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.

In this study, the YH consortium, an ethene-producing culture, was used to evaluate the effect of vitamin B₁₂ (VB₁₂) on trichloroethene (TCE) dechlorination by transferring the original TCE-reducing culture with or without adding exogenous VB₁₂. Ultra-high performance liquid chromatography - tandem mass spectrometry (UPLC-MS/MS) was applied to detect the concentrations of VB₁₂ and its lower ligand 5,6-dimethylbenzimidazole (DMB) in the cultures. After three successive VB₁₂ starvation cycles, the dechlorination of TCE stopped mostly at cis-dichloroethene (cDCE), and no ethene was found; methane production increased significantly, and no VB₁₂ was detected. Results suggest that the co-cultured microbes may not be able to provide enough VB₁₂ as a cofactor for the growth of Dehalococcoides in the YH culture, possibly due to the competition for corrinoids between Dehalococcoides and methanogens. The relative abundances of 16 S rRNA gene of Dehalococcoides and reductive dehalogenase genes tceA or vcrA were lower in the cultures without VB₁₂ compared with the cultures with VB₁₂. VB₁₂ limitation changed the microbial community structures of the consortia. In the absence of VB₁₂, the microbial community shifted from dominance of Chloroflexi to Proteobacteria after three consecutive VB₁₂ starvation cycles, and the dechlorinating genus Dehalococcoides declined from 42.9% to 13.5%. In addition, Geobacter, Clostridium, and Desulfovibrio were also present in the cultures without VB₁₂. Furthermore, the abundance of archaea increased under VB₁₂ limited conditions. Methanobacterium and Methanosarcina were the predominant archaea in the culture without VB₁₂.

A novel non-dsrAB (without dissimilatory sulfite reductase genes) sulfate-reducing bacterium (SRB) Clostridium sp. BXM was isolated from a paddy soil. Incubation experiments were then performed to investigate the formation of reduced sulfur compounds (RSC) by Clostridium sp. BXM, and RSC-induced dechlorination of p,p′-DDT in culture medium and soil solution. The RSCs produced were 5.8mM and 4.5mM in 28mM sulfate amended medium and soil solution respectively after 28-day cultivation. The p,p′-DDT dechlorination ratios were 74% and 45.8% for 5.8mM and 4.5mM RSCs respectively at 6h. The metabolites of p,p′-DDT found in the two reaction systems were identified as p,p′-DDD and p,p′-DDE. The dechlorination pathways of p,p′-DDT to p,p′-DDD and p,p′-DDE were proposed, based on mass balance and dechlorination time-courses. The results indicated that RSC-induced natural dechlorination may play an important role in the fate of organochlorines.

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.

Widespread nitrobenzene (NB) contamination in groundwater requires an economical and effective remediation technology. In situ microbial reactive zone enhanced by injecting emulsified vegetable oil (EVO) is an effective method for remediating NB-contaminated groundwater, which can be reduced to aniline (AN) effectively in the reactive zone. However, the bio-mechanism of NB remediation in a real contaminated site is still unclear. Thus, a 3-D tank was established to conduct a pilot-scale experiment and the bacterial communities in the tank were analyzed by 16S rDNA high-throughput sequencing. The results suggested that the injection of EVO can stimulate some certain microorganisms to grow, and reduce NB though biological and biochemical processes. There were three degradation pathways of NB: (1) direct oxidation by Pseudomonas; (2) direct mineralization by Clostridium sensu stricto; and (3) coupled reduction of NB through microbial dissimilatory iron reduction by Geobacter and Arthrobacter. Among these pathways, the coupled reduction process is the main degradation pathway.

Production of rice grains at non-toxic levels of arsenic (As) to meet the demands of an ever-increasing population is a global challenge. There is currently a lack of investigation into integrated approaches for decreasing As levels in rice agro-ecosystems. By examining the integrated iron-modified rice hull biochar (Fe-RBC) and water management approaches on As dynamics in the paddy agro-ecosystem, this study aims to reduce As accumulation in rice grains. The rice cultivar, Ishikari, was grown and irrigated with As-containing water (1 mg L⁻¹ of As(V)), under the following treatments: (1) Fe-RBC-flooded water management, (2) Fe-RBC-intermittent water management, (3) conventional flooded water management, and (4) intermittent water management. Compared to the conventional flooded water management, grain weight per pot and Fe and Si concentrations in the paddy pore water under Fe-RBC-intermittent and Fe-RBC-flooded treatments increased by 24%–39%, 100%–142%, and 93%–184%, respectively. The supplementation of Fe-RBC decreased the As/Fe ratio and the abundance of Fe(III) reducing bacteria (i.e. Bacillus, Clostridium, Geobacter, and Anaeromyxobacter) by 57%–88% and 24%–64%, respectively, in Fe-RBC-flooded and Fe-RBC-intermittent treatments compared to the conventional flooded treatment. Most importantly, Fe-RBC-intermittent treatment significantly (p ≤ 0.05) decreased As accumulation in rice roots, shoots, husks, and unpolished rice grains by 62%, 37%, 79%, and 59%, respectively, compared to the conventional flooded treatment. Overall, integrated Fe-RBC-intermittent treatment could be proposed for As endemic areas to produce rice grains with safer As levels, while sustaining rice yields to meet the demands of growing populations.

