Many naturally seleniferous soils are faced with Cd contamination problem, which severely limits crop cultivation in these areas. Straw returning has been widely applied in agricultural production due to its various benefits to soil physicochemical properties, soil fertility, and crops yield. However, effects of straw application on the fates of Se and Cd in Cd-contaminated seleniferous soils remain largely unclear. Therefore, the effects of straw application on the fates of Se and Cd in Cd-contaminated seleniferous soils were investigated in this study. The results showed that iron reduction driven by Clostridium and Anaeromyxbacter was responsible for the variations in Se and Cd fates in soil. Straw application respectively increased the gene copy numbers of Clostridium and Anaeromyxbacter by 19.5–56.3% and 33.6–39.8%, thus promoting iron reductive dissolution, eventually resulting in a high release amount of Se and Cd from Fe(III) (oxyhydr) oxides. Under reducing conditions, the released Cd was adsorbed by the newly formed metal sulfides or reacted with sulfides to generate CdS precipitates. Straw application decreased the soil exchangeable Se and soil exchangeable Cd concentration during flooding phase. However, straw application significantly increased Se/Cd in soil solution which had the highest bioavailability during flooding. In addition, straw application increased soil exchangeable Se concentration, but it had no significant effects on soil exchangeable Cd concentration after soil drainage. Taken together, straw application increased Se bioavailability and Cd mobility. Therefore, straw application is an effective method for improving Se bioavailability, but it is not suitable for the application to Cd-contaminated paddy soils. In the actual agricultural production, straw could be applied in seleniferous soils to improve Se bioavailability. At the same time, straw application should be cautious to avoid the release of Cd from Cd-contaminated soil.

This study examined the effect of tetracycline addition on arsenic (As) mobilization and biotransformation in two contrasting soils (upland soil and paddy soil) under flooded conditions. The soils with added tetracycline (0–50 mg kg⁻¹) were incubated for 30 days, and soil properties and microbial functional genes over time were quantified. Tetracycline significantly promoted As reduction and As release into porewater in both soils. The enhancement had resulted from an increase in the concentration of dissolved organic carbon and a decrease in soil redox potential. Tetracycline also increased the abundances of As-reducing genes (arsC and arrA) and the relative abundances of As-reducing bacteria Streptomyces, Bacillus, Burkholderia, Clostridium and Rhodococcus, all of which have been found resistant to tetracycline. These genera play a key part in stimulating As reduction in the presence of tetracycline. The study indicated the significance of tetracycline in the biochemical behavior of As in flooded soils and provided new insights into the potential effects of tetracycline on the quality and safety of agricultural products in the future.

Tetrabromobisphenol A (TBBPA) is the most used flame retardant worldwide and has become a threat to aquatic ecosystems. Previous research into the degradation of this micropollutant in anaerobic bioreactors has suggested several identities of putative TBBPA degraders. However, the organisms actively degrading TBBPA under in situ conditions have so far not been identified. Protein-stable isotope probing (protein-SIP) has become a cutting-edge technique in microbial ecology for enabling the link between identity and function under in situ conditions. Therefore, it was hypothesized that combining protein-based stable isotope probing with metagenomics could be used to identify and provide genomic insight into the TBBPA-degrading organisms. The identified ¹³C-labelled peptides were found to belong to organisms affiliated to Phytobacter, Clostridium, Sporolactobacillus, and Klebsilla genera. The functional classification of identified labelled peptides revealed that TBBPA is not only transformed by cometabolic reactions, but also assimilated into the biomass. By application of the proteogenomics with labelled micropollutants (protein-SIP) and metagenome-assembled genomes, it was possible to extend the current perspective of the diversity of TBBPA degraders in wastewater and predict putative TBBPA degradation pathways. The study provides a link to the active TBBPA degraders and which organisms to favor for optimized biodegradation.

Exposure to toxic metals from nonferrous metal(loid) smelter soils can pose serious threats to the surrounding ecosystems, crop production, and human health. Bioremediation using microorganisms is a promising strategy for treating metal(loid)-contaminated soils. Here, a native microbial consortium with sulfate-reducing function (SRB1) enriched from smelter soils can tolerate exposures to mixtures of heavy metal(loid)s (e.g., As and Pb) or various organic flotation reagents (e.g., ethylthionocarbamate). The addition of Fe²⁺ greatly increased As³⁺ immobilization compared to treatment without Fe²⁺, with the immobilization efficiencies of 81.0% and 58.9%, respectively. Scanning electronic microscopy-energy dispersive spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopy confirmed that the As³⁺ immobilizing activity was related to the formation of arsenic sulfides (AsS, As₄S₄, and As₂S₃) and sorption/co-precipitation of pyrite (FeS₂). High-throughput 16S rRNA gene sequencing of SRB1 suggests that members of Clostridium, Desulfosporosinus, and Desulfovibrio genera play an important role in maintaining and stabilizing As³⁺ immobilization activity. Metal(loid)s immobilizing activity of SRB1 was not observed at high and toxic total exposure concentrations (220–1181 mg As/kg or 63–222 mg Pb/kg). However, at lower concentrations, SRB1 treatment decreased bioavailable fractions of As (9.0%) and Pb (28.6%) compared to without treatment. Results indicate that enriched native SRB1 consortia exhibited metal(loid) transformation capacities under non-toxic concentrations of metal(loid)s for future bioremediation strategies to decrease mixed metal(loid)s exposure from smelter polluted soils.

