In situ anoxic bioremediation is an easy-to-use technology to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated soil. Degradation of PAHs mediated by soil bacteria and archaea using CO₂ as the electron acceptor is an important process for eliminating PAHs under methanogenic conditions; however, knowledge of the performance and mechanisms involved is poorly unveiled. In this study, the effectiveness and efficiency of NaHCO₃ (CO₂) as an electron acceptor to stimulate the degradation of PAHs by bacteria and archaea in highly contaminated soil were investigated. The results showed that CO₂ addition (EC2000) promoted PAH degradation compared to soil without added CO₂ (EC0), with 4.18%, 9.01%–8.05%, and 6.19%–12.45% increases for 2-, 3- and 4-ring PAHs after 250 days of incubation, respectively. Soil bacterial abundances increased with increasing incubation time, especially for EC2000 (2.90 × 10⁸ g⁻¹ soil higher than EC0, p < 0.05). Different succession patterns of the soil bacterial and archaeal communities during PAH degradation were observed. According to the PCoA and ANOSIM results, the soil bacterial communities were greatly (ANOSIM: R = 0.7232, P = 0.001) impacted by electron acceptors, whereas significant differences in the archaeal communities were not observed (ANOSIM: R = 0.553, P = 0.001). Soil bacterial and archaeal co-occurrence network analyses showed that positive correlations outnumbered the negative correlations throughout the incubation period for both treatments (e.g., EC0 and EC2000), suggesting the prevalence of coexistence/cooperation within and between these two domains rather than competition. The higher complexity, connectance, edge, and node numbers in EC2000 revealed stronger linkage and a more stable co-occurrence network compared to EC0. The results of this study could improve the knowledge on the removal of PAHs and the responses of soil bacteria and archaea to CO₂ application, as well as a scientific basis for the in situ anoxic bioremediation of PAH-contaminated industrial sites.

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.

Next-generation sequencing method employing the sphingomonads-specific and universal 16s rRNA primers were applied to analyze the response of soil bacterial community to continuous stress of nanoscale zero-valent iron (nZVI) and/or polycyclic aromatic hydrocarbons (PAHs) under suspended conditions. The group specific primer greatly improves taxonomic resolution, the overall OTU numbers increased from 12 by universal primer to 42 by sphingomonads-specific primer. It was found that nZVI and PAHs had opposite selection effects on bacterial community composition, furthermore, the abundance of Sphingopyxis was positively related to nZVI while negatively related to PAHs, whereas abundances of Sphingobium and Sphingosinicella were positively related to PAHs (p < 0.01). The improved taxonomic resolution helps identify the potential keystone taxa, which provides valuable information for future bioremediation technology such as synthetic microbiome.

The use of reclaimed water in agriculture represents a promising alternative to relieve pressure on freshwater supplies, especially in arid or semiarid regions facing water scarcity. However, this implies introducing micropollutants such as pharmaceutical residues into the environment. The fate and the ecotoxicological impact of valsartan, an antihypertensive drug frequently detected in wastewater effluents, were evaluated in soil-earthworm microcosms. Valsartan dissipation in the soil was concomitant with valsartan acid formation. Although both valsartan and valsartan acid accumulated in earthworms, no effect was observed on biomarkers of exposure (acetylcholinesterase, glutathione S-transferase and carboxylesterase activities). The geometric mean index of soil enzyme activity increased in the soils containing earthworms, regardless of the presence of valsartan. Therefore, earthworms increased soil carboxylesterase, dehydrogenase, alkaline phosphatase, β-glucosidase, urease and protease activities. Although bacterial richness significantly decreased following valsartan exposure, this trend was enhanced in the presence of earthworms with a significant impact on both alpha and beta microbial diversity. The operational taxonomic units involved in these changes were related to four (Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes) of the eight most abundant phyla. Their relative abundances significantly increased in the valsartan-treated soils containing earthworms, suggesting the presence of potential valsartan degraders. The ecotoxicological effect of valsartan on microbes was strongly altered in the earthworm-added soils, hence the importance of considering synergistic effects of different soil organisms in the environmental risk assessment of pharmaceutical active compounds.

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.

Steroid hormones are prevalent in the environment and have become emerging pollutants, but little is known about their effects on soil microbial community composition and function. In the present study, three representative soils in China were amended with environmentally relevant concentrations of testosterone and responses of soil bacterial community composition and soil function were assessed using high-throughput sequencing and nontargeted metabolomics. Our results showed that testosterone exposure significantly shifted bacterial community structure and metabolic profiles in soils at Ningbo (NB) and Kunming (KM), which may reflect high bioavailability of the hormone. Abundances of several bacterial taxa associated with nutrient cycling were reduced by testosterone and metabolites related to amino acid metabolism were downregulated. A close connection between bacterial taxa and specific metabolites was observed and confirmed by Procrustes tests and a co-occurrence network. These results provide an insight into the effects of steroid hormones on soil microbial community and highlight that nontargeted metabolomics is an effective tool for investigating the impacts of pollutants.

