Effects of co-contamination of heavy metals and total petroleum hydrocarbons on soil bacterial community and function network reconstitution

Co-pollution risk of petroleum hydrocarbons and heavy metals in typically polluted estuarine wetlands: Insights from the Xiaoqing River

Excessive accumulation of total petroleum hydrocarbons (TPH) and heavy metals (HMs) in sediments poses a significant threat to the estuarine ecosystem. In this study, the spatial and temporal distribution, ecological risks, sources, and their impacts on the microbial communities of TPH and nine HMs in the estuarine sediments of the Xiaoqing River were determined. Results showed that the spatial distribution of TPH and HMs were similar but opposite in temporal. Ni, Cr, Pb, and Co concentrations were similar to the reference values (RVs). However, the other five HMs (Cu, Zn, Cd, As, and Hg) and TPH concentrations were 2.00-763.44 times higher than RVs; hence, this deserves attention, particularly for Hg. Owing to the water content of the sediments, Hg was mainly concentrated on the surface during the wet season and on the bottom during the dry season. Moreover, because of weak hydrodynamics and upstream pollutant sinks, TPH-HMs in the river were higher than those in the estuary. TPH and HM concentrations were negatively correlated with microbial diversity. Structural equation modeling showed that HMs (path coefficient = -0.50, p < 0.001) had a negative direct effect on microbial community structure and a positive indirect effect on TPH. The microbial community (path coefficient = 0.31, 0.01 < p < 0.05) was significantly correlated with TPH. In summary, this study explores both the chemical analysis of pollutants and their interaction with microbial communities, providing a better understanding of the co-pollution of TPH and HMs in estuarine sediments.

Enhancing soil petrochemical contaminant remediation through nutrient addition and exogenous bacterial introduction

Biostimulation (providing favorable environmental conditions for microbial growth) and bioaugmentation (introducing exogenous microorganisms) are effective approaches in the bioremediation of petroleum-contaminated soil. However, uncertainty remains in the effectiveness of these two approaches in practical application. In this study, we constructed mesocosms using petroleum hydrocarbon-contaminated soil. We compared the effects of adding nutrients, introducing exogenous bacterial degraders, and their combination on remediating petroleum contamination in the soil. Adding nutrients more effectively accelerated total petroleum hydrocarbon (TPH) degradation than other treatments in the initial 60 days' incubation. Despite both approaches stimulating bacterial richness, the community turnover caused by nutrient addition was gentler than bacterial degrader introduction. As TPH concentrations decreased, we observed a succession in microbial communities characterized by a decline in copiotrophic, fast-growing bacterial r-strategists with high rRNA operon (rrn) copy numbers. Ecological network analysis indicated that both nutrient addition and bacterial degrader introduction enhanced the complexity and stability of bacterial networks. Compared to the other treatment, the bacterial network with nutrient addition had more keystone species and a higher proportion of negative associations, factors that may enhance microbial community stability. Our study demonstrated that nutrient addition effectively regulates community succession and ecological interaction to accelerate the soil TPH degradation.

Combined toxicity of Cd and aniline to soil bacteria varying with exposure sequence

Joint toxicity of organic-metal co-contamination can vary depending on organisms, toxicants, and even the sequence of exposure. This study examines how the combined toxicity of aniline (An) and cadmium (Cd) to soil bacteria in microcosms changes when the order of contaminant introduction is altered. Through analyzing biodiversity, molecular ecological network, functional redundancy, functional genes and pathways, we find the treatment of Cd followed by An brings about the strongest adverse impact to the bacterial consortium, followed by the reverse-ordered exposure and the simple mixture of the two chemicals. On the level of individual organisms, exposure sequence also affects the bacteria that are otherwise resistant to the standalone toxicity of both An and Cd. The dynamic behavior of aniline-cadmium composite is interpreted by considering the tolerance of organisms to individual chemicals, the interactions of the two toxicants, the recovery time, as well as the priority effect. The overall effect of the composite contamination is conceptualized by treating the chemicals as environmental filters screening the growth of the community.

Exploring the diversity and functional profile of microbial communities of Brazilian soils with high salinity and oil contamination

Environmental pollution associated with the petroleum industry is a major problem worldwide. Microbial degradation is extremely important whether in the extractive process or in bioremediation of contaminants. Assessing the local microbiota and its potential for degradation is crucial for implementing effective bioremediation strategies. Herein, contaminated soil samples of onshore oil fields from a semiarid region in the Northeast of Brazil were investigated using metagenomics and metataxonomics. These soils exhibited hydrocarbon contamination and high salinity indices, while a control sample was collected from an uncontaminated area. The shotgun analysis revealed the predominance of Actinomycetota and Pseudomonadota, while 16S rRNA gene amplicon analysis of the samples showed Actinomycetota, Bacillota, and Pseudomonadota as the most abundant. The Archaea domain phylotypes were assigned to Thermoproteota and Methanobacteriota. Functional analysis and metabolic profile of the soil microbiomes exhibited a broader metabolic repertoire in the uncontaminated soil, while degradation pathways and surfactant biosynthesis presented higher values in the contaminated soils, where degradation pathways of xenobiotic and aromatic compounds were also present. Biosurfactant synthetic pathways were abundant, with predominance of lipopeptides. The present work uncovers several microbial drivers of oil degradation and mechanisms of adaptation to high salinity, which are pivotal traits for sustainable soil recovery strategies.

