ARG types, accounting for 89.9–94.3% of the total ARGs. Additionally, 15 MRG types consisting of 146 MRG subtypes were identified. In all samples, MRGs of the same type presented resistance to Pb, Ni, Hg, W, Zn, Ag, Cr, Fe, As, Cu, and multimetals. Overall, the distribution and diversity of antibiotic and metal resistance genes showed no significant differences in the samples. Plasmids (91.03–91.82%) were the most dominant mobile genetic elements in the sediments of Daihai Lake. Network analysis indicated that the target ARGs and MRGs were significantly positively correlated with the microorganisms. Potential hosts for various ARGs and MRGs include Proteobacteria, Euryarchaeota, Actinobacteria, Chloroflexi, and Bacteroidetes.

Landfills are considered an anthropogenic source of arsenic (As). The As species mediated by microbes in landfills vary significantly in toxicity. Based on random matrix theory, 16S rRNA genes were used to construct four microbial networks associated with different stages over 12 years of landfill ages. The results indicated that network size and microbial structure varied with landfill age. According to the network scores, about 208 taxa were identified as putative keystones for the whole landfill; the majority of them were Firmicutes, which accounted for 66.8% of all specialists. Random Forest analysis was performed to predict the keystone taxa most responsible for As species distribution under different landfill conditions; 17, 10 and 14 keystone taxa were identified as drivers affecting As species distribution at early, middle, and later landfill stages, respectively.

Distillery sludge is a major source of aquatic pollution, but little is known about their microbial community and their association with the organic and metal pollutants. Sugarcane molasses-based distillery is an important industry in India, although the waste is usually treated prior to disposal, the treatment is often inadequate. The adverse effects of the organic and metal pollutants in sugarcane molasses-based distillery sludge on the microbial biodiversity and abundance in the disposal site have not been elucidated. This study aims to address this gap of knowledge. Samples were collected from the discharge point, 1 and 2 km downstream (D1, D2, and D3, respectively) of a sugarcane distillery in Uttar Pradesh, India, and their physico-chemical properties characterised. Using QIIME, taxonomic assignment for the V3 and V4 hypervariable regions of 16 S rRNA was performed. The phyla Proteobacteria (28–39%), Firmicutes (20–28%), Bacteriodetes (9–10%), Actinobacteria (5–10%), Tenericutes (1–9%) and Patescibacteria (2%) were the predominant bacteria in all three sites. Euryechaeota, were detected in sites D1 and D2 (1–2%) but absent in D3. Spirochaetes (5%), Sinergistetes (2%) and Cloacimonetes (1%) were only detected in samples from site D1. Shannon, Simpson, Chao1, and Observed-species indices indicated that site D1 (10.18, 0.0013, 36706.55 and 45653.84, respectively) has higher bacterial diversity and richness than D2 (6.66, 0.0001, 25987.71 and 49655.89, respectively) and D3 (8.31, 0.002, 30345.53 and 30654.88, respectively), suggesting the organic and metal pollutants provided the stressors to favour the survival of microbial community that can biodegrade and detoxify them in the distillery sludge. This study confirmed that the treatment of the distillery waste was not sufficiently effective and provided new metagenomic information on its impact on the surrounding microbial community. It also offered new insights into potential bioremediation candidates.

The use of reclaimed water in agriculture represents a promising alternative to relieve pressure on freshwater supplies, especially in arid or semiarid regions facing water scarcity. However, this implies introducing micropollutants such as pharmaceutical residues into the environment. The fate and the ecotoxicological impact of valsartan, an antihypertensive drug frequently detected in wastewater effluents, were evaluated in soil-earthworm microcosms. Valsartan dissipation in the soil was concomitant with valsartan acid formation. Although both valsartan and valsartan acid accumulated in earthworms, no effect was observed on biomarkers of exposure (acetylcholinesterase, glutathione S-transferase and carboxylesterase activities). The geometric mean index of soil enzyme activity increased in the soils containing earthworms, regardless of the presence of valsartan. Therefore, earthworms increased soil carboxylesterase, dehydrogenase, alkaline phosphatase, β-glucosidase, urease and protease activities. Although bacterial richness significantly decreased following valsartan exposure, this trend was enhanced in the presence of earthworms with a significant impact on both alpha and beta microbial diversity. The operational taxonomic units involved in these changes were related to four (Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes) of the eight most abundant phyla. Their relative abundances significantly increased in the valsartan-treated soils containing earthworms, suggesting the presence of potential valsartan degraders. The ecotoxicological effect of valsartan on microbes was strongly altered in the earthworm-added soils, hence the importance of considering synergistic effects of different soil organisms in the environmental risk assessment of pharmaceutical active compounds.

