Abandoned nonferrous metal(loid) tailings sites are anthropogenic, and represent unique and extreme ecological niches for microbial communities. Tailings contain elevated and toxic content of metal(loid)s that had negative effects on local human health and regional ecosystems. Microbial communities in these typical tailings undergoing natural attenuation are often very poorly examined. The diversity and inferred functions of bacterial communities were examined at seven nonferrous metal(loid) tailings sites in Guangxi (China), which were abandoned between 3 and 31 years ago. The acidity of the tailings sites rose over 31 years of site inactivity. Desulfurivibrio, which were always coupled with sulfur/sulfide oxidation to dissimilate the reduction of nitrate/nitrite, were specific in tailings with 3 years abandonment. However, genus beneficial to plant growth (Rhizobium), and iron/sulfur-oxidizing bacteria and metal(loid)-related genera (Acidiferrobacter and Acidithiobacillus) were specific within tailings abandoned for 23 years or more. The increased abundance of acid-generating iron/sulfur-oxidizing and metal(loid)-related bacteria and specific bacterial communities during the natural attenuation could provide new insights for understanding microbial ecosystem functioning in mine tailings. OTUs related to Sulfuriferula, Bacillus, Sulfurifustis, Gaiella, and Thiobacillus genera were the main contributors differentiating the bacterial communities between the different tailing sites. Multiple correlation analyses between bacterial communities and geochemical parameters indicated that pH, TOC, TN, As, Pb, and Cu were the main drivers influencing the bacterial community structures. PICRUSt functional exploration revealed that the main functions were related to DNA repair and recombination, important functions for bacterial adaptation to cope with the multi-contamination of tailings. Such information provides new insights to guide future metagenomic studies for the identification of key functions beyond metal-transformation/resistance. As well, our results offers novel outlooks for the management of bacterial communities during natural attenuation of multi-contaminated nonferrous metal(loid) tailings sites.

Rhizospheric microorganisms such as denitrifying bacteria are able to affect ‘rhizobioaugmention’ in aquatic plants and can help boost wastewater purification by benefiting plant growth, but little is known about their effects on the production of plant root exudates, and how such exudates may affect microorganismal nitrogen removal. Here, we assess the effects of the rhizospheric Pseudomonas inoculant strain RWX31 on the root exudate profile of the duckweed Spirodela polyrrhiza, using gas chromatography/mass spectrometry. Compared to untreated plants, inoculation with RWX31 specifically induced the exudation of two sterols, stigmasterol and β-sitosterol. An authentic standard assay revealed that stigmasterol significantly promoted nitrogen removal and biofilm formation by the denitrifying bacterial strain RWX31, whereas β-sitosterol had no effect. Assays for denitrifying enzyme activity were conducted to show that stigmasterol stimulated nitrogen removal by targeting nitrite reductase in bacteria. Enhanced N removal from water by stigmasterol, and a synergistic stimulatory effect with RWX31, was observed in open duckweed cultivation systems. We suggest that this is linked to a modulation of community composition of nirS- and nirK-type denitrifying bacteria in the rhizosphere, with a higher abundance of Bosea, Rhizobium, and Brucella, and a lower abundance of Rubrivivax. Our findings provide important new insights into the interaction of duckweed with the rhizospheric bacterial strain RWX31 and their involvement in the aquatic N cycle and offer a new path toward more effective bio-formulations for the purification of N-polluted waters.

Mine tailings contain toxic metals and can lead to serious pollutions of soil environment. Phytoremediation using legumes has been regarded as an eco-friendly way for the rehabilitation of tailings-laden lands but little is known about the changes of microbial structure during the process. In the present study, we monitored the dynamic change of microbiota in the rhizosphere of Pongamia pinnata during a 2-year on-site remediation of vanadium-titanium magnetite tailings. After remediation, overall soil health conditions were significantly improved as increased available N and P contents and enzyme activities were discovered. There was also an increase of microbial carbon and nitrogen contents. The Illumina sequencing technique revealed that the abundance of taxa under Proteobacteria was increased and rhizobia-related OTUs were preferentially enriched. A significant difference was discovered for sample groups before and after remediation. Rhizobium and Nordella were identified as the keystone taxa at genus rank. Functional predictions indicated that nitrogen fixation was enhanced, corresponding well with qPCR results which showed a significant increase of nifH gene copy numbers by the 2nd year. Our findings for the first time elucidated that legume phytoremediation can effectively cause microbial communities to shift in favour of rhizobia in heavy metal contaminated soil.