Brucella pituitosa strain BU72, a new hydrocarbonoclastic bacterium through exopolysaccharide-based surfactant production

Hydrocarbon and heavy metal pollution are amongst the most severe and prevalent environmental problems due to their toxicity and persistence. Bioremediation using microorganisms is considered one of the most effective ways to treat polluted sites. In the present study, we unveil the bioremediation potential of Brucella pituitosa strain BU72. Besides its ability to grow on multiple hydrocarbons as the sole carbon source and highly tolerant to several heavy metals, BU72 produces different exopolysaccharide-based surfactants (EBS) when grown with glucose or with crude oil as sole carbon source. These EBS demonstrated particular and specific functional groups as determined by Fourier transform infrared (FTIR) spectral analysis that showed a strong absorption peak at 3250 cm-1 generated by the -OH group for both EBS. The FTIR spectra of the produced EBS revealed major differences in functional groups and protein content. To better understand the EBS production coupled with the degradation of hydrocarbons and heavy metal resistance, the genome of strain BU72 was sequenced. Annotation of the genome revealed multiple genes putatively involved in EBS production pathways coupled with resistance to heavy metals genes such as arsenic tolerance and cobalt-zinc-cadmium resistance. The genome sequence analysis showed the potential of BU72 to synthesise secondary metabolites and the presence of genes involved in plant growth promotion. Here, we describe the physiological, metabolic, and genomic characteristics of Brucella pituitosa strain BU72, indicating its potential as a bioremediation agent.

Soil amendments alter cadmium distribution and bacterial community structure in paddy soils

Soil amendments play a pivotal role in ensuring the safety of food production by inhibiting the transfer of heavy metal ions from soils to crops. Nevertheless, their impact on soil characteristics and the microbial community and their role in reducing cadmium (Cd) accumulation in rice remain unclear. In this study, pot experiments were conducted to investigate the effects of three soil amendments (mineral, organic, and microbial) on the distribution of Cd speciation, organic components, iron oxides, and microbial community structure. The application of soil amendments resulted in significant reductions in the soil available Cd content (16 %-51 %) and brown rice Cd content (16 %-78 %), facilitating the transformation of Cd from unstable forms (decreasing 10 %-20 %) to stable forms (increasing 77 %-150 %) in the soil. The mineral and organic amendments increased the soil cation exchange capacity (CEC) and plant-derived organic carbon (OC), respectively, leading to reduced Cd accumulation in brown rice, while the microbial amendment enhanced OC complexity and the abundances of Firmicutes and Bacteroidota, contributing to the decreased rice Cd uptake. The synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectroscopy indicated that soil amendments regulated soil Cd species by promoting iron oxides and OC coupling. Moreover, both organic and microbial amendments significantly reduced the diversity and richness of the bacterial communities and altered their compositions and structures, by increasing the relative abundances of Bacteroidota and Firmicutes and decreasing those of Acidobacteria, Actinobacteria, and Myxococcota. Soil microbiome analysis revealed that the increase of Firmicutes and Bacteroidota associated with Cd adsorption and sequestration contributed to the suppression of soil Cd reactivity. These findings offer valuable insights into the potential mechanisms by which soil amendments regulate the speciation and bioavailability of Cd, and improve the bacterial communities, thereby providing guidance for agricultural management practices.

Biostimulation effect of different amendments on Cr(VI) recovering microbial community

The present study used Cr(VI)-polluted microcosms amended with lactate or yeast extract, and nonamended microcosms as control, to investigate how a native bacterial community varied in response to the treatment and during the pollutant removal. Results suggested that providing electron donors resulted in a proliferation of a few bacterial species, with the consequent decrease in observed species richness and evenness, and was a driving force for the bacterial compositional shift. Lactate promoted, in the first instance, the enrichment of fermentative bacteria belonging to Chromobacteriaceae, including Paludibacterium, and Micrococcaceae as observed after 4 days. When the rate of Cr(VI) removal was maximum in microcosms amended with lactate, the most represented taxa were Pseudarcicella and Azospirillum. Using yeast extract as a carbon source and electron donor led instead to the significant enrichment of Shewanella, followed by Vogesella and Acinetobacter on the 4th day, corresponding to 90% of Cr(VI) removed from the system. After the complete Cr(VI) removal, achieved in 7 days in the presence of yeast extract, α-diversity was notably increased. The amendment-specific turnover of the enriched bacterial taxa resulted in a different kinetic of pollutant removal. In particular, yeast extract promoted the quickest Cr(VI) reduction, while lactate supported a slower, but also considerable, pollutant removal from water. Since it is reasonable to assume that a macroscopic effect, such as the observed Cr(VI) removal, involved the overrepresented taxa, deepening the knowledge of the native bacterial community and its changes were used to hypothesize the possible microbial pathways involved.