Tebuconazole is a broad-spectrum triazole fungicide that has been extensively applied in agriculture, but its toxicity on soil ecology remains unknown after repeated introduction to soil. This study investigated the degradation of tebuconazole and the changes in soil microbial community composition and functional diversity as well as network complexity in soil repeatedly treated with tebuconazole. Tebuconazole degraded slowly as the degradation half-life initially increased and then decreased during the four repeated treatments. High concentration of tebuconazole treatment significantly delayed the degradation of tebuconazole. The soil microbial functional diversity in tebuconazole-treated soils showed an inhibition-recovery-stimulation trend with increasing treatment frequency, which was related to the increased degradation rates of tebuconazole. Tebuconazole significantly decreased soil microbial biomass and bacterial community diversity, and this decreasing trend became more pronounced with increasing treatment frequency and concentration. Moreover, tebuconazole significantly decreased soil bacterial community network complexity, particularly at high concentration of tebuconazole treatment. Notably, four bacterial genera, Methylobacterium, Burkholderia, Hyphomicrobium, and Dermacoccus, were identified as the potential tebuconazole-degrading bacteria, with the relative abundances in the tebuconazole treatment significantly increasing by 42.1–34687.1% compared to the control. High concentration of tebuconazole treatment delayed increases in the relative abundances of Methylobacterium but promoted those of Burkholderia, Hyphomicrobium and Dermacoccus. Additionally, repeated tebuconazole treatments improved only four metabolic pathways, cell motility, membrane transport, environmental information processing, and xenobiotics biodegradation and metabolism, which were associated with the degradation of tebuconazole. The above results indicated that repeated tebuconazole treatments resulted in the significant accumulation of residues and long-term negative effects on soil ecology, and also emphasized the potential roles of dominant indigenous microbial bacteria in the degradation of tebuconazole.

Biofumigation is an effective, non-chemical method to control soil-borne pests and diseases and to maximize crop yield. We studied the responses of soil bacterial and fungal communities, the soil’s nutritional state and strawberry yield, when the soil was biofumigated each year for five consecutive years using fresh chicken manure (BioFum). BioFum significantly increased the soil’s NH4+-N, NO3−-N, available P and K and organic matter. Fusarium spp. and Phytophthora spp. which are known to cause plant disease, were significantly decreased after BioFum. In addition, Biofum increased the soil’s temperature, enhanced chlorophyll levels in the leaves of strawberry plants, and the soluble sugar and ascorbic acid content in strawberry fruit. We used high-throughput gene sequencing to monitor changes in the soil’s bacterial and fungal communities. Although BioFum significantly decreased the diversity of these communities, it increased the relative abundance of some biological control agents in the phylum Actinobacteria and the genera Pseudomonas, Bacillus and Chaetomium. An increase in these biological control agents would reduce the incidence of soil-borne pathogens and plant disease. Although strawberry marketable yield using BioFum was higher in the first three years, the decline in the final two years could be due to the accumulation of P and K which may have delayed flowering and fruiting. Methods to overcome yield losses using BioFum need to be developed in the future. Our research, however, showed that BioFum enhanced soil fertility, reduced the presence of soil pathogens, increased the relative abundance of beneficial bacteria and fungi and improved strawberry quality. Unlike chemical soil treatments that can cause pest and disease resistance when used continuously over many years, our multi-year research program on BioFum showed that this treatment provided significant benefits to the soil, plant and strawberry fruit.

Environmental pollution can disrupt the interactions between animals and their symbiotic bacteria, which can lead to adverse effects on the host even in the absence of direct chemical toxicity. It is therefore crucial to understand how environmental pollutants affect animal microbiomes, especially for those chemicals that are designed to target microbes. Here, we study the effects of two biocidal nanoparticles (NPs) (Ag and CuO) on the soil bacterial community and the resident gut microbiome of the earthworm Eisenia fetida over a 28-day period using metabarcoding techniques. Exposures to NPs were conducted following OECD test guidelines and effects on earthworm reproduction and juvenile biomass were additionally recorded in order to compare effects on the host to effects on microbiomes. By employing a full concentration series, we were able to link pollutants to microbiome effects in high resolution. Multivariate analysis, differential abundance analysis and species sensitivity distribution analysis showed that Ag-NPs are more toxic to soil bacteria than CuO-NPs. In contrast to the strong effects of CuO-NPs and Ag-NPs on the soil bacterial community, the earthworm gut microbiome is largely resilient to exposure to biocidal NPs. Despite this buffering effect, CuO-NPs did negatively affect the relative abundance of some earthworm symbionts, including ‘Candidatus Lumbricincola’. Changes in the soil bacterial community and the earthworm microbiome occur at total copper concentrations often found or modelled to occur in agricultural fields, demonstrating that soil bacterial communities and individual taxa in the earthworm microbiome may be at risk from environmental copper exposure including in nanomaterial form.

Lincomycin mycelial residues (LMRs) are one kind of byproduct of the pharmaceutical industry. Hydrothermal treatment has been used to dispose of them and land application is an attractive way to reuse the treated LMRs. However, the safe dose for soil amendment remains unclear. In this study, a lab-scale incubation experiment was conducted to investigate the influence of the amendment dosage on lincomycin resistance genes and soil bacterial communities via quantitative PCR and 16S rRNA sequencing. The results showed that introduced lincomycin degraded quickly in soil and became undetectable after 50 days. Degradation rate of the high amendment amount (100 mg kg−1) was almost 4 times faster than that of low amendment amount (10 mg kg−1). Moreover, the introduced LMRs induced the increase of lincomycin resistance genes after incubation for 8 days, and two genes (lmrA and lnuB) showed a dosage-related increase. For example, the abundance of gene lmrA was 17.78, 74.13 and 128.82 copies g−1 soil for lincomycin concentration of 10, 50 and 100 mg kg−1, respectively. However, the abundance of lincomycin resistance genes recovered to the control level as the incubation period extended to 50 days, indicating a low persistence in soil. In addition, LMRs application markedly shifted the bacterial composition and significant difference was found between control soil, 10 mg kg−1 and 50 mg kg−1 lincomycin amended soil. Actually, several genera bacteria were significantly related to the elevation of lincomycin resistance genes. These results provided a comprehensive understanding of the effects of lincomycin dosage on the fate of resistance genes and microbial communities in LMRs applied soil.