Soil Cd and Zn contamination has become a serious environmental problem. This work explored the performance of wood vinegar (WV) in enhancing the phytoextraction of Cd/Zn by hyperaccumulator Sedum alfredii Hance. Rhizosphere chemical properties, enzyme activities and bacterial community were analyzed to determine the mechanisms of metal accumulation in this process. Results demonstrated that, after 120 days growth, different times dilution of WV increased the shoot biomass of S. alfredii by 85.2%–148%. In addition, WV application significantly increased soil available Cd and Zn by lowing soil pH, which facilitated plant uptake. The optimal Cd and Zn phytoextraction occurred from the 100 times diluted WV (D100), which increased the Cd and Zn extraction by 188% and 164%, compared to CK. The 100 and 50 times diluted WV significantly increased soil total and available carbon, nitrogen and phosphorus, and enhancing enzyme activities of urease, acid phosphatase, invertase and protease by 10.1–21.4%, 29.1–42.7%,12.2–38.3% and 26.8–85.7%, respectively, compared to CK. High-throughput sequencing revealed that the D 100 significantly increased the bacterial diversity compared to CK. Soil bacterial compositions at phylum, family and genera level were changed by WV addition. Compared to CK, WV application increased the relative abundances of genus with plant growth promotion and metal mobilization function such as, Bacillus, Gemmatimonas, Streptomyces, Sphingomonas and Polycyclovorans, which was positively correlated to biomass, Cd/Zn concentrations and extractions by S. alfredii. Structural equation modeling analysis showed that, soil chemical properties, enzyme activities and bacterial abundance directly or indirectly contributed to the biomass promotion, Cd, and Zn extraction by S. alfredii. To sum up, WV improved phytoextraction efficiency by enhancing plant growth, Cd and Zn extraction and increasing soil nutrients, enzyme activities, and modifying bacterial community.

With the rapid development of nanotechnology in agriculture, there is increasing urgency to assess the impacts of nanoparticles (NPs) on the soil environment. This study merged raw high-throughput sequencing (HTS) data sets generated from 365 soil samples to reveal the potential ecological effects of NPs on soil microbial community by means of metadata analysis and machine learning methods. Metadata analysis showed that treatment with nanoparticles did not have a significant impact on the alpha diversity of the microbial community, but significantly altered the beta diversity. Unfortunately, the abundance of several beneficial bacteria, such as Dyella, Methylophilus, Streptomyces, which promote the growth of plants, and improve pathogenic resistance, was reduced under the addition of synthetic nanoparticles. Furthermore, metadata demonstrated that nanoparticles treatment weakened the biosynthesis ability of cofactors, carriers, and vitamins, and enhanced the degradation ability of aromatic compounds, amino acids, etc. This is unfavorable for the performance of soil functions. Besides the soil heterogeneity, machine learning uncovered that a) the exposure time of nanoparticles was the most important factor to reshape the soil microbial community, and b) long-term exposure decreased the diversity of microbial community and the abundance of beneficial bacteria. This study is the first to use a machine learning model and metadata analysis to investigate the relationship between the properties of nanoparticles and the hazards to the soil microbial community from a macro perspective. This guides the rational use of nanoparticles for which the impacts on soil microbiota are minimized.

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.

Pesticides may alter soil microbial community structure or diversity, but their impact on microbial co-occurrence patterns remains unclear. Here, the effect of the widely used neonicotinoid insecticide thiamethoxam on the bacterial community in five arable soils was deciphered using the 16S rRNA gene amplicon sequencing technique. The degradation half-life of thiamethoxam in nonsterilized soils was significantly lower than that in sterilized soils, suggesting a considerable contribution from biodegradation. Soil bacterial community diversity diminished in high concentration thiamethoxam treatment and its impact varied with treatment concentration and soil type. Bacterial co-occurrence network complexity significantly decreased after exposure to thiamethoxam. Under thiamethoxam stress, the relative changes in bacterial co-occurrence networks were closely related (the majority of p-values < 0.05) to the soil physicochemical properties, yet the diversity and dominant phyla were slightly related (the majority of p-values > 0.05). Additionally, three bacterial genera, Sphingomonas, Streptomyces, and Catenulispora, were identified to be relevant to the degradation of thiamethoxam in soils. This finding deciphers the succession of the bacterial community under thiamethoxam stress across multiple soils, and emphasizes the potential role of physicochemical properties in regulating the ecotoxicological effect of pesticides on the soil microbiome.