Polydopamine and calcium functionalized fiber carrier for enhancing microbial attachment and Cr(VI) resistance

The formation of biofilm determines the performance and stability of biofilm system. Increasing the hydrophilicity of the carrier surface could efficiently accelerate the attachment and growth of microorganisms. Here, the surface of polypropylene (PP) fiber carrier was modified with polydopamine (PDA) and calcium (Ca(II)) to enhance microbial attachment and toxicity resistance. The results of surface characteristic confirmed the self-polymerization of PDA and the chelation mechanism of Ca(II). Subsequently, the biofilm formation experiments were conducted in sequencing batch biofilm reactors using both normal and chromium-containing wastewater. The biofilm on the surface of the modified carrier exhibited better nitrogen removal and Cr(VI) reduction ability. The biomass of the modified carrier was significantly increased, and the maximum microbial attachment amounts in normal wastewater and chrome-containing wastewater were 1153.34 and 511.78 mg/g carrier, respectively. Furthermore, the confocal laser scanning microscope (CLSM) indicated that the modified carrier coated with PDA and Ca(II) were both biocompatible, and the cell activity was significantly increased. 16S rRNA sequencing results showed that the modified carrier efficiently enriched both denitrification bacteria (Thauera and Flavobacterium) and chrome-reducing bacteria (Simplicispira and Arenimonas) to improve system stability and Cr(VI) resistance. Microbial phenotype prediction based on BugBase analysis further verified the enrichment effect of modified carriers on microorganisms responsible for biofilm formation and oxidative stress resistance. Overall, this work proposed a novel functional carrier that could provide references for advancing the application of biofilm systems in wastewater treatment.

Effects of single and combined contamination of total petroleum hydrocarbons and heavy metals on soil microecosystems: Insights into bacterial diversity, assembly, and ecological function

Deciphering the impact of single and combined contamination of total petroleum hydrocarbons (TPH) and heavy metals on soil microecosystems is essential for the remediation of contaminated habitats, yet it remains incompletely understood. In this study, we employed high-throughput sequencing to investigate the impact of single TPH contamination, single metal contamination, and their co-contamination on soil microbial diversity, assembly mechanisms, composition, ecological function, and resistome. Our results revealed that contamination led to a reduction in alpha diversity, with single contamination displaying lower diversity compared to co-contamination, depending on the concentration of pollutants. Community beta diversity was primarily driven by turnover rather than nestedness, and narrower ecological niches were detected under pollution conditions. The neutral community model suggested that homogenizing dispersal played a significant role in the community assembly process under single TPH or co-contamination, while homogeneous selection dominated under heavy metals pollution. Procrustes analysis demonstrated a correlation between community composition and functional divergence, while Mantel tests linked this divergence to concentrations of Cr, Cr6+, Pb, and TPH. Interestingly, soils co-polluted with TPH and heavy metals exhibited similar genera, community functions, and resistomes as soils contaminated with only metals, highlighting the significant impact of heavy metals. Ecological functions related to carbon (C), nitrogen (N), and sulfur (S) cycles were enhanced under TPH pollution but impaired under heavy metals stress. These findings enhance our understanding of soil microecosystems subjected to TPH, heavy metals, and their co-contamination, and carry significant implications for environmental microecology and pollutant risk assessment.

Differences in microbial community structure and metabolic activity among tea plantation soils under different management strategies

Introduction

Microorganisms play an important role in the multifunctionality of soil ecosystems. Soil microbial diversity and functions have a great impact on plant growth and development. The interactions between tea trees and soil microbiota can be linked with planting patterns and management strategies, whose effects on soil microbial community structure and metabolites are still unclear.

Methods

Here we used amplicon sequencing and metabolomic analysis to investigate the differences in soil microbial composition and metabolites among three tea production systems: organic, non-organic, and intercropping.

Results

We detected significant differences among the three systems and found that Firmicutes, Proteobacteria, Acidobacteriota, Actinobacteriota and Chloroflexi were the main bacteria in the three soil groups, although they varied in relative abundance. Acidobacteria bacterium increased significantly in the organic and intercropping groups. For fungi, Ascomycota and Basidiomycota were the main differential fungal phyla. Fungi alpha-diversity in the non-organic group was significantly higher than that in the other two groups, and was correlated with multiple soil physical and chemical factors. Moreover, network analysis showed that bacteria and fungi were strongly correlated. The changes in soil microorganisms caused by management and planting patterns may affect soil quality through corresponding changes in metabolites. Metabolomic analysis showed differences in metabolite composition among different groups. It was also found that the arachidonic acid metabolic pathway was affected by changes in soil microorganisms, and may further affect soil quality in an essential manner.

Discussion

Planting patterns and management strategies may significantly affect soil microorganisms and therefore metabolites. Changes in soil microorganisms, especially in fungi, may alter soil quality by affecting soil physicochemical properties and metabolites. This study will provide new insights into soil quality monitoring from a microbiological perspective.

