Dissipation of Sulfonamides in Soil Emphasizing Taxonomy and Function of Microbiomes by Metagenomic Analysis

New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms

BACKGROUND

Bioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low viability of the exogenous degraders limits their practical application. Understanding the mechanism is important to enhance and optimize performance of the bioaugmentation, which requires a multifaceted analysis of the microbial communities. Here, DNA-stable isotope probing (DNA-SIP) and metagenomic analysis were conducted to decipher the bioaugmentation mechanisms in stabilization pond sediment microcosms inoculated with sulfamethoxazole (SMX)-degrading bacteria (Pseudomonas sp. M2 or Paenarthrobacter sp. R1).

RESULTS

The bioaugmentation with both strains M2 and R1, especially strain R1, significantly improved the biodegradation rate of SMX, and its biodegradation capacity was sustainable within a certain cycle (subjected to three repeated SMX additions). The removal strategy using exogenous degrading bacteria also significantly abated the accumulation and transmission risk of antibiotic resistance genes (ARGs). Strain M2 inoculation significantly lowered bacterial diversity and altered the sediment bacterial community, while strain R1 inoculation had a slight effect on the bacterial community and was closely associated with indigenous microorganisms. Paenarthrobacter was identified as the primary SMX-assimilating bacteria in both bioaugmentation systems based on DNA-SIP analysis. Combining genomic information with pure culture evidence, strain R1 enhanced SMX removal by directly participating in SMX degradation, while strain M2 did it by both participating in SMX degradation and stimulating SMX-degrading activity of indigenous microorganisms (Paenarthrobacter) in the community.

CONCLUSIONS

Our findings demonstrate that bioaugmentation using SMX-degrading bacteria was a feasible strategy for SMX clean-up in terms of the degradation efficiency of SMX, the risk of ARG transmission, as well as the impact on the bacterial community, and the advantage of bioaugmentation with Paenarthrobacter sp. R1 was also highlighted. Video Abstract.

Identification of sulfamethazine degraders in swine farm-impacted river and farmland: A comparative study of aerobic and anaerobic environments

Sulfonamides (SAs) are extensively used antibiotics in the prevention and treatment of animal diseases, leading to significant SAs pollution in surrounding environments. Microbial degradation has been proposed as a crucial mechanism for removing SAs, but the taxonomic identification of microbial functional guilds responsible for SAs degradation in nature remain largely unexplored. Here, we employed 13C-sulfamethazine (SMZ)-based DNA-stable isotope probing (SIP) and metagenomic sequencing to investigate SMZ degraders in three distinct swine farm wastewater-receiving environments within an agricultural ecosystem. These environments include the aerobic riparian wetland soil, agricultural soil, and anaerobic river sediment. SMZ mineralization activities exhibited significant variation, with the highest rate observed in aerobic riparian wetland soil. SMZ had a substantial impact on the microbial community compositions across all samples. DNA-SIP analysis demonstrated that Thiobacillus, Auicella, Sphingomonas, and Rhodobacter were dominant active SMZ degraders in the wetland soil, whereas Ellin6067, Ilumatobacter, Dongia, and Steroidobacter predominated in the agricultural soil. The genus MND1 and family Vicinamibacteraceae were identified as SMZ degrader in both soils. In contrast, anaerobic SMZ degradation in the river sediment was mainly performed by genera Microvirga, Flavobacterium, Dechlorobacter, Atopostipes, and families Nocardioidaceae, Micrococcaceae, Anaerolineaceae. Metagenomic analysis of 13C-DNA identified key SAs degradation genes (sadA and sadC), and various of dioxygenases, and aromatic hydrocarbon degradation-related functional genes, indicating their involvement in degradation of SMZ and its intermediate products. These findings highlight the variations of indigenous SAs oxidizers in complex natural habitats and emphasize the consideration of applying these naturally active degraders in future antibiotic bioremediation.

Structural effects of sulfonamides on the proliferation dynamics of sulfonamide resistance genes in the sequencing batch reactors and the mechanism

Antibiotic resistance genes (ARGs) can be easily promoted by antibiotics, however, the structural effects of antibiotics on the proliferation of ARGs dynamic and the associated mechanisms remain obscure in, especially, activated sludge sequencing batch reactors. In the present study, the effects of 9 sulfonamides (SAs) with different structures on the proliferation dynamic of sulfonamide resistance genes (Suls) in the activated sludge sequencing batch reactors and the corresponding mechanisms were determined (30 days), and the results showed that the largest proliferation value (∆AR) of Suls dynamic for SAs (sulfachloropyridazine) was approximately 2.9 times than that of the smallest one (sulfadiazine). The proliferation of Suls was significantly related to the structural features (minHBint6, SssNH, SHBd and SpMax2_Bhm) that represent the biological activity of SAs. To interpret the phenomenon, a mechanistic model was developed and the results indicated that the biodegradation of SAs (T1/2) rather than conjugative transfer frequency or mutation frequency tends to be the key process for affecting Suls proliferation. T1/2 was proved to be dependent on the interactions between SAs and receptors (Ebinding), the cleavage mode (bond dissociation energy), and the site of nucleophilic assault. Besides, the metagenomic analysis showed that SAs posed significant effect on antibiotic resistome and Tnp31 played a vital role in the proliferation of Suls. Overall, our findings provide important insight into a theoretical basis for understanding the structural effects of SAs on the proliferation of ARGs in SBR systems.

