Soil fumigants aim to control soil-borne diseases below levels that affect economic crop production, but their use also reduces the abundance of beneficial microorganisms. Previous studies have shown that adding various types of fertilizers to soil after fumigation can reshape the soil microbial community and regulate crop growth. We fumigated soil with dazomet (DZ) that had been cropped continuously for more than 20 years. After fumigation we applied silicon fertilizer, potassium humate organic fertilizer, Bacillus microbial fertilizer or a mixture of the last two. We studied the effects of different fertilizers treatments on the soil's physicochemical properties, enzyme activities, key soil pathogens and beneficial microbes. We found that fertilizers applied after fumigation promoted soil beneficial microorganisms (such as Fimicutes, Chloroflexi, Bacillus and Actinomadura) restoration; increased Fusarium and Phytophthora pathogen mortality, the content of ammonium nitrogen, sucrase enzyme activity; and increased strawberry fruit yield. A significant increase in strawberry yield was positively correlated with increases in beneficial microorganisms such as Gemmatimonadota, Firmicutes, Bacillus and Flavisolibacter. We concluded that organic fertilizer applied after fumigation significantly increased the number of beneficial microorganisms, improved the physicochemical properties of the soil, increased soil enzyme activities, inhibited the growth of soil pathogens to increase strawberry fruit yield. In summary, organic fertilizer activated soil beneficial microorganisms after soil fumigation, promoted soil health, and increased strawberry fruit yield.

Cadmium (Cd) and lead (Pb) are ubiquitously present in surface soils, due to anthropogenic activities, causing threat to ecological and human health because of their carcinogenic nature. They accumulate in large quantities in the environment and affect negatively soil microbiota, plants, animals, and humans. For the cleanup of Cd/Pb polluted soils, different plant species have been studied. Many plants have shown the potential to hyperaccumulate Cd/Pb in their above-ground tissues. These plants decrease soil pH by root exudation or by releasing H⁺ ions, and this, in turn, increases the bioavailability of Cd/Pb for plant uptake. Different environmental processes related to soil organic matter, microorganisms, pH, genetic modifications, and various soil-borne chelating agents affect the potential of phytoremediation technology. Review papers trying to identify a single factor influencing the phytoremediation of heavy metals are available in the literature. However, an integrated approach dealing with different factors involved in the remediation of both metals is scarcely discussed. The main focus of this review is to discuss the phytoextraction technique for Cd/Pb removal from contaminated sites along with detoxification mechanisms. Further, the challenges in the Cd/Pb phytoextraction and different options available to cope with these challenges are also discussed. The update on the relevant findings on the use of microorganisms and amendments in enhancing the Cd/Pb phytoextraction is also provided. Finally, the areas to be explored in future research for the removal of Cd/Pb by integrated strategies have been discussed.

This experiment was conducted to evaluate the ecotoxicity of typical explosives and their mechanisms in the soil microenvironment. Here, TNT (trinitrotoluene), RDX (cyclotrimethylene trinitramine), and HMX (cyclotetramethylene tetranitramine) were used to simulate the soil pollution of single explosives and their combination. The changes in soil enzyme activity and microbial community structure and function were analyzed in soil, and the effects of explosives exposure on the soil metabolic spectrum were revealed by non-targeted metabonomics. TNT, RDX, and HMX exposure significantly inhibited soil microbial respiration and urease and dehydrogenase activities. Explosives treatment reduced the diversity and richness of the soil microbial community structure, and the microorganisms able to degrade explosives began to occupy the soil niche, with the Sphingomonadaceae, Actinobacteria, and Gammaproteobacteria showing significantly increased relative abundances. Non-targeted metabonomics analysis showed that the main soil differential metabolites under explosives stress were lipids and lipid-like molecules, organic acids and derivatives, with the phosphotransferase system (PTS) pathway the most enriched pathway. The metabolic pathways for carbohydrates, lipids, and amino acids in soil were specifically inhibited. Therefore, residues of TNT, RDX, and HMX in the soil could inhibit soil metabolic processes and change the structure of the soil microbial community.

