Simultaneous 3-/4-Hydroxybenzoates Biodegradation and Arsenite Oxidation by Hydrogenophaga sp. H7

The ecology of bacterial communities in groundwater of industrial areas: Diversity, composition, network, and assembly

Groundwater provides freshwater resources necessary for mankind, but its quality is significantly impacted by anthropologic activities. The unique characteristics of groundwater provide a special niche for bacterial colonization. To maintain the sustainability of groundwater ecosystem, a good understanding of the influencing factors and assembly mechanisms for bacterial communities is necessary. Here, we investigated the bacterial communities of groundwater from two industrial zones in Shanghai, a highly industrialized city, during the wet and dry seasons using the high-throughput sequencing technology. Our study uncovered the significant effects of season, geographical location, and industrial type on the diversity and composition of groundwater bacterial communities, particularly, we found that season was the most dominant factor with much stronger influences (give the explanation 17.7%) in comparison with geographical location (8.8%) and industrial type (7.5%). Co-occurrence networks revealed that geographical location explained more variations of bacterial ecological network than season did. Both distance-decay of similarities and variation partitioning analyses indicated that the assembly of groundwater bacterial communities was more governed by environmental filtering compared to spatial-related dispersal. Finally, null model analysis suggested the role of stochastic processes, including dispersal and drift, in shaping the groundwater bacterial communities cannot be ignored. These findings would benefit to improve our understanding of the bacterial communities in groundwater ecosystem and provide a theoretical foundation for groundwater health management.

Mechanism of β-blocker biodegradation by wastewater microorganisms

The recalcitrant β-blockers have been widely detected in aquatic environments up to several hundred μg/L, which are major contributors to β1 antagonistic activities in wastewater. Their biodegradation mechanisms remain obscure, hindering the development of efficient removal techniques. This study constructed the biodegradation pathways for three typical β-blockers, namely atenolol, metoprolol, and propranolol, assessed the toxicity of their major biotransformation products, and identified the key enzyme catalyzing the O-dealkylation reaction leading to pollutant mineralization. Atenolol and metoprolol degradation was more efficient than that of propranolol by activated sludge, producing metoprolol acid (MTPA) as a major intermediate. Hydrogenophaga sp. YM1 isolated from activated sludge possess the α-ketoglutarate dependent dioxygenase (TfdA) responsible for O-dealkylation of MTPA and propranolol, producing 4-hydroxyphenylacetic acid (4-HPA) that can be further degraded and ultimately enters the TCA cycle. The role of TfdA was verified by proteomics, enzyme stimulation/inhibition tests, and gene knockout experiments. Molecular docking suggests its different interactions with MTPA and propranolol. Acetate facilitated the degradation of β-blockers efficiently. The results may shed light on enhanced biological removals of broader β-blockers and their transformation products in the environment.

Characterization of arsenic-metabolizing bacteria in an alkaline soil

Arsenite (As(III)) is more toxic, mobilizable and bioavailable than arsenate (As(V)). Hence, the transformations between As(III) and As(V) are crucial for the toxicity and mobility of arsenic (As). However, As transformation and microbial communities involved in alkaline soils are largely unknown. Here we investigate two major pathways of As transformation, i.e., As(III) oxidation and As(V) reduction, and identify the bacteria involved in the alkaline soil by combining stable isotope probing with shotgun metagenomic sequencing. As(III) oxidation and significant increase of the aioA genes copies were observed in the treatments amended with As(III) and NO₃^-, suggesting that As(III) oxidation can couple with nitrate reduction and was mainly catalyzed by the microorganisms containing aioA genes. As(V) reduction was detected in the treatments amended with As(V) and acetate where the abundance of arrA gene significantly increased, indicating that microorganisms with arrA genes were the key As(V) reducers. Acidovorax, Hydrogenophaga, and Ramlibacter were the putative nitrate-dependent As(III) oxidizers, and Deinococcus and Serratia were the putative respiratory As(V) reducers. These findings will improve our understanding of As metabolism and are meaningful for mapping out bioremediation strategies of As contamination in alkaline environment.