Responses of antibiotic resistance genes in the enhanced biological phosphorus removal system under various antibiotics: Mechanisms and implications

The effects of antibiotics on the proliferation of antibiotic resistant genes (ARGs) in WWTPs have drawn great attention in recent years. The effects of antibiotics on ARGs in the enhanced biological phosphorus removal (EBPR) system and its mechanisms, however, are still not well understood. In this study, EBPR systems were constructed using activated sludge to investigate the effects of ten commonly detected antibiotics in the environment on the proliferation of ARGs and the mechanisms involved. The results showed that the total abundance of ARGs increased to varying degrees with the addition of different antibiotics (0.05 mmol/L), and the top 30 ARGs increased by 271.1 % to 370.0 %. Mobile genetic elements (MGEs), functional modules, and the bacteria community were consistently related to the changes in ARGs. Refractory antibiotics, in particular, have a stronger promoting effect on transduction in the EBPR system. The insertion sequence common region (ISCR) and transposon (Tnp) were identified as crucial factors in the proliferation of ARGs. Moreover, the risk of polyphosphate accumulating organisms (PAOs) carrying ARGs in the presence of antibiotics should not be ignored. Our findings emphasize the potential efficacy of employing strategies that target the reduction of MGEs, regulation of cellular communication, and management of microbial communities to effectively mitigate the risks associated with ARGs.

Fabrication and application of molecularly imprinted polymer doped carbon dots coated silica stationary phase

Facing the difficulties in chromatographic separation of polar compounds, this investigation devotes to developing novel stationary phase. Molecularly imprinted polymers (MIPs) have aroused wide attention, owing to their outstanding selectivity, high stability, and low cost. In this work, a novel stationary phase based on carbon dots (CDs), MIP layer, and silica beads was synthesized to exploit high selectivity of MIPs, excellent physicochemical property of CDs, and outstanding chromatographic performances of silica microspheres simultaneously. The MIP doped CDs coated silica (MIP-CDs/SiO₂) stationary phase was systematically characterized by scanning electron microscopy (SEM), Brunauer-Emmett-Teller (BET) surface area measurement, and carbon elemental analysis. Furthermore, the chromatographic performance of the MIP-CDs/SiO₂ column was thoroughly assessed by using a wide variety of compounds (including nucleosides, sulfonamides, benzoic acids, and some other antibiotics). Meanwhile, the separation efficiency of the MIP-CDs/SiO₂ stationary phase was superior to other kinds of stationary phases (e.g. nonimprinted NIP-CDs/SiO₂, MIP/SiO₂, and C18-SiO₂). The results demonstrated that MIP-CDs/SiO₂ column exhibited best performance in terms of chromatographic separation. For all tested compounds, the resolution value was not less than 1.60, and the column efficiency of MIP-CDs/SiO₂ for thymidine was 22,740 plates/m. The results further indicate that the MIP-CDs/SiO₂ column can combine the good properties of MIP, CDs, with those of silica microbeads. Therefore, the developed MIP-CDs/SiO₂ stationary phase can be applied in the separation science and chromatography-based techniques.

Impact of clomazone on bacterial communities in two soils

Introduction

Bacterial communities are important for soil functions, but the effect of clomazone on network complexity, composition, and stability is not well studied.

Method

In this study, two agricultural soils were used to test the impact of clomazone on bacterial communities, and the two soils were treated with three concentrations of clomazone (0, 0.8, 8, and 80 mg kg1) in an incubator.

Results and discussion

Bacterial network nodes, links, and average degrees were all decreased by 9-384, 648-829, and 0.703-2.429, respectively. Based on keystone nodes, the topological roles of the nodes were also influenced by clomazone. Bacterial network composition was also impacted based on the analysis of similarity (ANOSIM) and network dissimilarity. Compared with control and clomazone treatments in both soils, the ANOSIM between control and all clomazone treatments was higher than 0.6, network dissimilarities were 0.97-0.98, shared nodes were 131-260, and shared links were 12-100. The bacterial network stability was decreased by clomazone, with decreased robustness by 0.01-0.016 and increased vulnerability by 0.00023-0.00147 in both soils. There were fewer bacterial network modules preserved after clomazone treatment, and the bacterial network community functions were also impacted in both soils. Based on these results, soil bacterial species connections, modularization, and network stability were significantly impacted by clomazone.