Rice growing in flooded paddy soil often accumulates considerable levels of inorganic and organic arsenic (As) species, which may cause toxicity to plants and/or pose a risk to human health. The bioavailability and toxicity of As in soil depends on its chemical species, which undergo multiple transformations driven primarily by soil microbes. However, the role of endophytes inside rice roots in As species transformation remains largely unknown. We quantified the abundances of microbial functional genes involved in As transformation in the endosphere and rhizosphere of rice roots growing in three paddy soils in a pot experiment. We also isolated 46 different bacterial endophytes and tested their abilities to transform various As species. The absolute abundances of the arsenate reductase gene arsC and the dissimilatory arsenate reductase gene arrA in the endosphere were comparable to those in the rhizosphere, whereas the absolute abundances of the arsenite methylation gene arsM and arsenite oxidation gene aioA in the endosphere were lower. After normalization based on the bacterial 16S rRNA gene, all four As transformation genes showed higher relative abundances in the endosphere than in the rhizosphere. Consistent with the functional gene data, all of the 30 aerobic endophytic isolates were able to reduce arsenate, but only 3 strains could oxidize arsenite. Among the 16 anaerobic endophytic isolates, 4 strains belonging to Desulfovibrio, Terrisporobacter or Clostridium could methylate arsenite and/or methylarsenite. Six strains of aerobic endophytes could demethylate methylarsenite, among which three strains also could reduce and demethylate methylarsenate. None of the isolates could demethylate dimethylarsenate. These results suggest that diverse endophytes living inside rice roots could participate in As species transformation and affect As accumulation and species distribution in rice plants.

Combining biochar with irrigation management to alter the microbial community is a sustainable method for remediating soils contaminated by heavy metals. However, studies on how these treatments promote Cr(VI) reduction are limited, and the corresponding microbial mechanisms are unclear. Therefore, we conducted a pot experiment to explore the responses of soil microbial communities to combined biochar amendment and irrigation management strategies and their involvement in Cr transformation in paddy soils. Six treatments were established using varying concentrations of biochar (0, 1, and 2% [w/w]) combined with two irrigation management strategies (continuous flooding [CF] and dry–wet alternation [DWA]). The results showed that the combined biochar addition and irrigation management strategy significantly altered soil pH, redox potential, organic matter content, and Fe(II) and sulfide concentrations. In addition, the Cr(VI) concentration under CF irrigation management was conspicuously lower (48.2–54.4%) than that under DWA irrigation management. Biochar amendment also resulted in a substantial reduction (8.8–27.4%) in Cr(VI) concentration. Moreover, the changes in soil physicochemical properties remarkably affected the soil microbial community. The microbial diversity and abundance significantly increased with biochar amendment. Furthermore, the combined biochar amendment and CF strategy stimulated the growth of Geobacter- and Anaeromyxobacter-related Fe(III)-reducing bacteria, Gallionella-related Fe(II)-oxidizing bacteria, and Desulfovibro- and Clostridium-related sulfate-reducing bacteria, which simultaneously facilitated the generation of Fe(II) and sulfide, thereby enhancing Cr(VI) reduction. Consequently, our results suggest that the effectively increased abundance of Fe-reducing/oxidizing bacteria and sulfate-reducing bacteria via combined CF irrigation management and biochar addition may be a key factor in reducing Cr(VI) in paddy soil. The keystone genera responsible for Cr(VI) reduction were Geobacter, Anaeromyxobacter, Gallionella, Desulfovibro, and Clostridium. This study provides novel insights into the coupling mechanism of the Fe/S/Cr transformation mediated by Fe-reducing/oxidizing bacteria and sulfate-reducing bacteria.