Novel pathway and acetate-facilitated complete atenolol degradation by Hydrogenophaga sp. YM1 isolated from activated sludge

Atenolol is a widely prescribed beta-blocker that has been detected in wastewater at concentrations up to 300 μg/L. The parent compound and its transformation products pose risks to aquatic organisms. Efficient atenolol degrading microorganism has yet to be identified, and its biodegradation pathway is unknown. In this study, Hydrogenophaga sp. YM1 isolated from activated sludge can degrade atenolol efficiently (286.1 ± 4.0 μg/g dry wt/h in actual wastewater), where atenolol acid, and four newly detected products (4-hydroxyphenylacetic acid, 3-(isopropylamino)-1,2-propanediol, 3-amino-1,2-propanediol and 4-(1-amino-2-hydroxy-3-propoxy) benzeneacetic acid) were the main intermediates. Key genes involved in atenolol degradation were proposed based on RNA-seq and validated by RT-qPCR. The ether bond cleavage of atenolol acid was the rate-limiting step likely catalyzed by the α-ketoglutarate dependent 2,4-dichlorophenoxyacetate dioxygenase. The further degradation of 4-hydroxyphenylacetic acid followed the homoprotocatechuate degradation pathway, enabling complete conversion to CO₂. Acetate addition (39-156 mg COD/L) under aerobic condition enhanced atenolol degradation by 29-37% and decreased the accumulation of atenolol acid, likely because acetate oxidation provided α-ketoglutarate and additional reducing power. Activated sludge core microorganisms have limited atenolol mineralization potentials. Enriching Hydrogenophaga-like populations and/or providing such as acetate can drive more complete conversion of atenolol in natural and engineered biosystems.

Simultaneous removal of nitrogen and arsenite by heterotrophic nitrification and aerobic denitrification bacterium Hydrogenophaga sp. H7

Introduction

Nitrogen and arsenic contaminants often coexist in groundwater, and microbes show the potential for simultaneous removal of nitrogen and arsenic. Here, we reported that Hydrogenophaga sp. H7 was heterotrophic nitrification and aerobic denitrification (HNAD) and arsenite [As(III)] oxidation bacterium.

Methods

The appearance of nitrogen removal and As(III) oxidation of Hydrogenophaga sp. H7 in liquid culture medium was studied. The effect of carbon source, C/N ratio, temperature, pH values, and shaking speeds were analyzed. The impact of strains H7 treatment with FeCl3 on nitrogen and As(III) in wastewater was assessed. The key pathways that participate in simultaneous nitrogen removal and As(III) oxidation was analyzed by genome and proteomic analysis.

Results and discussion

Strain H7 presented efficient capacities for simultaneous NH₄ ⁺-N, NO₃ ^--N, or NO₂ ^--N removal with As(III) oxidation during aerobic cultivation. Strikingly, the bacterial ability to remove nitrogen and oxidize As(III) has remained high across a wide range of pH values, and shaking speeds, exceeding that of the most commonly reported HNAD bacteria. Additionally, the previous HNAD strains exhibited a high denitrification efficiency, but a suboptimal concentration of nitrogen remained in the wastewater. Here, strain H7 combined with FeCl3 efficiently removed 96.14% of NH₄ ⁺-N, 99.08% of NO₃ ^--N, and 94.68% of total nitrogen (TN), and it oxidized 100% of As(III), even at a low nitrogen concentration (35 mg/L). The residues in the wastewater still met the V of Surface Water Environmental Quality Standard of China after five continuous wastewater treatment cycles. Furthermore, genome and proteomic analyses led us to propose that the shortcut nitrification-denitrification pathway and As(III) oxidase AioBA are the key pathways that participate in simultaneous nitrogen removal and As(III) oxidation.