Antibiotic resistance genes (ARGs) are emerging contaminants in the environment and have been highlighted as a worldwide environmental and health concern. As important participants in the biogeochemical cycles, mangrove ecosystems are subject to various anthropogenic disturbances, and its microbiota may be affected by various contaminants such as ARGs. This study selected 13 transects of mangrove-covered areas in Hainan, China for sediment sample collection. The abundance and diversity of ARGs and mobile genetic elements (MGEs) were investigated using high-throughput quantitative polymerase chain reaction (HT-qPCR), and high-throughput sequencing was used to study microbial structure and diversity. A total of 179 ARGs belonging to 9 ARG types were detected in the study area, and the detection rates of vanXD and vatE-01 were 100%. The abundance of ARGs was 8.30 × 10⁷–6.88 × 10⁸ copies per g sediment (1.27 × 10⁻²–3.39 × 10⁻² copies per 16S rRNA gene), which was higher than similar studies, and there were differences in the abundance of ARGs in these sampling transects. The multidrug resistance genes (MRGs) accounted for the highest proportion (69.0%), which indicates that the contamination of ARGs in the study area was very complicated. The ARGs significantly positively correlated with MGEs, which showed that the high level of ARGs was related to its self-enhancement. The dominant bacteria at the genus level were Desulfococcus, Clostridium, Rhodoplanes, Bacillus, Vibrio, Enterococcus, Sedimentibacter, Pseudoalteromonas, Paracoccus, Oscillospira, Mariprofundus, Sulfurimonas, Aminobacterium, and Novosphingobium. There was a significant positive correlation between 133 bacterial genera and some ARGs. Chthoniobacter, Flavisolibacter, Formivibrio, Kaistia, Moryella, MSBL3, Perlucidibaca, and Zhouia were the main potential hosts of ARGs in the sediments of Hainan mangrove area, and many of these bacteria are important participants in biogeochemical cycles. The results contribute to our understanding of the distribution and potential hosts of ARGs and provide a scientific basis for the protection and management of Hainan mangrove ecosystem.

Heat stress (HS) during gestation has been associated with negative outcomes, such as preterm birth or postnatal metabolic syndromes. The intestinal microbiota is a unique ecosystem playing an essential role in mediating the metabolism and health of mammals. Here we hypothesize late gestational HS alters maternal microbial transmission and structures offspring’s intestinal microbiota and serum metabolic profiles. Our results show maternal HS alters bacterial β-diversity and composition in sows and their piglets. In the maternal intestine, genera Ruminococcaceae UCG-005, [Eubacterium] coprostanoligenes group and Halomonas are higher by HS (q < 0.05), whereas the populations of Streptococcus, Bacteroidales RF16 group_norank and Roseburia are decreased (q < 0.05). In the maternal vagina, HS mainly elevates the proportions of phylum Bacteroidetes and Fusobacteria (q < 0.05), whereas reduces the population of Clostridiales Family XI (q < 0.05). In the neonatal intestine, maternal HS promotes the population of Proteobacteria but reduces the relative abundance of Firmicutes (q < 0.05). Moreover, the core Operational taxonomic units (OTU) analysis indicates the proportions of Clostridium sensu stricto 1, Romboutsia and Turicibacter are decreased by maternal HS in the intestinal and vaginal co-transmission, whereas that of phylum Proteobacteria and Epsilonbacteraeota, such as Escherichia-Shigella, Klebsiella, Acinetobacter, and Comamonas are increased in both the intestinal and vaginal co-transmission and the vagina. Additionally, Aeromonas is the only genus that is transmitted from environmental sources. Lastly, we evaluate the importance of neonatal differential OTU for the differential serum metabolites. The results indicate Acinetobacter significantly contributes to the differences in the adrenocorticotropic hormone (ACTH) and glucose levels due to HS (P < 0.05). Further, Stenotrophomonas is the most important variable for Cholesterol, low-density lipoprotein (LDL), diamine oxidase (DAO), blood urea nitrogen (BUN) and 5-hydroxytryptamine (5-HT) (P < 0.10). Overall, our data provides evidence for the maternal HS in establishing the neonatal microbiota via affecting maternal transmission, which in turn affects the maintenance of metabolic health.

Excessive use of antibiotics in breeding industry leads to accumulation of antibiotic residuals and antibiotic resistance genes (ARGs) in environment from improperly treated livestock excrements. Four commonly used veterinary antibiotics including chlortetracycline (CTC), sulfamerazine (SMZ), enrofloxacin (ENR) and erythromycin (ERY) were monitored in the swine manure composting. Co-resistance and cross-resistance effects among relative ARGs, correlations between ARGs and bacterial community under multiple antibiotics residual during the composting were investigated in this research. With CTC addition up to 20 mg/kg, more than 99% of CTC removal was achieved after composting, and most of the other antibiotics can be thoroughly removed as well. The variations in ARGs during the composting were strongly correlated to the compositions of the microbial community, Bacteroides and Sporosarcina were main ARGs carriers in the thermophlic phase. Clostridium Ⅺ, Clostridium sensu stricto, and Pseudoxanthomonas, might spread ARGs in cooling and maturing stage. Most of the tested ARGs in swine manure can be effectively reduced through composting, thus makes the compost products safe for soil fertilization.