Penicillin fermentation dreg (PFD) is a solid waste discharged by pharmaceutical enterprises in the fermentation production process. Due to the residual antibiotic of PFD, the risk of antibiotic resistance bacteria (ARB) generation should be considered in the disposal process. High-throughput quantitative PCR (HT-qPCR) and 16S rRNA gene sequencing were performed to investigate the effect of PFD on the dynamics of antibiotic resistance genes (ARGs) and bacterial community during a lab-scale soil experiment. After the application of PFD, the bacterial number and diversity showed an obvious decrease in the initial days. The abundances of Streptomyces and Bacillus, which are the most widespread predicted source phyla of ARGs, increased remarkably from 4.42% to 2.59%–22.97% and 21.35%. The increase of ARGs was observed during the PFD application and the ARGs carried by PFD itself contributed to the initiation of soil ARGs. The results of redundancy analysis (RDA) show that the shift in bacterial community induced by variation of penicillin content is the primary driver shaping ARGs compositions.

The bioremediation of historic industrial contaminated sites is a complex process. Co-contamination, often with lead which was commonly added to gasoline until 16 years ago is one of the biggest challenges affecting the clean-up of these sites. In this study, the effect of heavy metals, as co-contaminant, together with total petroleum hydrocarbons (TPH) is reported, in terms of remaining soil toxicity and the structure of the microbial communities. Contaminated soil samples from a relatively hot and dry climate in Western Australia were collected (n = 27). Analysis of soils showed the presence of both contaminants, TPHs and heavy metals. The Microtox test confirmed that their co-presence elevated the remaining ecotoxicity. Toxicity was correlated with the presence of lead, zinc and TPH (0.893, 0.599 and 0.488), respectively, assessed using Pearson Correlation coefficient factor. Next Generation Sequencing of soil bacterial 16S rRNA, revealed a lack of dominate genera; however, despite the variation in soil type, a few genera including Azospirillum spp. and Conexibacter were present in most soil samples (85% and 82% of all soils, respectively). Likewise, many genera of hydrocarbon-degrading bacteria were identified in all soil samples. Streptomyces spp. was presented in 93% of the samples with abundance between 7% and 40%. In contrast, Acinetobacter spp. was found in only one sample but was a dominant member of (45%) of the microbial community. In addition, some bacterial genera were correlated to the presence of the heavy metals, such as Geodermatophilus spp., Rhodovibrio spp. and Rubrobacter spp. which were correlated with copper, lead and zinc, respectively. This study concludes that TPH and heavy metal co-contamination significantly elevated the associated toxicity. This is an important consideration when carrying out risk assessment associated with natural attenuation. This study also improves knowledge about the dynamics of microbial communities in mixed contamination scenarios.

Microbial degradation of polycyclic aromatic hydrocarbons (PAHs) is the major channel for their decontamination from different environments. Aerobic and anaerobic biodegradations of PAHs in batch reactors with single or multiple bacterial strains have been intensively studied, but the cooperative mechanism of functional PAH-degrading populations at the community level under field conditions remains to be explored. We determined the composition of PAH-degrading populations in the bacterial community and PAHs in farmland and wasteland soils contaminated by coking plants using high-throughput sequencing and high-performance liquid chromatography (HPLC), respectively. The results indicated that the PAH content of farmland was significantly lower than that of wasteland, which was attributed to the lower content of low molecular weight (LMW) PAHs and benzo [k]fluoranthene. The soil physicochemical properties were significantly different between farmland and wasteland. The naphthalene content was related to the soil organic carbon (SOC) and pH, while phenanthrene was related to the nitrate nitrogen (NO₃⁻-N) and water content (WC). The pH, nitrite (NO₂⁻-N), SOC, NO₃⁻-N and WC were correlated with the content of high molecular weight (HMW) PAHs and total PAHs. The relative abundances of the phyla Actinobacteria, Chloroflexi, Acidobacteria, and Firmicutes and the genera Nocardioides, Bacillus, Lysobacter, Mycobacterium, Streptomyces, and Steroidobacter in farmland soil were higher than those in wasteland soil. The soil physicochemical characteristics of farmland increased the diversities of the PAH degrader and total bacterial communities, which were significantly negatively related to the total PAHs and LMW PAHs. Subsequently, the connectivity and complexity of the network in farmland were lower than those in wasteland, while the module containing a module hub capable of degrading PAHs was identified in the network of farmland soil. Structural equation modelling (SEM) analysis showed that the soil characteristics and optimized abundance and diversity of the bacterial community in farmland were beneficial for the dissipation efficiency of PAHs.