Ethidium monoazide bromide (EMA) and propidium monoazide (PMA), in combination with amplicon-based sequencing (ABS) and quantitative polymerase chain reaction (qPCR) assays, were compared for the detection of viable bacterial species in rainwater. The ABS α- and β-diversity indices indicated that, in comparison to the untreated samples, both EMA and PMA reduced the detection of non-viable bacteria in the rainwater samples. However, while comparable results were obtained for the detection of the most abundant bacterial families and genera in the rainwater samples for both the EMA and PMA pre-treatments; the EMA pre-treatment produced highly significant differences in the relative abundance of the dominant bacterial families and genera, and significantly decreased the detection of “unclassified” bacteria in comparison to the untreated samples (i.e. unclassified genera: untreated 46.7% versus EMA-treated 39.7%). Additionally, the inclusion of EMA and PMA allowed for the increased detection of less abundant pathogenic bacteria in the rainwater samples, such as Clostridium, Listeria and Streptococcus spp. The qPCR assays also indicated that the EMA and PMA pre-treatments were comparable for the detection of intact and potentially viable Acinetobacter, Legionella and Pseudomonas spp. The combination of viability pre-treatments with ABS thus offers a comprehensive monitoring approach to detect less abundant bacterial genera and/or pathogens, which may pose a health risk to the end-users (prioritise target organisms) of unpiped environmental water sources. Moreover, the subsequent combination of the viability pre-treatments with qPCR allows for the specific detection and quantification of these pathogenic genera, which increases analysis sensitivity and allows for the application of risk assessment and water safety strategies.

Sulfate-reducing bacteria (SRB) can be used to remove metals from wastewater, sewage, and contaminated areas. However, metals can be toxic to this group of bacteria. Sediments from port areas present abundance of SRB and also metal contamination. Their microbial community has been exposed to metals and can be a good inoculum for isolation of metal-resistant SRB. The objective of the study was to analyze how metals influence activity and composition of sulfate-reducing bacteria. Enrichment cultures were prepared with a different metal (Zn, Cr, Cu, and Cd) range concentration tracking activity of SRB and 16S rRNA sequencing in order to access the community. The SRB activity decreased when there was an increase in the concentration of the metals tested. The highest concentration of metals precipitated were 0.2 mM of Cd, 5.4 mM of Zn, 4.5 mM of Cu, and 9.6 mM of Cr. The more toxic metals were Cd and Cu and had a greater community similarity with less SRB and more fermenters (e.g., Citrobacter and Clostridium). Meanwhile, the enrichments with less toxic metals (Cr and Zn) had more sequences affiliated to SRB genera (mainly Desulfovibrio). A new Desulfovibrio species was isolated. This type of study can be useful to understand the effects of metals in SRB communities and help to optimize wastewater treatment processes contaminated by metals. The new Desulfovibrio species may be important in future studies on bioremediation of neutral pH effluents contaminated by metals.

Volatile organic compounds (VOCs) harm human health and the ecological environment. This work demonstrated manganese oxide catalytic membrane coupled to biodegradation of toluene in a catalytic membrane biofilm rector (CMBfR). Toluene removal efficiency in CMBfR was up to 91% in a 200-day operation. Manganese oxide combined to membrane biofilm reactor could promote degradation of toluene. Manganese oxide catalysts were characterized by XRD, Raman, XPS, and FT-IR. Raman and XPS spectra verified the existence of Mn defects, adsorbed oxygen species, and the oxygen vacancy, which was catalytic of toluene on the Mn oxides coated membranes significantly. Pseudomonas, Hydrogenophaga, Flavobacterium, Bacillus, Clostridium and Prosthecobacter were the dominant bacteria of toluene degradation. Mn oxides catalysis could degrade toluene into intermediate products; these products were entered into the biological phase eventually metabolized to CO₂ and H₂O. These results show that the catalytic membrane biofilm reactor is achievable and opens new possibilities for applying the catalytic membrane biofilm reactor to VOCs treatment.

Fludioxonil is a post-harvest fungicide contained in effluents produced by fruit packaging plants, which should be treated prior to environmental dispersal. We developed and evaluated an immobilized cell bioreactor, operating under microaerophilic conditions and gradually reduced hydraulic retention times (HRTs) from 10 to 3.9 days, for the biotreatment of fludioxonil-rich wastewater. Fludioxonil removal efficiency was consistently above 96%, even at the shortest HRT applied. A total of 12 transformation products were tentatively identified during fludioxonil degradation by using liquid chromatography coupled to quadrupole time-of-flight Mass spectrometry (LC-QTOF-MS). Fludioxonil degradation pathway was initiated by successive hydroxylation and carbonylation of the pyrrole moiety and disruption of the oxidized cyanopyrrole ring at the NH-C bond. The detection of 2,2-difluoro-2H-1,3-benzodioxole-4-carboxylic acid verified the decyanation and deamination of the molecule, whereas its conversion to the tentatively identified compound 2,3-dihydroxybenzoic acid indicated its defluorination. High-throughput amplicon sequencing revealed that HRT shortening led to reduced α-diversity, significant changes in the β-diversity, and a shift in the bacterial community composition from an initial activated sludge system typical community to a community composed of bacterial taxa like Clostridium, Oligotropha, Pseudomonas, and Terrimonas capable of performing advanced degradation and/or aerobic denitrification. Overall, the immobilized cell bioreactor operation under microaerophilic conditions, which minimizes the cost for aeration, can provide a sustainable solution for the depuration of fludioxonil-contaminated agro-industrial effluents.