Methylotrophs and Hydrocarbon-Degrading Bacteria Are Key Players in the Microbial Community of an Abandoned Century-Old Oil Exploration Well

In this work, we studied the microbial community and the physicochemical conditions prevailing in an exploratory oil well, abandoned a century ago, located in the Cahuita National Park (Costa Rica). According to our analysis, Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including phenanthrene/anthracene, fluoranthene, pyrene, dibenzothiophene, tricyclic terpanes, pyrene, sesquiterpenes, sterane, and n-alkanes. Based on the analysis of 16S rRNA gene amplicons, we detected a significant abundance of methylotrophic bacteria such as Methylobacillus (6.3-26.0% of total reads) and Methylococcus (4.1-30.6%) and the presence of common genera associated with hydrocarbon degradation, such as Comamonas (0.8-4.6%), Hydrogenophaga (1.5-3.3%) Rhodobacter (1.0-4.9%), and Flavobacterium (1.1-6.5%). The importance of C1 metabolism in this niche was confirmed by amplifying the methane monooxygenase (MMO)-encoding gene (pmo) from environmental DNA and the isolation of two strains closely related to Methylorubrum rhodesianum and Paracoccus communis with the ability to growth using methanol and formate as sole carbon source respectively. In addition, we were able to isolated 20 bacterial strains from the genera Pseudomonas, Acinetobacter, and Microbacterium which showed the capability to grow using the hydrocarbons detected in the oil well as sole carbon source. This work describes the physicochemical properties and microbiota of an environment exposed to hydrocarbons for 100 years, and it not only represents a contribution to the understanding of microbial communities in environments with permanently high concentrations of these compounds but also has biotechnological implications for bioremediation of petroleum-polluted sites.

Dynamics of Soil Microbial Communities During Diazepam and Oxazepam Biodegradation in Soil Flooded by Water From a WWTP

The demand for energy and chemicals is constantly growing, leading to an increase of the amounts of contaminants discharged to the environment. Among these, pharmaceutical molecules are frequently found in treated wastewater that is discharged into superficial waters. Indeed, wastewater treatment plants (WWTPs) are designed to remove organic pollution from urban effluents but are not specific, especially toward contaminants of emerging concern (CECs), which finally reach the natural environment. In this context, it is important to study the fate of micropollutants, especially in a soil aquifer treatment (SAT) context for water from WWTPs, and for the most persistent molecules such as benzodiazepines. In the present study, soils sampled in a reed bed frequently flooded by water from a WWTP were spiked with diazepam and oxazepam in microcosms, and their concentrations were monitored for 97 days. It appeared that the two molecules were completely degraded after 15 days of incubation. Samples were collected during the experiment in order to follow the dynamics of the microbial communities, based on 16S rRNA gene sequencing for Archaea and Bacteria, and ITS2 gene for Fungi. The evolution of diversity and of specific operating taxonomic units (OTUs) highlighted an impact of the addition of benzodiazepines, a rapid resilience of the fungal community and an evolution of the bacterial community. It appeared that OTUs from the Brevibacillus genus were more abundant at the beginning of the biodegradation process, for diazepam and oxazepam conditions. Additionally, Tax4Fun tool was applied to 16S rRNA gene sequencing data to infer on the evolution of specific metabolic functions during biodegradation. It finally appeared that the microbial community in soils frequently exposed to water from WWTP, potentially containing CECs such as diazepam and oxazepam, may be adapted to the degradation of persistent contaminants.

Recent Progress and Prospects in Catalytic Water Treatment

Presently, conventional technologies in water treatment are not efficient enough to completely mineralize refractory water contaminants. In this context, the implementation of catalytic processes could be an alternative. Despite the advantages provided in terms of kinetics of transformation, selectivity, and energy saving, numerous attempts have not yet led to implementation at an industrial scale. This review examines investigations at different scales for which controversies and limitations must be solved to bridge the gap between fundamentals and practical developments. Particular attention has been paid to the development of solar-driven catalytic technologies and some other emerging processes, such as microwave assisted catalysis, plasma-catalytic processes, or biocatalytic remediation, taking into account their specific advantages and the drawbacks. Challenges for which a better understanding related to the complexity of the systems and the coexistence of various solid-liquid-gas interfaces have been identified.