Combinations of waste seaweed liquid fertilizer and biochar on tomato (Solanum lycopersicum L.) seedling growth in an acid-affected soil of Jiaodong Peninsula, China

Biochar application is an effective strategy for improving soil degradation and productivity. However, the effects of the combination of biochar and other fertilizers to improve seedling growth in abiotic stress-affected soils remains unknown. We investigate the effect of biochar derived from reed straw (RBC) and waste seaweed liquid fertilizer (SLF) on tomato (Solanum lycopersicum L.) seedling growth in an acid-affected soil of Jiaodong Peninsula, China. The results revealed RBC, SLF, and the combination of RBC with SLF (RBC+SLF) significantly elevated the dry weight of tomatoes by 23.33 %, 29.93 %, and 63.66 %, respectively. The malondialdehyde content in the tomato seedling roots, stems, and leaves was significantly lower in the RBC+SLF treatment, which might be related to the enhanced contents of proline, soluble sugar, and soluble protein. The synthesis and accumulation of zeatin riboside, indole-3-acetic acid, and gibberellic acid 3 in tomato under RBC+SLF amendment may be attributed to the enhanced plant growth. Moreover, RBC, SLF, and RBC+SLF improved the soil status (including ammonium nitrogen, nitrate nitrogen, laccase, and urease) in the acid-affected soil. Biochar and waste seaweed liquid fertilizer significantly increased the relative abundance of Pseudomonas and Azospira (beneficial bacteria) in tomato rhizosphere. The microbial amino acid metabolism was associated with changes in soil properties and enzyme activities. Consequently, biochar and waste seaweed liquid fertilizer are viable soil conditioners for acid-affected soil.

Metagenomics-metabolomics analysis of microbial function and metabolism in petroleum-contaminated soil

Contamination of soil by petroleum is becoming increasingly serious in the world today. However, the research on gene functional characteristics, metabolites and distribution of microbial genomes in oil-contaminated soil is limited. Considering that, metagenomic and metabonomic were used to detect microbes and metabolites in oil-contaminated soil, and the changes of functional pathways were analyzed. We found that oil pollution significantly changed the composition of soil microorganisms and metabolites, and promoted the relative abundance of Pseudoxanthomonas, Pseudomonas, Mycobacterium, Immundisolibacter, etc. The degradation of toluene, xylene, polycyclic aromatic hydrocarbon and fluorobenzoate increased in Xenobiotics biodegradation and metabolism. Key monooxygenases and dioxygenase systems were regulated to promote ring opening and degradation of aromatic hydrocarbons. Metabolite contents of polycyclic aromatic hydrocarbons (PAHs) such as 9-fluoronone and gentisic acid increased significantly. The soil microbiome degraded petroleum pollutants into small molecular substances and promoted the bioremediation of petroleum-contaminated soil. Besides, we discovered the complete degradation pathway of petroleum-contaminated soil microorganisms to generate gentisic acid from the hydroxylation of naphthalene in PAHs by salicylic acid. This study offers important insights into bioremediation of oil-contaminated soil from the aspect of molecular regulation mechanism and provides a theoretical basis for the screening of new oil degrading bacteria.

Biodegradation of petroleum hydrocarbons based pollutants in contaminated soil by exogenous effective microorganisms and indigenous microbiome

Microbial remediation is an eco-friendly and promising approach for the restoration of sites contaminated by petroleum hydrocarbons (PHCs). The degradation of total petroleum hydrocarbons (TPHs), semi volatile organic compounds (SVOCs) and volatile organic compounds (VOCs) of the soil samples collected from a petrochemical site by indigenous microbiome and exogenous microbes (Saccharomyces cerevisiae ATCC 204508/S288c, Candida utilis AS2.281, Rhodotorula benthica CBS9124, Lactobacillus plantarum S1L6, Bacillus thuringiensis GDMCC1.817) was evaluated. Community structure and function of soil microbiome and the mechanism involved in degradation were also revealed. After bioremediation for two weeks, the concentration of TPHs in soil samples was reduced from 17,800 to 13,100 mg/kg. The biodegradation efficiencies of naphthalene, benzo[a]anthracene, benzo[b]fluoranthene, benzo[a]pyrene, indeno[1,2,3-cd]pyrene, dibenzo[a,h]anthracene, 1,2,3-trichloropropane, 1,2-dichloropropane, ethylbenzene and benzene in soil samples with the addition of S. cerevisiae were 38.0%, 35.7%, 36.2%, 40.4%, 33.6%, 36.2%, 12.0%, 43.9%, 43.3% and 43.0%, respectively. The microbial diversity and community structure were improved during the biodegradation process. S. cerevisiae supplemented soil samples exhibited the highest relative abundance of the genus Acinetobacter for bacteria and Saccharomyces for yeast. The findings offer insight into the correlation between microbes and the degradation of PHC-based pollutants during the bioremediation process.

Bio-organic fertilizers improve Dendrocalamus farinosus growth by remolding the soil microbiome and metabolome

