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.

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.

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.

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.

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.

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.

Rice (Oryza sativa) tends to accumulate elevated levels of arsenic (As) in grain, threatening food safety and human health. The rice rhizosphere has a micro-environment that differs markedly from the bulk soil. Yet, little is known about how this micro-environment influences the mobility of As in the rhizosphere. Using rhizoboxes with two rice cultivars (cv. Shenyou 957 and Yangdao 6) differing in their radial oxygen loss (ROL), we investigated the in situ transformation of As in the rhizosphere associated with changes in microbial communities and As-related functional genes. Contrary to expectation, dissolved (porewater) As concentrations within the rhizosphere increased by 1.3–2.4 fold compared to the bulk soil during the seedling stage, with the magnitude of this difference gradually decreasing over time. The increased As mobilization in the rhizosphere was associated with increased soluble Fe. This increasing trend was associated with the increased abundance of both Fe-reducing bacteria (FeRB) and As-related functional genes within the rhizosphere. Furthermore, bacterial 16S rRNA gene sequencing data showed that the abundances of Geobacter and Clostridium were 3.1 times and 12.4 times higher in the rhizosphere, respectively. The importance of FeRB was also suggested by the fact that dissolved As concentrations were highly correlated with dissolved Fe concentrations (r² = 0.83) and also with the relative abundance of genus Clostridium_sensu_stricto_10 (r² = 0.85). This study highlights that although the rice rhizosphere favors a more aerobic condition compared to the bulk soil, As is more mobilized in the rhizosphere, and that Geobacter and some species of Clostridium play a critical role in controlling As mobilization in the rhizosphere.

In situ immobilization of heavy metals in contaminated soils using industrial by-products is an attractive remediation technique. In this work, titanium gypsum (TG) was applied at two levels (TG-L: 0.15% and TG-H: 0.30%) to simultaneously reduce the uptake of cadmium (Cd), lead (Pb) and arsenic (As) in rice grown in heavy metal contaminated paddy soils. The results showed that the addition of TG significantly decreased the pH and dissolved organic carbon (DOC) in the bulk soil. TG addition significantly improved the rice plants growth and reduced the bioavailability of Cd, Pb and As. Particularly, bioavailable Cd, Pb and As decreased by 35.2%, 38.1% and 38.0% in TG-H treatment during the tillering stage, respectively. Moreover, TG application significantly reduced the accumulation of Cd, Pb and As in brown rice. Real-time PCR analysis demonstrated that the relative abundance of sulfate-reducing bacteria increased with the TG application, but not for the iron-reducing bacteria. In addition, 16S rRNA sequencing analysis revealed that the relative abundances of heavy metal-resistant bacteria such as Bacillus, Sulfuritalea, Clostridium, Sulfuricella, Geobacter, Nocardioides and Sulfuricurvum at the genus level significantly increased with the TG addition. In conclusion, the present study implied that TG is a potential and effective amendment to immobilize metal(loid)s in soil and thereby reduce the exposure risk of metal(loid)s associated with rice consumption.