Motor vehicles emit a variety of pollutants including metals, petroleum hydrocarbons and polycyclic aromatic hydrocarbons (PAHs). The relationships between metals, petroleum hydrocarbons and PAHs, soil respiration and microbial diversity (fungi and bacteria) were studied using control (n = 3) and roadside soils (n = 27) with different exposure periods to vehicle emissions (2–63 years). Bacterial diversity was found to be higher than control sites (P = 0.002) but was the same across different categories of road age (P = 0.328). Significant (r = −0.49, P = 0.007) contrasting behaviour of fungal and bacterial diversity was reported, with diversity increasing across all road types for bacteria and decreasing across all road types for fungi compared to control soils. Analysis of the bacterial community identified three distinct clusters, separated on age of contamination, suggesting that roadside bacterial communities change over time with pollution from vehicles with the potential development of metal resistant bacteria in roadside soils. In contrast, for fungal communities, a reduction in diversity with time of exposure to roadside vehicle emissions was observed suggesting the potential for reduced ecosystem functionality and soil health in roadside soils. This is the first study in the published literature to include both bacterial and fungal responses from aged roadside soils. The results from this study suggest that normal functionality of soil ecosystem services is being affected in roadside soils, potentially globally.

Polycyclic aromatic hydrocarbons (PAHs) are hazardous organic compounds with mutagenic, genotoxic and carcinogenic properties. Although PAHs in soil can cause toxicity to microorganisms, the microbial community is able to degrade these compounds. For this reason, it is important to study acute and short-term effects of PAH contamination on soil microbial community, also to shed light on its possible exploitation in soil restoration.The effects of acute PAH contamination on the structure and metabolic activity of microbial communities in three forest (beech, holm oak, black pine) soils were studied. The soils were spiked with phenanthrene, pyrene or benzo[a]pyrene and incubated in experimental mesocosms, under controlled conditions. Enzymatic activities (laccase, total peroxidase and hydrolase), as well as microbial biomass and community structure (through phospholipid fatty acid and ergosterol analyses), were evaluated in the three soil systems 4 days after contamination and compared to no-spiked soils. In soil under holm oak, there was a stimulation of Gram+ bacteria after contamination with all the 3 PAHs, whereas in soil under pine, pyrene and phenanthrene additions mainly stimulated fungi and actinomycetes.

Co-presence of organic pollutants and heavy metals in soil is causing increasing concerns, but the lack of knowledge of relation between soil ecology and pollutant fate is limiting the developing of specific control strategy. This study investigated soil change under pyrene stress and its interaction with cadmium (Cd). Soil physicochemical properties were not seriously influenced. However, pollutants’ presence easily varied soil microbial activity, quantity, and diversity. Under high-level pyrene, Cd presence contributed to soil indigenous microorganisms’ adaption and soil microbial community structure stability. Soils with both pyrene and Cd presented 7.11–12.0% higher pyrene degradation compared with single pyrene treatment. High-throughput sequencing analysis indicated the proportion of Mycobacterium sp., a commonly known PAHs degrader, increased to 25.2–48.5% in treatments from 0.52% in control. This phenomenon was consistent with the increase of PAHs probable degraders (the ratio increased to 2.86–6.57% from 0.24% in control). Higher Cd bioavailability was also observed in soils with both pollutants than that with Cd alone. And Cd existence caused the elevation of Cd resistant bacterium Limnobacter sp. (increased to 12.2% in CdCK from 2.06% in control). Functional gene prediction also indicated that abundance of genes related to nutrient metabolism decreased dramatically with pollutants, while the abundances of energy metabolism, lipid metabolism, secondary metabolites biosynthesis-related genes increased (especially for aromatic compound degradation related genes). These results indicated the mutual effect and internal-interaction existed between pollutants and soils resulted in pollutants’ fate and soil microbial changes, providing further information regarding pollutants dissipation and transformation under soil microbial response.

Clonal plants can share information and resources among connected ramets (asexual individuals). Such clonal integration can promote ramet growth, which may further influence soil microbial communities in the rooting zone. Crude oil contamination can negatively affect plant growth and alter soil microbial community composition. However, we still know little about how clonal integration affects soil microbial communities, especially under crude oil contamination. In a coastal wetland, ramets of the rhizomatous plant Phragmites australis in circular plots (60 cm in diameter) were subjected to 0, 5 and 10 mm depth of crude oil, and the rhizomes at the edge of the plots were either severed (preventing clonal integration) or left intact (allowing clonal integration). After three years of treatment, we analysed in each plot soil physiochemical properties and soil microbial community composition. The alpha-diversity of the soil microbial communities did not differ between intact and severed plots, but was overall lower in 10-mm than in 0-mm and 5-mm oil plots. Considering all three oil treatments together, soil microbial community dissimilarity (beta-diversity) was positively correlated with soil property distance in both severed and intact plots. Considering the three oil treatments separately, this pattern was also observed in 10-mm oil plots, but not in 0-mm or 5-mm oil plots. The soil microbial community composition was more sensitive to the oil addition than to the clonal integration. Moreover, the relative abundance of the nitrogen-cycling bacterial taxa was lower in intact than in severed plots, and that of the oil-degrading bacterial taxa increased with increasing oil-addition levels. Our results indicate that clonal integration and oil contamination can influence soil microbial communities independently through changing the relative abundance of the component bacteria taxa, which has important implications for ecosystem functions of the soil food web mediated by clonal plants.