Organic and microbial fertilizers have potential advantages over inorganic fertilizers in improving soil fertility and crop yield without harmful side-effects. However, the effects of these bio-organic fertilizers on the soil microbiome and metabolome remain largely unknown, especially in the context of bamboo cultivation. In this study, we cultivated Dendrocalamus farinosus (D. farinosus) plants under five different fertilization conditions: organic fertilizer (OF), Bacillus amyloliquefaciens bio-fertilizer (Ba), Bacillus mucilaginosus Krassilnikov bio-fertilizer (BmK), organic fertilizer plus Bacillus amyloliquefaciens bio-fertilizer (OFBa), and organic fertilizer plus Bacillus mucilaginosus Krassilnikov bio-fertilizer (OFBmK). We conducted 16S rRNA sequencing and liquid chromatography/mass spectrometry (LC-MS) to evaluate the soil bacterial composition and soil metabolic activity in the different treatment groups. The results demonstrate that all the fertilization conditions altered the soil bacterial community composition. Moreover, the combination of organic and microbial fertilizers (i.e., in the OFBa and OFBmK groups) significantly affected the relative abundance of soil bacterial species; the largest number of dominant microbial communities were found in the OFBa group, which were strongly correlated with each other. Additionally, non-targeted metabolomics revealed that the levels of soil lipids and lipid-like molecules, and organic acids and their derivatives, were greatly altered under all treatment conditions. The levels of galactitol, guanine, and deoxycytidine were also markedly decreased in the OFBa and OFBmK groups. Moreover, we constructed a regulatory network to delineated the relationships between bamboo phenotype, soil enzymatic activity, soil differential metabolites, and dominant microbial. The network revealed that bio-organic fertilizers promoted bamboo growth by modifying the soil microbiome and metabolome. Accordingly, we concluded that the use of organic fertilizers, microbial fertilizers, or their combination regulated bacterial composition and soil metabolic processes. These findings provide new insights into how D. farinosus-bacterial interactions are affected by different fertilization regiments, which are directly applicable to the agricultural cultivation of bamboo.

Effect of calcination temperatures on the performance of rectorite for cadmium immobilization in soil: Freeze-thaw, plant growth, and microbial diversity

The immobilization of cadmium (Cd(II)) in soil using calcined rectorite (REC) was investigated in this research. The results of immobilization show that a small amount of REC calcined at 700 °C (REC-700 °C) could effectively immobilize 90% of Cd(II) in soil, while the immobilization efficiency of REC only reached 42%. Moreover, the immobilization efficiency of REC calcined at 300 °C and 500 °C (REC-300 °C and REC-500 °C) were lower than REC. To investigate the mechanism, the materials before and after immobilization were fully analyzed by Fourier transform infrared spectroscopy (FT-IR), powdery X-ray diffraction analysis (XRD), and scanning electron microscopy (SEM). The results indicate that the structure of REC has been changed after calcination at different temperatures and Cd(II) was successfully immobilized on materials. Losing free water, structural water and OH groups respectively, the layer spacing of REC-300 °C and REC-500 °C was shrunk. However, the crystal structure of REC was destroyed after calcination at 700 °C, resulting in the generation of new phases. According to the XRD result, more cadmium hydroxide (Cd(OH)₂) were produced on REC-700 °C, indicating that more OH groups were formed during immobilization. Furthermore, Tessier test demonstrates that Cd(II) in soil changed from exchangeable state and water soluble state to carbonate bound state and iron manganese oxide bound state during immobilization. The result of microbial community indicates that REC-700 °C can restore the microbial composition of Cd(II)-contaminated soil. The effects of pH, freeze-thaw, REC dosage, and initial heavy metal concentration were also evaluated to provide a theoretical basis for the subsequent application of the material in the remediation of contaminated soil.

Short-term responses of soil nutrients, heavy metals and microbial community to partial substitution of chemical fertilizer with spent mushroom substrates (SMS)

Currently, many spent mushroom substrates (SMS) are produced each year, which have the great potential to replace partial chemical fertilizer in agricultural production due to the high content of organic matter in SMS. However, how the replacement of chemical fertilizer by different SMS affected soil nutrients and contamination was less reported. Therefore, this study applied Enoki mushroom substrates (EMR), Agaricus bisporus substrates (ABR), or Auricularia auricula substrates (AAR) to replace 25 % chemical fertilizers (based on N fertilizer) with understanding the role of SMS replacement in affecting soil nutrients, heavy metals, and microbial community via the short-term field study, respectively. Compared to chemical fertilizer (CF), the contents of organic matter (OM), total P (TP), and K (TK) in SMS replaced soils were significantly increased by 1.96-4.22, 0.08-0.12, and 0.03-0.53 g kg^-1, respectively. Among three SMS replacements, AAR demonstrated the highest increment of soil nutrients. On the other hand, EMR and ABR replacements reduced the contents of total and acid-soluble Cd, Pb, and As by 7.94-30.32 % and 0-31.61 % in soils relative to CF, respectively. Unlike EMR and ABR, AAR reduced 11.08-16.04 % of total Cd, Pb, and As but increased 62.58 % acid-soluble As in soils. Furthermore, it was found that all SMS replacements increased the relative abundance of Proteobacteria, while ABR also increased the relative abundance of Actinobacteria in soils compared to CF. Besides, EMR and ABR replacements increased the relative abundance of Mortierellomycota relative to CF. Finally, it can be known that partial replacement of chemical fertilizer by SMS could elevate soil nutrients (especially AAR) and reduce heavy metals (especially EMR), which further improved microbial diversity and community composition. This study provides information on applying SMS to replace partial chemical fertilizer to elevate nutrients and reduce heavy metals contamination.

