Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils.

Microbial arsenic transformations play essential roles in controlling pollution and ameliorating risk. This study combined high-throughput sequencing and PCR-based approaches targeting both the 16 S rRNA and arsenic functional genes to investigate the temporal and spatial dynamics of the soil microbiomes impacted by high arsenic contamination (9.13 to 911.88 mg/kg) and to investigate the diversity and abundance of arsenic functional genes in soils influenced by an arsenic gradient. The results showed that the soil microbiomes were relatively consistent and mainly composed of Actinobacteria (uncultured Gaiellales and an unknown_67 - 14 bacterium), Proteobacteria, Firmicutes (particularly, Bacillus), Chloroflexi, and Acidobacteria (unknown_Subgroup_6). Although a range of arsenic functional genes (e.g., arsM, arsC, arrA, and aioA) were identified by shotgun metagenomics, only the arsM gene was detected by the PCR-based method. The relative abundance of the arsM gene accounted for 0.20%-1.57% of the total microbial abundance. Combining all analyses, arsenic methylation mediated by the arsM gene was proposed to be a key process involved in the arsenic biogeochemical cycle and mitigation of arsenic toxicity. This study advances our knowledge about arsenic mechanisms over the long-term in highly contaminated soils.

Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons.

Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg-1), moderate (600 mg kg-1), and high (1200 mg kg-1) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11.58, 14.51, and 8.94 mg kg-1 sediment day-1) than in the dry-season sediments (3.51, 12.56, and 5.91 mg kg-1 sediment day-1) possibly due to higher nutrient accumulation caused by rainfall and higher diversity of potential phenanthrene-degrading bacteria. The results suggested that the mangrove sediment microbiome significantly clustered according to season. Although Gram-negative phenanthrene-degrading bacteria (i.e., Anaerolineaceae, Marinobacter, and Rhodobacteraceae) played a key role in both dry and wet seasons, distinctly different phenanthrene-degrading bacterial taxa were observed in each season. Halomonas and Porticoccus were potentially responsible for the degradation of phenanthrene in the dry and wet seasons, respectively. The knowledge gained from this study contributes to the development of effective and rationally designed microbiome innovations for oil removal.

Arsenic speciation, the abundance of arsenite-oxidizing bacteria and microbial community structures in groundwater, surface water, and soil from a gold mine.

The arsenic speciation, the abundance of arsenite-oxidizing bacteria, and microbial community structures in the groundwater, surface water, and soil from a gold mining area were explored using the PHREEQC model, cloning-ddPCR of the aioA gene, and high-throughput sequencing of the 16S rRNA gene, respectively. The analysis of the aioA gene showed that arsenite-oxidizing bacteria retrieved from groundwater, surface water, and soil were associated with Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. In groundwaters from the mining area, there were relatively high ratios of aioA/total 16S rRNA gene copies and the dominance of As5+, which suggested the presence and activity of arsenite-oxidizing bacteria. Metagenomic analysis revealed that the majority of the soil and surface water microbiomes were Proteobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi, whereas the groundwater microbiomes were dominated exclusively by Betaproteobacteria and Alphaproteobacteria. Geochemical factors influencing the microbial structure in the groundwater were As, residence time, and groundwater flowrate, while those showing a positive correlation to the microbial structure in the surface water were TOC, ORP, and DO. This study provides insights into the groundwater, surface water, and soil microbiomes from a gold mine and expands the current understanding of the diversity and abundance of arsenite-oxidizing bacteria, playing a vital role in global As cycling.

Photolytic fate of (E)- and (Z)-endoxifen in water and treated wastewater exposed to sunlight.

Endoxifen is the main active metabolite of a common cytostatic drug, tamoxifen. Endoxifen has been recently detected in the final effluent of municipal wastewater treatment plants. The antiestrogenic activity of endoxifen could bring negative effects to aquatic life if released to the water environment. This study elucidated the fate and susceptibility of (E)- and (Z)-endoxifen (2 µg mL-1, 1:1 wt ratio between the two easily interchangeable isomers) in wastewater and receiving surface water to sunlight. Phototransformation by-products (PBPs) and their toxicity were determined. Sunlight reduced at least 83% of endoxifen concentration in wastewater samples, whereas in surface water samples, 60% of endoxifen was photodegraded after 180 min of the irradiation. In ultrapure water samples spiked with endoxifen, PBPs were mainly generated via con-rotatory 6π-photocyclization, followed by oxidative aromatization. These PBPs underwent secondary reactions leading to a series of PBPs with different molecular weights. Eight PBPs were identified and the toxicity analysis via the Toxicity Estimation Software Tool revealed that seven of these PBPs are more toxic than endoxifen itself. This is likely due to the formation of poly-aromatic core in the PBPs due to exposure to sunlight. Therefore, highly toxic PBPs may be generated if endoxifen is present in water and wastewater exposed to sunlight. The presence, fates and activities of these PBPs in surface water especially at locations close to treated wastewater discharge points should be investigated.