Although abundant evidence has suggested that early-life antibiotic exposure was associated with adipogenesis later in life, limited data were available on the effect of intrauterine antibiotic exposure on infant growth and growth speed. Additionally, few studies have investigated the role of the neonatal gut microbiota in the above association. In this study, we examined the association between intrauterine cumulative antibiotic exposure and infant growth and explored the potential role of the neonatal gut microbiota in the association. 295 mother-child pairs from the Shanghai Maternal-Child Pairs Cohort (MCPC) study were included, and meconium samples and infant growth measurements were assessed. Z-scores of length-for-age, weight-for-age (weight-for-age), and body mass index (BMI)-for-age (BMI-for-age) were calculated. Eighteen common antibiotics were measured in meconium. Multivariable linear regression models were applied to test the interrelationships between antibiotic exposure, diversity indicators, and the relative abundance of selected bacterial taxa from phylum to genus levels from least absolute shrinkage and selection operator (LASSO) and infant growth indicators. The detection rates of the 18 antibiotics, except for chlortetracycline, penicillin, and chloramphenicol, were below 10 %. Penicillin was found to be positively associated with infant growth at birth and with growth speed from 2 to 6 months. The Pielou and Simpson indexes were negatively associated with meconium penicillin. Nominally significant associations between penicillin and the relative abundances of several bacterial taxa from the phyla Proteobacteria, Bacteroidetes, and Firmicutes were found. The Pielou and Simpson indexes were also found to be negatively associated with infant growth. Among taxa selected from LASSO regression, the relative abundances of the phyla Actinobacteria and Firmicutes and order Bifidobacteriales were found to be significantly associated with weight and BMI growth speeds from 2 to 6 months. In conclusion, intrauterine antibiotic exposure can affect infant growth. The neonatal gut microbiota might play a role in the abovementioned association.

Heavy metals (HMs) in an aquatic environment mainly affects fish, and thus, fish are convenient pollution bio-indicators. In this study, the toxic effects of HM mixture (chromium (Cr), cadmium (Cd), copper (Cu)) in 0 mg/L to 3.2 mg/L concentration range was investigated in Cyprinus carpio (28 days). HM accumulation, histopathology, oxidative stress, and gut microbial changes were evaluated. HMs accumulated in the order of Cr > Cu > Cd, primarily in the kidneys and finally scales. Reactive oxygen species generation increased in all exposure groups up to day 14, with maximum generation at 3.2 mg/L mixture, which later decreased on day 28 in all. Malondialdehydeand and superoxide dismutase levels increased from day 7 to 28 with increased HM concentrations, while total protein showed an inverse trend. Gill histopathology showed major changes such as uplifted and disintegrated primary lamella, and secondary lamella shortening. The kidneys were characterized by glomerular necrosis, Bowman’s capsule expansion, and tubular space dilatation. Proteobacteria and Firmicutes abundance increased up to 59.4% and 99.16% in 0.8 mg/L and 3.2 mg/L treatment groups, respectively. This study provided a better understanding on the physiology and gut microbiota alteration in C. carpio under multiple HM stress.

Despite their ecological and socioeconomic importance, mangroves are among the most threatened tropical environments in the world. In the past two decades, the world's mangrove degradation and loss were estimated to lie between an 35% and >80%. However, appropriate bioindicators for assessing the impact of external factors, and for differentiating polluted from unpolluted areas are still scarce. Here, we determine the physicochemical profiles of the soils of two mangroves, one exposed to and one not exposed to anthropogenic factors. By metagenomic analysis based on 16S rRNA, we generated the bacterial diversity profiles of the soils and estimated their functional profiles. Our results showed that the two examined mangrove forests differed significantly in the physicochemical properties of the soils, especially regarding organic carbon, phosphorus and metal content, as well as in their microbial communities, which was likely caused by anthropogenic pollution. The physicochemical differences between the soils explained 76% of the differential bacterial composition, and 64% depended solely on gradients of phosphorus, metal ions and potassium. We found two genera JL-ETNP-Z39 and TA06 exclusively in polluted and non-polluted mangroves, respectively. Additionally, the polluted mangrove was enriched in Gemmatimonadetes, Cyanobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Nitrospirae. A total of 77 genera were affected by anthropic contamination, of which we propose 33 as bioindicators; 26 enriched, and 7 depleted upon pollution.