Diversity and Metabolic Potentials of As(III)-Oxidizing Bacteria in Activated Sludge

Biological arsenite [As(III)] oxidation is an important process in the removal of toxic arsenic (As) from contaminated water. However, the diversity and metabolic potentials of As(III)-oxidizing bacteria (AOB) responsible for As(III) oxidation in wastewater treatment facilities are not well documented. In this study, two groups of bioreactors inoculated with activated sludge were operated under anoxic or oxic conditions to treat As-containing synthetic wastewater. Batch tests of inoculated sludges from the bioreactors further indicated that microorganisms could use nitrate or oxygen as electron acceptors to stimulate biological As(III) oxidation, suggesting the potentials of this process in wastewater treatment facilities. In addition, DNA-based stable isotope probing (DNA-SIP) was performed to identify the putative AOB in the activated sludge. Bacteria associated with Thiobacillus were identified as nitrate-dependent AOB, while bacteria associated with Hydrogenophaga were identified as aerobic AOB in activated sludge. Metagenomic binning reconstructed a number of high-quality metagenome-assembled genomes (MAGs) associated with the putative AOB. Functional genes encoding As resistance, As(III) oxidation, denitrification, and carbon fixation were identified in these MAGs, suggesting their potentials for chemoautotrophic As(III) oxidation. In addition, the presence of genes encoding secondary metabolite biosynthesis and extracellular polymeric substance metabolism in these MAGs may facilitate the proliferation of these AOB in activated sludge and enhance their capacity for As(III) oxidation. IMPORTANCE AOB play an important role in the removal of toxic arsenic from wastewater. Most of the AOB have been isolated from natural environments. However, knowledge regarding the structure and functional roles of As(III)-oxidizing communities in wastewater treatment facilities is not well documented. The combination of DNA-SIP and metagenomic binning provides an opportunity to elucidate the diversity of in situ AOB community inhabiting the activated sludges. In this study, the putative AOB responsible for As(III) oxidation in wastewater treatment facilities were identified, and their metabolic potentials, including As(III) oxidation, denitrification, carbon fixation, secondary metabolite biosynthesis, and extracellular polymeric substance metabolism, were investigated. This observation provides an understanding of anoxic and/or oxic AOB during the As(III) oxidation process in wastewater treatment facilities, which may contribute to the removal of As from contaminated water.

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.

Bacteria responsible for antimonite oxidation in antimony-contaminated soil revealed by DNA-SIP coupled to metagenomics

Antimony (Sb), the analog of arsenic (As), is a toxic metalloid that poses risks to the environment and human health. Antimonite (Sb(III)) oxidation can decrease Sb toxicity, which contributes to the bioremediation of Sb contamination. Bacteria can oxidize Sb(III), but the current knowledge regarding Sb(III)-oxidizing bacteria (SbOB) is limited to pure culture studies, thus underestimating the diversity of SbOB. In this study, Sb(III)-oxidizing microcosms were set up using Sb-contaminated rice paddies as inocula. Sb(III) oxidation driven by microorganisms was observed in the microcosms. The increasing copies and transcription of the arsenate-oxidizing gene, aioA, in the microcosms during biotic Sb(III) oxidation indicated that microorganisms mediated Sb(III) oxidation via the aioA genes. Furthermore, a novel combination of DNA-SIP and shotgun metagenomic was applied to identify the SbOB and predict their metabolic potential. Several putative SbOB were identified, including Paracoccus, Rhizobium, Achromobacter and Hydrogenophaga. Furthermore, the metagenomic analysis indicated that all of these putative SbOB contained aioA genes, confirming their roles in Sb(III) oxidation. These results suggested the concept of proof of combining DNA-SIP and shotgun metagenomics directly. In addition, the identification of the novel putative SbOB expands the current knowledge regarding the diversity of SbOB.

Immobilization of Cd Using Mixed Enterobacter and Comamonas Bacterial Reagents in Pot Experiments with Brassica rapa L