In this study, two proficient Cadmium (Cd) resistant and plant growth-promoting actinobacterial strains were isolated from metal-polluted soils and identified as Streptomyces sp. strain RA04 and Nocardiopsis sp. strain RA07. Multiple abiotic stress tolerances were found in these two actinobacterial strains, including Cd stress (CdS), drought stress (DS) and high-temperature stress (HTS). Both actinobacterial strains exhibited multifarious plant growth-promoting (PGP) traits such as phosphate solubilization, and production of indole-3-acetic acid, siderophores and 1-aminocyclopropane-1-carboxylate deaminase under CdS, DS and HTS conditions. The inoculation of strains RA04 and RA07 significantly increased Sorghum bicolor growth and photosynthetic pigments under CdS, DS, HTS, CdS + DS and CdS + HTS conditions as compared to their respective uninoculated plants. The actinobacterial inoculants reduced malondialdehyde concentration and enhanced antioxidant enzymes in plants cultivated under various abiotic stress conditions, indicating that actinobacterial inoculants reduced oxidative damage. Furthermore, strains RA04 and RA07 enhanced the accumulation of Cd in plant tissues and the translocation of Cd from root to shoot under CdS, CdS + DS and CdS + HTS treatments as compared to their respective uninoculated plants. These findings suggest that RA04 and RA07 strains could be effective bio-inoculants to accelerate phytoremediation of Cd polluted soil even in DS and HTS conditions.

Chloropicrin (CP) controls soil-borne plant diseases caused by pathogenic microbes, increases crop yield, but has a long-term inhibitory effect on beneficial soil microorganisms. Therefore, we evaluated the effects of biofumigation material fresh chicken manure (FCM) on soil microorganisms, and the duration of those effects in this experiment. Our results showed that in the laboratory, FCM significantly increased substrate-induced respiration (SIR) of soil microorganisms by 2.2–3.2 times at 80 d compared to the control, however, CP significantly inhibited the SIR of soil microorganisms. FCM and CP increased NH4+-N concentration within 40 days which then returned to the control level. FCM increased NO3--N by 2.82–5.78 times by 80 days, compared with the control, while the concentration of NO3--N in the CP treatment was not significantly different from the control at the 80 day. Although in the laboratory FCM inhibited the relative abundance of 16 S rRNA and the nitrogen cycle functional genes AOA amoA, AOB amoA, nirK and nosZ over a 40-day period, the taxonomic diversity of soil bacteria and fungi in the FCM treatment were restored to unfumigated level within 90 days in the field. However, CP treatment has a strong inhibitory effect on soil microorganisms after 90 days. Importantly, the relative abundance of some beneficial microorganisms that control soil-borne pathogenic microbes or degrade pollutants increased significantly in FCM, including Bacillus, Pseudomonas and Streptomyces bacterial genera and Chaetomium and Mycothermus fungal genera. Noteworthy, like CP, FCM still had a strong inhibitory effect on Fusarium at 90 d. Our results indicated that FCM not only increased the content of inorganic nitrogen and improved the respiration rate of soil microorganisms, but it also shortened the recovery time of beneficial soil microorganisms and increased taxonomic diversity. Our previous reports showed that FCM and CP treatments had the same effect in disease control and crop growth. Combined with the results of this experiment, we believe that FCM has the potential to replace CP, which would eliminate CP's detrimental environmental impact, improve farmer safety and promote sustainable crop production.

Metagenomics has provided the discovery of genes and metabolic pathways involved in the degradation of xenobiotics. Some microorganisms can metabolize these compounds, potentiating phytoremediation in association with plant. This study aimed to study the metagenome and the occurrence of atrazine degradation genes in rhizospheric soils of the phytoremediation species Inga striata and Caesalphinea ferrea. The genera of microorganisms predominant in the rhizospheric soils of I. striata and C. ferrea were Mycobacterium, Conexibacter, Bradyrhizobium, Solirubrobacter, Rhodoplanes, Streptomyces, Geothrix, Gaiella, Nitrospira, and Haliangium. The atzD, atzE, and atzF genes were detected in the rhizospheric soils of I. striata and atzE and atzF in the rhizospheric soils of C. ferrea. The rhizodegradation by both tree species accelerates the degradation of atrazine residues, eliminating toxic effects on plants highly sensitive to this herbicide. This is the first report for the species Agrobacterium rhizogenes and Candidatus Muproteobacteria bacterium and Micromonospora genera as atrazine degraders.