Fish-associated antibiotic resistance genes (ARGs) have attracted increasing attention due to their potential risks to human beings via the food chain. However, data are scarce regarding the antibiotic resistance in fish themselves. Herein, the antibiotic resistance genes (ARGs) were assessed in the gut of four major Chinese freshwater carp (i.e., silver carp, grass carp, bighead carp, and crucian carp) from food retail markets. Results show that the abundances of target ARGs (e.g., tetA, tetO, tetQ, tetW, sulI, sulII, and blaTEM₋₁) and class 1 integrase (intI1) were in the range 9.4 × 10⁻⁶ - 1.6 × 10⁻¹ and 6.7 × 10⁻⁵ - 5.2 × 10⁻² gene copies per 16S rRNA gene, respectively. The sulI, sulII, and tetQ strongly correlated with silver and mercury resistance genes (e.g., silE and merR). The microbial taxa of fish gut could be partly separated among retail markets based on the PCA analysis. About 15.0% of the OTUs in fish gut were shared and 74.5% of the shared OTUs were identified as Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, and Proteobacteria. These phyla may constitute the core microbiota in the guts of the four Chinese freshwater carp. The possible ARG hosts were revealed based on the network analysis, and the presence of pathogen-associated resistant genera in fish gut highlights the need to fully understand their potential human health risks.

The response of sediment bacterial communities in subtropical freshwater benthic microcosms to sediment-associated triclosan (TCS; 28 d exposure) was analysed using Illumina high-throughput sequencing. This study highlights the interactive effects of TCS and the presence of benthic macroinvertebrates (Limnodrilus hoffmeisteri and Viviparidae bellamya) on sediment bacterial communities. Our results show that TCS alone significantly altered the taxonomic composition and decreased alpha diversity of sediment bacterial communities at concentrations ≥80 μg TCS/g dry weight (dw) sediment (sed). Regarding dominant phyla, TCS significantly reduced the relative abundance of Bacteroidetes and Firmicutes at these concentrations, whereas the relative abundance of Chloroflexi and Cyanobacteria increased. In the presence of benthic macroinvertebrates, the sediment bacterial community was affected by 8 μg TCS/g dw sed as well. However, the presence of benthic macroinvertebrates did not cause measurable changes to bacterial community in unspiked (i.e., control) sediment. These results indicate that TCS alone would not alter the sediment bacterial community at environmentally relevant concentrations (up till 8 μg/g dw sed), but may have an effect in combination with the presence of benthic macroinvertebrates. Therefore, we recommend to include benthic macroinvertebrates when assessing the response of sediment bacterial communities during exposure to environmental stress such as organic contaminants.

Microbes in sediments contribute to nutrient release and play an important role in lake eutrophication. However, information about the profiles of functional genes and bacterial communities and the most important environmental factor affecting them in the sediments of eutrophic lake remains unrevealed. In this work, the real-time fluorescent quantitative polymerase chain reaction (qPCR) assay and 16S ribosomal RNA gene next generation sequencing analysis were used to explore the profiles of functional genes and bacterial communities in the sediments of Chaohu Lake. The selected 18 functional genes involved in C, N and P cycles were detected in most of samples. Seasonal variation and sediment variables were found to affect the profiles of functional genes and bacterial communities, and total nitrogen was the dominant environmental factor to drive the formation of bacterial community structure. Proteobacteria and Firmicutes were observed to be the two dominant phyla in the sediments with relative abundance ranging from 10.8% to 36.0% and 7.7%–46.7%, respectively. Three bacterial phyla, i.e., Actinobacteria, Proteobacteria, and Spirochaetes, were found to be significantly positively correlated with the C, N and P-cycle related functional genes. Bacterial community structure was the most important driver to shape the profiles of functional genes. Seasonal variation also influenced the co-occurrence patterns between functional genes and bacterial taxa as revealed by network analysis. The findings from this work facilitate a better understanding about the C, N, and P cycles in the sediments of eutrophic lakes.