Enterobacter sp. A11 and Comamonas sp. A23 were isolated and identified. Coculturing these two strains with Cd(II) led to the production of biofilm, H₂S, and succinic acid (SA), and Cd(II) was adsorbed by cells and formed CdS precipitates. After centrifugation, 97% Cd(II) was removed from the coculture. Proteomic and metabolomic analyses of the cocultured bacteria revealed that H₂S and SA production pathways, metal transportation, and TCA cycle were active under Cd(II) stress. In vitro addition of SA enhanced the production of H₂S and biofilm formation and Cd(II) adsorption. Two-season greenhouse pot experiments with Brassica rapa L. were performed with and without the coculture bacteria. Compared with the control, the average Cd amounts of the two-season pot experiments of the aboveground plants were decreased by 71.3%, 62.8%, and 38.6%, and the nonbioavailable and immobilized Cd in the soils were increased by 211.8%, 213.4%, and 116.7%, for low-, medium-, and high- Cd-spiked soils, respectively. The two strains survived well in soil during plant growth using plate counting, quantitative real-time PCR, and metagenomics analysis. Our results indicate that the combination of Enterobacter and Comamonas strains with the production of H₂S and biofilm are important effectors for the highly efficient immobilization of Cd.

Complex effects of pH and organic shocks on arsenic oxidation and removal by manganese-oxidizing aerobic granular sludge in sequencing batch reactors

Biological technologies are efficient and economical methods for removing toxic arsenic (As) from organic wastewaters. In this study, four sequencing batch reactors of manganese-oxidizing aerobic granular sludge (Mn-AGS) were operated in duplicate and imposed with acidic pH and high organic shocks. Batch experiments with different initial conditions were conducted to investigate the effects of pH and organic load on As(III) oxidation and removal. The results indicate that acidic pH shocks (influent pH decreased to 4.0/3.0) unexpectedly increased the As removal efficiency from 23.4-38.2% to 64.7-72.5%. The effects of high organic shocks were very complicated, as the results of the shocks were opposite twice. According to the results of the batch experiments, it was estimated that the suitable pH range for high performance was 5.0-8.5 in reaction liquid. Although acidic pH shocks initially inhibited As(III) oxidation and removal, they largely extended the reaction time of the suitable pH range and finally improved the As removal efficiency. There were many negative and positive factors affecting the As removal during the high organic shocks, leading to the unstable responses. Moreover, the microbial community was not largely changed by pH or organic shocks, and genus Hydrogenophaga (∼8%) might be responsible for the microbial As(III) oxidation. Finally, several operation strategies were proposed to obtain high performance, such as liquid pH control and aeration improvement.

Simultaneous removal of chromate and arsenite by the immobilized Enterobacter bacterium in combination with chemical reagents

Simultaneous chromate [Cr(VI)] reduction and arsenite [As(III)] oxidation is a promising pretreatment process for Cr and As removal. Here, a facultative anaerobic bacterium, Enterobacter sp. Z1, presented capacities of simultaneous Cr(VI) reduction and As(III) oxidation during anoxic cultivation in a wild range of temperature (20-45 °C) and pH (Cerkez et al., 2015; Chen et al., 2015; China Environmental Prote, 1996; Fan et al., 2008, 2019) conditions. Strikingly, strain Z1 could simultaneously contribute up to 92.8% of the reduction of Cr(VI) and 45.8% of the oxidation of As(III) in wastewater. The cells of strain Z1 were embedded with sodium alginate to produce biobeads, and the biobeads exhibited stable ratio of Cr(VI) reduction (91.8%) and As(III) oxidation (29.6%) even in the 5 continuous cycles of wastewater treatment. Moreover, in a process pretreated with the Z1 biobeads followed a precipitation with Ca(OH)₂ and FeCl₃, the removal efficiencies in wastewater were 98.9% and 98.3% for total Cr and As, respectively, which were 44.1% and 9.8% higher than those of using Ca(OH)₂ and FeCl₃, only. The residual amounts of Cr and As met the national standard levels of wastewater discharge. Proteomics analysis showed that cysteine, sulfur and methionine metabolisms, As resistance and oxidoreductase (CysH, CysI, CysJ, NemA and HemF) were induced by Cr(VI) and As(III). Moreover, the addition of cysteine to the medium also significantly improved bacterial Cr(VI) reduction rate. Our results provide a novel microbial pretreatment approach for enhancing remediation of Cr(VI) and As(III) pollution in wastewater, and reveal the evident that cysteine, sulfur and methionine metabolisms, As resistance and oxidoreductases are associated with the redox conversion of Cr(VI) and As(III).