Selenium engineered nanomaterials (Se ENMs)-enabled agriculture has developed rapidly, however, the roles of surface charge in the bioavailability and enrichment efficiency of Se ENMs are still unknown. Herein, various Se ENMs of homogenous size (40–60 nm) and different surface charges (3.2 ± 0.7, −29.0 ± 0.4, and 45.5 ± 1.3 mV) were prepared to explore the Se content and nutritional quality in Brassica chinensis L. The results demonstrated that soil application of various Se ENMs (0.05 mg kg⁻¹) displayed different bio-availabilities via modulating the secretion of root exudates (e.g., tartaric, malic, and citric acids), microbial community composition (e.g., Flavobacterium, Pseudomonas, Paracoccus, Bacillus and Rhizobium) and root cell wall. Negatively charged Se ENMs (Se (−)) showed the highest Se content in the shoot of B. chinensis (3.7-folds). Se (−) also significantly increased yield (156.9%) and improved nutritional quality (e.g., ascorbic acid, amino acids, flavonoids, fatty acids, and tricarboxylic acid) of B. chinensis. Moreover, after harvest, the Se (−) did not lead to significant change in Se residue in soil, but the amount of Se residue in soil was increased by 5.5% after applying the traditional Se fertilizer (selenite). Therefore, this study provides useful information for producing Se-fortified agricultural products, while minimizing environmental risk.

Compound-specific stable isotope analysis of micropollutants has become an established method for the qualitative and quantitative assessment of biodegradation in the field. However, many of environmental factors may have an influence on the observed isotope fractionation. Herein, we investigate the impact of substrate concentration on the observed enrichment factor derived from Rayleigh plot of batch laboratory experiments conducted to measure the atrazine carbon isotope fractionation of Rhizobium sp. CX-Z subjected to the different initial concentration level of atrazine. The Rayleigh plot (changes in bulk concentration vs. isotopic composition) derived from batch experiments shown divergence from the linear relation towards the end of degradation, confirming bioavailability of atrazine changed along with the decay of substrate concentration, consequently, influenced the isotope fractionation and lowered the observed enrichment factor. When microbial degradation is coupled to a mass transfer step limiting the bioavailability of substrate, the observed enrichment factor displays a dependence on initial atrazine concentration. Observed enrichment factors (ε) (absolute value) derived from the low concentration (i.e. 9.5 μM) are below 3.5‰ to the value of −5.4‰ determined at high bioavailability (membrane-free cells). The observed enrichment factor depended significantly on the atrazine concentration, indicating the concentration level and the bioavailability of a substrate in realistic environments should be considered during the assessment of microbial degradation or in situ bioremediation based on compound-specific stable isotope analysis (CSIA) method.

In this work, soil contaminated by petroleum resins was remediated by electrokinetic-bioremediation (EK-BIO) technology for 60 days. A microbial consortium, comprising Rhizobium sp., Arthrobacter globiformis, Clavibacter xyli, Curtobacterium flaccumfaciens, Bacillus subtilis, Pseudomonas aeruginosa and Bacillus sp., was used to enhance the treatment performance. The results indicate that resin removal and phytotoxicity reduction were highest in the inoculated EK process, wherein 23.6% resins was removed from the soil and wheat seed germination ratio was increased from 47% to around 90% after treatment. The microbial counts, soil basal respiration and dehydrogenase activity were positively related to resins degradation, and they could be enhanced by direct current electric field. After remediation, the C/H ratio of resins decreased from 8.03 to 6.47. Furthermore, the structure of resins was analyzed by Fourier-transform infrared spectroscopy, elemental analysis, and ¹H nuclear magnetic resonance (¹H NMR) before and after treatment. It was found that the changes of the structure of resins took place during EK-BIO treatment and finally led to the reduction of aromaticity, aromaticity condensation and phytotoxicity.

The volatile metabolome of Rhizobium sp. strain E20-8 exposed to three concentrations of cadmium (2.5, 5.0 and 7.5 μM) was screened using comprehensive two-dimensional gas chromatography coupled to time of flight mass spectrometry (GC × GC–ToFMS), combined with headspace solid phase microextraction (HS-SPME). Cd exposure induced a global increase in the concentration of volatile organic compounds (VOCs) both intra and extracellularly. Peak areas of several linear alkanes, ketones, aldehydes, alcohols, terpenic and volatile sulfur compounds, and one ester (ethyl acetate), were especially increased when compared with the control condition (no Cd). These compounds might originate from the metabolization of toxic membrane peroxidation products, the proteolysis of oxidized proteins or the alteration of metabolic pathways, resulting from the oxidative stress imposed by Cd. Several VOCs are related to oxidative damage, but the production of VOCs involved in antioxidant response (menthol, α-pinene, dimethyl sulfide, disulfide and trisulfide, 1-butanol and 2-butanone) and in cell aggregation (2,3-butanedione, 3-methyl-1-butanol and 2-butanone) is also observed. These results bring new information that highlights the role of VOCs on bacteria response to Cd stress, identify a novel set of biomarkers related with metal stress and provide information to be applied in biotechnological and remediation contexts.