A microcosm approach for evaluating the microbial nonylphenol and butyltin biodegradation and bacterial community shifts in co-contaminated bottom sediments from the Gulf of Finland, the Baltic Sea

Pollution of aquatic ecosystems with nonylphenol (NP) and butyltins (BuTs) is of great concern due to their effects on endocrine activity, toxicity to aquatic organisms, and extended persistence in sediments. The impact of contamination with NP and/or BuTs on the microbial community structure in marine sediments was investigated using microcosms and high-throughput sequencing. Sediment microcosms with NP (300 mg/kg) and/or BuTs (95 mg/kg) were constructed. Complete removal of monobutyltin (MBT) occurred in the microcosms after 240 days of incubation, while a residual NP rate was 40%. The content of toxic tributyltin (TBT) and dibutyltin (DBT) in the sediments did not change notably. Co-contamination of the sediments with NP and BuTs did not affect the processes of their degradation. The pollutants in the microcosms could have been biodegraded by autochthonous microorganisms. Significantly different and less diverse bacterial communities were observed in the contaminated sediments compared to non-contaminated control. Firmicutes and Gammaproteobacteria dominated in the NP treatment, Actinobacteria and Alphaproteobacteria in the BuT treatment, and Gammaproteobacteria, Alphaproteobacteria, Firmicutes, and Acidobacteria in the NP-BuT mixture treatment. The prevalence of microorganisms from the bacterial genera Halothiobacillus, Geothrix, Methanosarcina, Dyella, Parvibaculum, Pseudomonas, Proteiniclasticum, and bacteria affiliated with the order Rhizobiales may indicate their role in biodegradation of NP and BuTs in the co-contaminated sediments. This study can provide some new insights towards NP and BuT biodegradation and microbial ecology in NP-BuT co-contaminated environment.

Decontamination of water co-polluted by copper, toluene and tetrahydrofuran using lauric acid

Co-contamination by organic solvents (e.g., toluene and tetrahydrofuran) and metal ions (e.g., Cu2+) is common in industrial wastewater and in industrial sites. This manuscript describes the separation of THF from water in the absence of copper ions, as well as the treatment of water co-polluted with either THF and copper, or toluene and copper. Tetrahydrofuran (THF) and water are freely miscible in the absence of lauric acid. Lauric acid separates the two solvents, as demonstrated by proton nuclear magnetic resonance (1H NMR) and Attenuated Total Reflection-Fourier Transform Infrared Spectroscopy (ATR-FTIR). The purity of the water phase separated from 3:7 (v/v) THF:water mixtures using 1 M lauric acid is ≈87%v/v. Synchrotron small angle X-Ray scattering (SAXS) indicates that lauric acid forms reverse micelles in THF, which swell in the presence of water (to host water in their interior) and ultimately lead to two free phases: 1) THF-rich and 2) water-rich. Deprotonated lauric acid (laurate ions) also induces the migration of Cu2+ ions in either THF (following separation from water) or in toluene (immiscible in water), enabling their removal from water. Laurate ions and copper ions likely interact through physical interactions (e.g., electrostatic interactions) rather than chemical bonds, as shown by ATR-FTIR. Inductively coupled plasma-optical emission spectrometry (ICP-OES) demonstrates up to 60% removal of Cu2+ ions from water co-polluted by CuSO4 or CuCl2 and toluene. While lauric acid emulsifies water and toluene in the absence of copper ions, copper salts destabilize emulsions. This is beneficial, to avoid that copper ions are re-entrained in the water phase alongside with toluene, following their migration in the toluene phase. The effect of copper ions on emulsion stability is explained based on the decreased interfacial activity and compressional rigidity of interfacial films, probed using a Langmuir trough. In wastewater treatment, lauric acid (a powder) can be mixed directly in the polluted water. In the context of groundwater remediation, lauric acid can be solubilized in canola oil to enable its injection to treat aquifers co-polluted by organic solvents and Cu2+. In this application, injectable filters obtained by injecting cationic hydroxyethylcellulose (HEC +) would impede the flow of toluene and copper ions partitioned in it, protecting downstream receptors. Co-contaminants can be subsequently extracted upstream of the filters (using pumping wells), to enable their simultaneous removal from aquifers.

New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions

Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.

Soil microbial ecological effect of shale gas oil-based drilling cuttings pyrolysis residue used as soil covering material

The residue derived from oil-based drilling cutting pyrolysis could be used as paving materials. Some petroleum hydrocarbons remain in the residue after pyrolysis and cause severe environmental pollution. In this study, the soil column leaching experiments were carried out under different leaching amounts, and the vertical migration characteristics of petroleum hydrocarbons in soil and the dynamic response mechanism of microorganisms to petroleum hydrocarbons were analyzed. The result showed that the soil pH value and water content with different leaching amounts did not differ significantly, but the vertical migration ability of each petroleum hydrocarbon component was different. In petroleum hydrocarbon contaminated soil, the relative abundance of Proteobacteria maintained a high level (23.6%-60.7%). At the genus level, the relative abundance of Massilia decreased with the leaching amount increased. According to PICRUSt, Monooxygenase [EC: 1.14.13.-] played a significant role in petroleum hydrocarbon degradation. While Long-chain-fatty-acid-CoA ligase [EC: 6.2.1.3] had the highest relative abundance. By studying the influence of shale gas oil-based drilling cuttings pyrolysis residue on soil physical and chemical properties and soil microorganisms, this work provides scientific ecological assessment for the resource application of pyrolysis residue.