Ecological insight into antibiotic resistome of ion-adsorption rare earth mining soils from south China by metagenomic analysis

Antibiotic resistome has led to growing global threat to public health. Rare earth elements play important roles in modern society and mining activity for them has caused serious impact on soil ecosystems. However, antibiotic resistome in, especially, ion-adsorption rare earth-related soils is still poorly understood. In this work, soils were collected from ion-adsorption rare earth mining areas and adjacent regions of south China and metagenomic analysis was employed for profile, driving factors and ecological assembly of antibiotic resistome in the soils. Results show prevalence of antibiotic resistance genes conferring resistance to tetracycline/fluoroquinolone (adeF), peptide (bcrA), aminoglycoside (rpsL), tetracycline (tet(A)) and mupirocin (mupB) in ion-adsorption rare earth mining soils. Profile of antibiotic resistome is accompanied by its driving factors, i.e., physicochemical properties (La, Ce, Pr, Nd and Y of rare earth elements in 12.50-487.90 mg kg^-1), taxonomy (Proteobacteria, Actinobacteria) and mobile genetic elements (MGEs, plasmid pYP1, Transposase_20). Variation partitioning analysis and partial least-squares-path modeling demonstrate that taxonomy is the most important individual contributor and pose most direct/indirect effect to antibiotic resistome. Further, null model analysis reveals stochastic processes as dominant ecological assembly of antibiotic resistome. This work advances our knowledge on antibiotic resistome with emphasis on ecological assembly in ion-adsorption rare earth-related soils for ARGs mitigation, mining management and mine restoration.

Plant rhizosphere defense system respond differently to emerging polyfluoroalkyl substances F-53B and PFOS stress

Chlorinated polyfluoroalkyl ether sulfonate (F-53B) and perfluorooctanesulfonate (PFOS) are used and emitted as fog inhibitors in the chromium plating industry, and they are widely detected worldwide. To study the effects of F-53B and PFOS on the rhizosphere defense system, they were added at two levels (0.1 and 50 mg L^-1) to the soil where different plants (Lythrum salicaria and Phragmites communis) were grown. In bulk soils, high concentrations of F-53B/PFOS resulted in significant increases in soil pH, NH₄⁺-N, and NO₃^--N (the effect of PFOS on NO₃^--N was not significant). Moreover, the extent of the effects of PFOS and F-53B on the physicochemical properties of bulk soils were different (e.g., PFOS caused an increase of NH₄⁺-N by 8.94%-45.97% compared to 1.63%-25.20% for F-53B). Root exudates and PFASs together influenced the physicochemical properties of rhizosphere soils (e.g., TOC increased significantly in contaminated rhizosphere soils but did not change in non-bulk soils). Under the influence of F-53B/PFOS, the root exudates regulated by plants were changed and weakened the effect of F-53B/PFOS on microbial community of rhizosphere soil. The rhizosphere defense systems of different plants have both similarities and differences in response to different substances and concentrations.

Clomazone impact on fungal network complexity and stability

Introduction

Soil fungal network composition and stability are important for soil functions, but there is less understanding of the impact of clomazone on network complexity and stability.

Methods

In this work, two agricultural soils were used to investigate the impact of clomazone on fungal network complexity, composition, and stability. The two soils were treated with clomazone solution (0, 0.8, 8, and 80  mg kg^-1) and kept in an incubator.

Results and Discussion

Under the influence of clomazone, the fungal network nodes were decreased by 12-42; however, the average degree was increased by 0.169-1.468 and fungal network density was increased by 0.003-0.054. The keystone nodes were significantly changed after clomazone treatment. Network composition was also impacted. Specifically, compared with control and clomazone treatments in both soils, the shared edges were fewer than 54 in all comparisons, and network dissimilarity was 0.97-0.98. These results suggested that fungal network composition was significantly impacted. The network robustness was increased by 0.0018-0.0209, and vulnerability was decreased by 0.00018-0.00059 in both soils, which indicated that fungal network stability was increased by clomazone. In addition, the functions of network communities were also changed in both soils. These results indicated that clomazone could significantly impact soil fungal networks.

Deciphering the fate of antibiotic resistance genes in norfloxacin wastewater treated by a bio-electro-Fenton system

The misuse of antibiotics has increased the prevalence of antibiotic resistance genes (ARGs), considered a class of critical environmental contaminants due to their ubiquitous and persistent nature. Previous studies reported the potentiality of bio-electro-Fenton processes for antibiotic removal and ARGs control. However, the production and fate of ARGs in bio-electro-Fenton processes triggered by microbial fuel cells are rare. In this study, the norfloxacin (NFLX) average residual concentrations within two days were 2.02, 6.07 and 14.84 mg/L, and the average removal efficiency of NFLX was 79.8 %, 69.6 % and 62.9 % at the initial antibiotic concentrations of 10, 20 and 40 mg/L, respectively. The most prevalent resistance gene type in all processes was the fluoroquinolone antibiotic gene. Furthermore, Proteobacteria was the dominant ARG-carrying bacteria. Overall, this study can provide theoretical support for the efficient treatment of high antibiotics-contained wastewater by bio-electro-Fenton systems to better control ARGs from the perspective of ecological security.