Marine microbial communities might be subjected to accidental petroleum spills; however, some bacteria can degrade it, making these specific bacteria valuable for bioremediation from petroleum contamination. Thus, characterizing the microbial communities exposed to varying types of petroleum is essential. We evaluated five enriched microbial communities from the northwest Gulf of Mexico (four from the water column and one from sediments). Enrichments were performed using five types of petroleum (extra light, light, medium, heavy and extra heavy), to reveal the microbial succession using a 16S rDNA amplicon approach. Four communities were capable of degrading from extra light to heavy petroleum. However, only the community from sediment was able to degrade the extra heavy petroleum. Successional changes in the microbial communities' structures were specific for each type of petroleum where genus Dietzia, Gordonia, Microvirga, Rhizobium, Paracoccus, Thalassobaculum, Sphingomonas, Moheibacter, Acinetobacter, Pseudohongiella, Porticoccus, Pseudoalteromonas, Pseudomonas, Shewanella, and Planctomyces presented differential abundance between the treatments.

Sukinda chromite mine of Odisha is a heavily polluted site, generating huge overburden dumps. The present experiment was designed to evaluate the potential of two native nodule endophytic bacterial strains, viz. Bacillus aryabhattai AS03 (MT645244) and Rhizobium pusense AS05 (MT645243), isolated from contaminated sites to be considered remediation tool to minimize the effect of Cr toxicity on Macrotyloma uniflorum var. Madhu. The two nodule endophytic bacterial strains AS03 and AS05 exhibited tolerance to 1800 and 3000 ppm of Cr(VI) respectively in vitro when cultured alone. AAS analysis confirmed higher accumulation of Cr(VI) in roots and less accumulation in shoots which is dose-specific (bio-inoculant) either treated alone or combined. Complete absence of Cr accumulation approximately 99% in shoots of Macrotyloma was observed owing to synergistic effect of both the strains (biochar-based formulation). This study also suggests increased shoot and root length, nodule nos., and leghemoglobin content of the plant at 60 days indicating the plant growth-promoting effects of both the strains. ROS and antioxidant enzymes of the plant recorded decreasing trend in inoculated plants. However, a significant increment in transpiration rate, total photosynthetic rate, intracellular CO₂ conc., and stomatal conductance in leaves was observed owing to dual inoculation. Our findings corroborate the supremacy of synergistic effect of both the strains applied in the form of biochar-based biofertilizer in enhancing growth and tolerance index of M. uniflorum cultivated in Cr(VI)-stressed soil. This investigation depicts the efficiency of the two nodule bacteria as a mixed inoculant to alleviate Cr toxicity and making the seeds safe for consumption.

Using an indoor microcosm assay, we analyzed the biodegradation of total petroleum hydrocarbons (TPHs) by autochthonous bacterial populations in mining soil in the presence of a surfactant (Tween 80). The kinetic behavior of TPH biodegradation involved fast and slow stages. Initially, heterotrophic and hydrocarbonoclastic bacteria increased in abundance by an order of magnitude, but both groups decreased to close to their initial population sizes by the end of experiment. The most efficient final biodegradation (61.5 %) was achieved using soil with 0.5 % added surfactant. Polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) were used to analyze changes in the bacterial community structure. During the fast biodegradation phase, bacterial species richness as indicated by DGGE profiles was reduced after long periods of TPH biodegradation with exposure to Tween 80. The distribution of families was modified, but no particular pattern could be identified. The main bacterial genera were Acinetobacter, Pedomicrobium, Halomonas, Rhizobium, Cryobacterium, Pseudomonas, Lysobacter, Thermomonas, and Stenotrophomonas. Acinetobacter exhibited the highest species richness and was the most abundant and persistent genus, followed by Pedomicrobium and Rhizobium. Decreasing TPH biodegradation can be attributed to a reduction in the microbial population and the disappearance of most of the initial bacterial genera. The correlation between TPH biodegradation and microbial population dynamics helps explain long bioremediation times and can facilitate actions for increasing bioremediation efficiency.