Remediation of Pb-diesel fuel co-contaminated soil using nano/bio process: subsequent use of nanoscale zero-valent iron and bioremediation approaches

The effectiveness of the nano/bio process was investigated as a remediation option for co-contaminated soils. Nano/bio process is a hybrid treatment method that may be defined as the use of nanoscale zero-valent iron (nZVI) and bioremediation approaches subsequently/concurrently. Different bioremediation approaches (bioattenuation, biostimulation, and/or bioaugmentation) were performed together with nZVI application to remediate Pb- and diesel fuel-spiked soils. Nutrient (N and P) and activated sludge amendment were made to realize biostimulation and bioaugmentation, respectively. The nZVI application decreased the total percentage of the most mobile and bioavailable soil Pb fractions (exchangeable and carbonate-bound) from 68.3 to 31.7%. The biodegradation levels of nZVI-applied co-contaminated soils were significantly higher than the soils without nZVI indicating the positive effect of the reduced mobility, bioavailability, and toxicity of Pb content. The use of nano/biostimulation or nano/bioaugmentation treatments resulted in higher than 60% total n-alkane degradation, whereas 89.5% degradation was obtained by using nano/biostimulation + bioaugmentation. Hydrocarbon-degrader strains belonging to phyla Actinobacteria, Proteobacteria, or Firmicutes were identified from samples subjected to nano/bio process and the strains from biostimulation and bioaugmentation treatments were different. These results indicate that the stress on the microbial population caused by the co-contamination might be subsided and the biodegradation of alkanes might be improved by using the nano/bio process.

Synergetic effects of microbial-phytoremediation reshape microbial communities and improve degradation of petroleum contaminants

Microbial-phytoremediation is an effective bioremediation technology that introduces petroleum-degrading bacteria and oil-tolerant plants into oil-contaminated soils in order to achieve effective degradation of total petroleum hydrocarbons (TPH). In this work, natural attenuation (NA), microbial remediation (MR, using Acinetobacter sp. Tust-DM21), phytoremediation (PR, using Suaeda glauca), and microbial-phytoremediation (MPR, using both species) were utilized to degrade petroleum hydrocarbons. We evaluated four different biological treatments, assessing TPH degradation rates, soil enzyme activities, and the structure of microbial community in the petroleum-contaminated soil. This finding revealed that the roots of Suaeda glauca adsorbed small amounts of polycyclic aromatic hydrocarbons, causing the structure of soil microbiota community to reshape. The abundance of petroleum-degrading bacteria and plant growth-promoting rhizobacteria (PGPR) has increased, as has microbial diversity. According to correlation research, these genera increased soil enzyme activity, boosted the number of degradation-functional genes in the petroleum hydrocarbon degradation pathway, and accelerated the dissipation and degradation of TPH in petroleum-contaminated soil. This evidence contributes to a better understanding of the mechanisms involved in the combined microbial-phytoremediation strategies for contaminated soil, specifically the interaction between microflora and plants in co-remediation and the effects on the structural reshaping of rhizosphere microbial communities.

Effect of nitrilotriacetic acid and tea saponin on the phytoremediation of Ni by Sudan grass (Sorghum sudanense (Piper) Stapf.) in Ni-pyrene contaminated soil

Phytoremediation is commonly used in the remediation of soils co-contaminated by heavy metals and polycyclic aromatic hydrocarbons (PAHs) because of its economy and effectiveness. Sudan grass (Sorghum sudanense (Piper) Stapf.) has well-developed roots and strong tolerance to heavy metals, so it has been widely concerned. In this study, nitrilotriacetic acid (NTA) and tea saponin (TS) were used as enhancers and combined with Sudan grass for improving the remediation efficiency of Ni-pyrene co-contaminated soil. The results of the pot experiment in soils showed that enhancers promoted the enrichment of Ni in plants. With the function of enhancers, more inorganic and water-soluble Ni were converted into low-toxic phosphate-bonded and residual Ni, so as to reinforce the tolerance of Sudan grass to Ni. In the pot experiment based on vermiculite, it was found that enhancers increased the accumulation of Ni in cell wall by 49.71-102.73%. Enhancers also had the positive effect on the relative abundance of Proteobacteria, Patescibacteria and Bacteroidetes that could tolerate heavy metals at phylum level. Simultaneously, the study found that pyrene reduced the exchangeable Ni in soils. More Ni entered the organelles and transfer to more high-toxic forms in Sudan grass when pynere coexisted. The study manifested that enhancers improved the phytoremediation effect of Ni significantly, yet the co-existence of pyrene weakened the process. Our results provided meaningful references for remediating actual co-contaminated soil of heavy metals and PAHs.