The bioavailability of the metalloid arsenic (As) in paddy soil is controlled by microbial cycling of As and other elements such as iron (Fe) and sulfur (S), which are strongly influenced by water management in paddy fields. In this study, we evaluated how water management affects As bioavailability by growing rice plants in a geogenic As-contaminated soil. We determined As speciation in soil porewater and the diversity of the associated microbial community. Continuous flooding enhanced the release of Fe and As and increased arsenite (As(III)) and methylated As species concentrations in the rice grain compared with aerobic treatment. Total inorganic and organic As in the grain was 84% and 81% lower, respectively, in the aerobic treatment compared with the continuous flooding treatment. The amounts of Fe(III)-reducing bacteria (FeRB) increased in the flooded rhizosphere soil. The abundance of FeRB in the soil correlated with the dissolution of Fe and As. Among the As-transformation genes quantified, the aioA gene for As(III) oxidation and arsM gene for As(III) methylation were most abundant. The arsM copy number correlated positively with the levels of dsrB (dissimilatory (bi) sulfite reductase β-subunit), suggesting that dissimilatory sulfate-reducing bacteria (SRB) may play an important role in dimethylarsenate (DMAs(V)) production in soil. Our results show that decreased populations of rhizosphere FeRB and SRB contributed to a lower bioavailability of As, and decreased production of methylated arsenicals under oxic conditions.

Degradation of metolachlor in surface soil is extremely important to its potential mobility and overall persistence. In this study, the effects of earthworms (Eisenia fetida) on the degradation of metolachlor at two concentration levels (5 and 20 mg kg⁻¹) in soil were investigated via the column experiment. The degradation kinetics of metolachlor indicate that addition of earthworms enhances metolachlor degradation significantly (P < 0.05), with the enhanced degradation rate of 30% and 63% in the low and high concentration treatments at the 15th day, respectively. Fungi rather than bacteria are primarily responsible for metolachlor degradation in soil, and earthworms stimulate metolachlor degradation mainly by stimulating the metolachlor-degrading functional microorganisms and improving fungal community structure. Earthworms prefer to promote the possible fungal degraders like order Sordariales, Microascales, Hypocreales and Mortierellales and the possible bacteria genus Rubritalea and strengthen the relationships between these primary fungi. Two metabolites metolachlor oxanilic (MOXA) and moetolachlor ethanesulfonic acid (MESA) are detected in soil and earthworms in the high concentration treatments. Earthworms stimulate the formation of MOXA and yet inhibit the formation of MESA in soil. Another metabolite metolachlor-2-hydroxy (M2H) is also detected in earthworms, which is reported firstly. The study provides an important information for the remediation of metolachlor-polluted soil.

Fomesafen, a long-lived protoporphyrinogen-oxidase inhibitor, specially developed for post-emergence control of broad-leaf weeds, is used widely in soybean fields in northern China (Dayan and Duke, 2010). The impact of fomesafen on microbial communities in rhizosphere soils, however, is unknown. In this study we examined fomesafen degradation as well as its effects in the rhizosphere of soybean plants grown in a greenhouse. Fomesafen had shorter half-life in rhizosphere soil than previously reported for bulk soil from the same location (87 vs 120 days). The enzyme activity of soil extracts and the microbial community composition of 16S rRNA genes (16S) amplified from soil DNA were also investigated. Although not immediately apparent, both the high (37.5 mg kg⁻¹) and low (18.75 mg kg⁻¹) doses of fomesafen significantly decreased urease and invertase activities in the rhizosphere soil from days 30 and 45 respectively until the end of the experiment (90 days). Analysis of 16S amplicons demonstrated that fomesafen had a dose dependent effect, decreasing alpha diversity and altering beta diversity. Significant phylum level decreases were observed in five of the ten phyla that were most abundant in the control. Proteobacteria was the only phylum whose relative abundance increased in the presence of fomesafen, driven by increases in the genera Methylophilacaea, Dyella, and Sphingomonas. The functional implications of changes in 16S abundance as predicted using PICRUSt suggested that fomesafen enriched for enzymes involved in xenobiotic metabolism and detoxification (cytochrome P450s and glutathione metabolism). Our data suggest that, despite being degraded more rapidly in the rhizosphere than in bulk soil, fomesafen had long-lasting functional impacts on the soil microbial community.