Effects of Arsenic and Iron on the Community and Abundance of Arsenite-Oxidizing Bacteria in an Arsenic-Affected Groundwater Aquifer.

Arsenic (As) contamination of groundwater aquifers is a global environmental problem, especially in South and Southeast Asian regions, and poses a risk to human health. Arsenite-oxidizing bacteria that transform As(III) to less toxic As(V) can be potentially used as a groundwater As remediation strategy. This study aimed to examine the community and abundance of arsenite-oxidizing bacteria in groundwater with various As concentrations from Rayong Province, Thailand using PCR-cloning-sequencing and quantitative PCR (qPCR) of catalytic subunit of arsenite oxidase gene (aioA). Key factors influencing their community and abundance were also identified. The results demonstrated that arsenite-oxidizing bacteria retrieved from groundwater were phylogenetically related to Betaproteobacteria and Alphaproteobacteria. The aioA gene abundances ranged from 8.6 × 101 to 1.1 × 104 copies per ng of genomic DNA, accounting for 0.16-1.37% of the total 16S rRNA bacterial gene copies. Although the abundance of arsenite-oxidizing bacteria in groundwater was low, groundwater with As(III) dominance likely promoted their abundance which possibly played an important role in chemolithoautotrophic oxidation of As(III) to As(V). Fe and As(III) were the major environmental factors influencing the community and abundance of arsenite-oxidizing bacteria. The knowledge gained from this study can be used to further contribute to the development of bioremediation strategies for As removal from groundwater resources.

Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes.

The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially controlled arsenic immobilization in the aquifers. Analysis of the aioA gene suggested that arsenite-oxidizing bacteria phylogenetically associated with Alpha-, Beta-, and Gamma proteobacteria were present at low abundance (0.85 to 37.13%) and were more prevalent in shallow aquifers and surface water. The concentrations of dissolved oxygen and total phosphorus significantly governed the microbiomes analyzed in this study, while the combination of NO3 --N concentration and oxidation-reduction potential significantly influenced the diversity and abundance of arsenite-oxidizing bacteria in the aquifers. The knowledge of microbial community structures and functions in relation to deep and shallow aquifers is required for further development of sustainable aquifer management.

Mechanisms of arsenic contamination associated with hydrochemical characteristics in coastal alluvial aquifers using multivariate statistical technique and hydrogeochemical modeling: a case study in Rayong province, eastern Thailand.

The rapid development of Rayong Province has resulted in increased demands on groundwater usage. This has potentially induced the release of contaminants such as arsenic (As), among others (i.e., NO3-, PO43-) from various land use types-especially in intensive agricultural areas and heavy industrial areas, including landfill sites. The objectives of this research are to investigate the As speciation and groundwater chemistry occurring due to different hydrogeological settings and the influence of human activities and to explain the mechanism of As release in the coastal alluvial aquifers in Rayong Province using multivariate statistical techniques and hydrogeochemical modeling (PHREEQC). Six major water facies, mainly consisting of Ca-Na-HCO3-Cl and Ca-Na-Cl, were included in the hydrochemical analysis. Arsenic levels were inversely correlated with NO3-, SO42-, DO, and ORP, confirming the reducing environment in the groundwater system. The results from the PHREEQC model show that most wells were strongly under-supersaturated with respect to arsenorite, scorodite, and arsenic pentoxide. Arsenic (As) is probably derived from the dissolution of Fe oxide and hydroxide (i.e., Fe(OH)3, goethite, maghemite, and magnetite). The multivariate statistical techniques revealed that the As species mainly consisted of As(III), governed by the reducing environment, while As(V) may be desorbed from Fe oxide and hydroxide as the pH increases. Anthropogenic inputs and intensive pumping may enhance the reducing environment, facilitating the release of As(III) into the groundwater. The knowledge gained from this study helps to better understand the mechanisms of As contamination in coastal groundwater aquifers, which is useful for groundwater management, including the optimum pumping rate and long-term monitoring of groundwater quality.