Hydrogen Peroxide Activated by Biochar-Supported Sulfidated Nano Zerovalent Iron for Removal of Sulfamethazine: Response Surface Method Approach

Biochar (BC)-supported sulfide-modified nanoscale zerovalent iron (S-nZVI/BC) was prepared using the liquid-phase reduction method for the application of the removal of sulfamethazine (SMZ) from water. The reaction conditions were optimized by the Box−Behnken response surface method (RSM). A model was constructed based on the influence factors of the removal rate, i.e., the carbon-to-iron ratio (C/Fe), iron-sulfur ratio (Fe/S), pH, and hydrogen peroxide (H2O2) concentration, and the influence of each factor on the removal efficiency was investigated. The optimal removal process parameters were determined based on theoretical and experimental results. The results showed that the removal efficiency was significantly affected by the C/Fe ratio and pH (p < 0.0001) but relatively weakly affected by the Fe/S ratio (p = 0.0973) and H2O2 concentration (p = 0.022). The optimal removal process parameters were as follows: 0.1 mol/L H2O2, a pH of 3.18, a C/Fe ratio of 0.411, and a Fe/S ratio of 59.75. The removal rate of SMZ by S-nZVI/BC was 100% under these conditions. Therefore, it is feasible to use the Box−Behnken RSM to optimize the removal of emerging pollutants in water bodies by S-nZVI/BC.

Sulfonamide-metabolizing microorganisms and mechanisms in antibiotic-contaminated wetland sediments revealed by stable isotope probing and metagenomics

Sulfonamide (SA) antibiotics are ubiquitous pollutants in livestock breeding and aquaculture wastewaters, which increases the propagation of antibiotic resistance genes. Microbes with the ability to degrade SA play important roles in SA dissipation, but their diversity and the degradation mechanism in the field remain unclear. In the present study, we employed DNA-stable isotope probing (SIP) combined with metagenomics to explore the active microorganisms and mechanisms of SA biodegradation in antibiotic-contaminated wetland sediments. DNA-SIP revealed various SA-assimilating bacteria dominated by members of Proteobacteria, such as Bradyrhizobium, Gemmatimonas, and unclassified Burkholderiaceae. Both sulfadiazine and sulfamethoxazole were dissipated mainly through the initial ipso-hydroxylation, and were driven by similar microbes. sadA gene, which encodes an NADH-dependent monooxygenase, was enriched in the ¹³C heavy DNA, confirming its catalytic capacity for the initial ipso-hydroxylation of SA in sediments. In addition, some genes encoding dioxygenases were also proposed to participate in SA hydroxylation and aromatic ring cleavage based on metagenomics analysis, which might play an important role in SA metabolism in the sediment ecosystem when Proteobacteria was the dominant active bacteria. Our work elucidates the ecological roles of uncultured microorganisms in their natural habitats and gives a deeper understanding of in-situ SA biodegradation mechanisms.

Impact of Dietary Vitamin D3 Supplementation on Growth, Molting, Antioxidant Capability, and Immunity of Juvenile Chinese Mitten Crabs (Eriocheir sinensis) by Metabolites and Vitamin D Receptor

Vitamin D₃ (vit-D₃), as an indispensable and fat-soluble nutrient, is associated with skeletal mineralization and health in mammals. However, such associations have not been well studied in economically important crustaceans. Six levels of vit-D₃ with isonitrogenous and isolipidic diets were used to feed Eriocheir sinensis. The range of optimal vit-D₃ requirements is 5685.43-10,000 IU/kg based on growth. The crabs fed 9000 IU/kg vit-D₃ showed the best growth performance. This vit-D₃ dose significantly increased antioxidant capacity in the hepatopancreas and intestine and was optimal for molting and innate immunity via quantitative polymerase chain reaction analysis. Transcriptomics analyses indicate that vit-D₃ could alter protein processing in the endoplasmic reticulum, steroid biosynthesis, and antigen processing and presentation. As shown by the enzyme-linked immunosorbent assay, vit-D₃ could improve vitamin D receptor, retinoic acid receptor, and C-type lectins concentrations. The 1α,25-dihydroxy vit-D₃ content in serum was significantly higher in 3000-9000 IU/kg vit-D₃. The study suggests that dietary vit-D₃ and its metabolites can regulate molting and innate immunity in crabs.