Microbial characteristics of the leachate contaminated soil of an informal landfill site

Because informal landfills are not constructed in a regulated manner, they will inevitably become a source of leachate pollution to the surrounding environment over time. Microbes are an important part of the soil system, playing a vital role in maintaining the normal functionality of soil. This study investigated the microbial composition and co-occurrence pattern in the leachate contaminated soil of an informal landfill site. The landfill leachate underwent horizontal and vertical migration through the contaminated soil, resulting in significant differences in the microbial compositions of horizontal surface soil (CS) and vertical subsurface soil (DS and ES) compared to uncontaminated soil (S). The microbial diversity of CS, DS, and ES was lower than that of S. Due to the migration of landfill leachate, the microbial composition of the surface soil was substantially changed. The dominant phyla in S included Proteobacteria (26.88%), Chloroflexi (23.68%), Actinobacteroita (17.36%), and Acidobacteroita (16.86%), but in contaminated soils, Firmicutes (35.27-86.68%) were the dominant bacteria. A network analysis indicated that Bacilli, Clostridia, and Thermacetogeniazai of the Firmicutes were the keystone taxa and played a vital role in maintaining the stability of the soil ecosystem. A functional annotation of prokaryotic taxa (FAPROTAX) analysis showed that the microbes involved in the C-, N-, and S-cycles in contaminated soil were significantly different to those in uncontaminated soil. The proportion of (aerobic)-chemoheterotrophy and cellulolysis functional communities in contaminated soils was significantly reduced, while there was an increase in functional communities, such as anammox and denitrification, which are not conducive to soil nitrogen fixation. This negatively affected the maintenance of normal soil ecological functions. This study identified the microbial characteristics in leachate contaminated soil and the results will be beneficial for the remediation of contaminated soil in informal landfill sites.

Effects of heavy metals on bacterial community structures in two lead-zinc tailings situated in northwestern China

We evaluated the variations of bacterial communities in six heavy metal contaminated soils sampled from Yanzi Bian (YZB) and Shanping Cun (SPC) tailings located in northwestern China. Statistical analysis showed that both the heavy metals and soil chemical properties could affect the structure and diversity of the bacterial communities in the tailing soils. Cd, Cu, Zn, Cr, Pb, pH, SOM (soil organic matters), TP (total phosphorus) and TN (total nitrogen) were the main driving factors of the bacterial community variations. As a consequence, the relative abundances of certain bacterial phyla including Proteobacteria, Chloroflexi, Firmicutes, Nitrospirota and Bacteroidota were significantly increased in the tailing soils. Further, we found that the abundance increasement of these phyla were mainly contributed by certain species, such as s__unclassified_g__Thiobacillus (Proteobacteria), s__unclassified_g__Sulfobacillus (Firmicutes) and Leptospirillum ferriphilum (Nitrospirota). Thus, these species were considered to be strongly heavy metal tolerant. Together, our findings will provide a useful insight for further bioremediations of these contaminated areas.

Microbial community structure and metabolome profiling characteristics of soil contaminated by TNT, RDX, and HMX

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.

Recovery of impregnated hydrocarbon in drill cuttings using supercritical carbon dioxide

Pollution due to waste generated by the oil industry has led to serious damage to ecosystems and the environment. Therefore, preventive and corrective actions must be taken to mitigate the ecological impact of waste resulting from oil-related activities, to explore and implement environment-friendly approaches, and achieve sustainable development. In this study, an alternative treatment for cuttings generated during the drilling of oil wells was investigated by extracting the hydrocarbons present in such cuttings through the use of carbon dioxide under supercritical conditions. The extractions were performed in a Supercritical Fluid Technologies Inc. Model SFT-150 extractor, under varying pressure (2300-6600 psi) and temperature (52-109 °C), while maintaining constant carbon dioxide flow rate and extraction time, to analyse the effect of these two thermodynamic variables on the extraction efficiency. During supercritical extraction, 21.51 g of total hydrocarbons from drill cuttings (oil/kg) were recovered at 6000 psi and 100 °C. The results indicated that pressure had the strongest effect on the extraction yield, with only a small amount of hydrocarbons recovered at the lowest pressure for all fractions. At <3000 psi pressure, increasing the temperature led to a decrease in the amount of recovered hydrocarbons; at >3000 psi pressure, increasing the temperature led to an increase in the extraction yield.

How the Soil Microbial Communities and Activities Respond to Long-Term Heavy Metal Contamination in Electroplating Contaminated Site

The effects of long-term heavy metal contamination on the soil biological processes and soil microbial communities were investigated in a typical electroplating site in Zhangjiakou, China. It was found that the soil of the electroplating plant at Zhangjiakou were heavily polluted by Cr, Cr (VI), Ni, Cu, and Zn, with concentrations ranged from 112.8 to 9727.2, 0 to 1083.3, 15.6 to 58.4, 10.8 to 510.0 and 69.6 to 631.6 mg/kg, respectively. Soil urease and phosphatase activities were significantly inhibited by the heavy metal contamination, while the microbial biomass carbon content and the bacterial community richness were much lower compared to noncontaminated samples, suggesting that the long-term heavy metal contamination had a severe negative effect on soil microorganisms. Differently, soil dehydrogenase was promoted in the presence of Chromate compared to noncontaminated samples. This might be due to the enrichment of Sphingomonadaceae, which have been proven to be able to secrete dehydrogenase. The high-throughput sequencing of the 16S rRNA gene documented that Proteobacteria, Actinobacteria, and Chloroflexi were the dominant bacterial phyla in the contaminated soil. The Spearman correlation analysis showed the Methylobacillus, Muribaculaceae, and Sphingomonadaceae were able to tolerate high concentrations of Cr, Cr (VI), Cu, and Zn, indicating their potential in soil remediation.