Photodegradation of (E)- and (Z)-Endoxifen in water by ultraviolet light: Efficiency, kinetics, by-products, and toxicity assessment.

Endoxifen is an effective metabolite of a common chemotherapy agent, tamoxifen. Endoxifen, which is toxic to aquatic animals, has been detected in wastewater treatment plant (WWTP) effluent. This research investigates ultraviolet (UV) radiation (253.7 nm) application to degrade (E)- and (Z)-endoxifen in water and wastewater and phototransformation by-products (PBPs) and their toxicity. The effects of light intensity, pH and initial concentrations of (E)- and (Z)-endoxifen on the photodegradation rate were examined. Endoxifen in water was eliminated ≥99.1% after 35 s of irradiation (light dose of 598.5 mJ cm-2). Light intensity and initial concentrations of (E)- and (Z)-endoxifen exhibited positive trends with the photodegradation rates while pH had no effect. Photodegradation of (E)- and (Z)-endoxifen in water resulted in three PBPs. Toxicity assessments through modeling of the identified PBPs suggest higher toxicity than the parent compounds. Photodegradation of (E)- and (Z)-endoxifen in wastewater at light doses used for disinfection in WWTPs (16, 30 and 97 mJ cm-2) resulted in reductions of (E)- and (Z)-endoxifen from 30 to 71%. Two of the three PBPs observed in the experiments with water were detected in the wastewater experiments. Therefore, toxic compounds are potentially generated at WWTPs by UV disinfection if (E)- and (Z)-endoxifen are present in treated wastewater.

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities.

Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.

Partial nitrification in entrapped-cell-based reactors with two different cell-to-matrix ratios: performance, microenvironment, and microbial community.

In this study, we investigated the effect of different cell-to-matrix ratios (1% and 4%) on the partial nitrification of phosphorylated polyvinyl alcohol-entrapped-cell-based reactors and evaluated the microenvironment, microbial community, and microbial localization within the gel matrices. The results indicated that the reactor with a 1% cell-to-matrix ratio required 184 days of operation to reach partial nitrification that produced anaerobic ammonium oxidation-suitable effluent. In contrast, partial nitrification was achieved from the beginning of the operation of the reactor with the 4% cell-to-matrix ratio. The oxygen-limiting zone (dissolved oxygen = 0.5-1.5 mg L-1), where nitrite-oxidizing activity has been suggested to be suppressed and ammonia-oxidizing activity was reported to be maintained, occurred at 10-230 µm from the gel matrices surface. In addition, the layer of ammonia-oxidizing bacteria observed in this zone is likely to have played a role in obstructing oxygen penetration into the inner region of the gel matrices. The next-generation sequencing results indicated that members of the family Nitrosomonadaceae accounted for 16.4-20.7% of the relative abundance of bacteria at the family level, while members of the family Bradyrhizobiaceae, to which the genus Nitrobacter belongs, accounted for approximately 10% of the relative abundance of bacteria at the genus level in the gel matrices.

Potential microbial consortium involved in the biodegradation of diesel, hexadecane and phenanthrene in mangrove sediment explored by metagenomics analysis.

Hydrocarbon contamination is a serious problem that degrades the quality of mangrove ecosystems, and bioremediation using autochthonous bacteria is a promising technology to recover an impacted environment. This research investigates the biodegradation rates of diesel, hexadecane and phenanthrene, by conducting a microcosm study and survey of the autochthonous microbial community in contaminated mangrove sediment, using an Illumina MiSeq platform. The biodegradation rates of diesel, hexadecane and phenanthrene were 82, 86 and 8 mg kg-1 sediment day-1, respectively. The removal efficiencies of hexadecane and phenanthrene were >99%, whereas the removal efficiency of diesel was 88%. A 16S rRNA gene amplicon sequence analysis revealed that the major bacterial assemblages detected were Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria. The bacterial compositions were relatively constant, while reductions of the supplemented hydrocarbons were observed. The results imply that the autochthonous microorganisms in the mangrove sediment were responsible for the degradation of the respective hydrocarbons. Diesel-, hexadecane- and phenanthrene-degrading bacteria, namely Bacillus sp., Pseudomonas sp., Acinetobacter sp. and Staphylococcus sp., were also isolated from the mangrove sediment. The mangrove sediment provides a potential resource of effective hydrocarbon-degrading bacteria that can be used as an inoculum or further developed as a ready-to-use microbial consortium for the purpose of bioremediation.