High PAH degradation and activity of degrading bacteria during alfalfa growth where a contrasted active community developed in comparison to unplanted soil

Polycyclic aromatic hydrocarbons in coastal rivers in Jiangsu Province, China: Spatial distribution, source apportionment and human impacts

The ocean is the ultimate sink for all pollutants, rivers are important channels for land-based pollutants to enter the oceans. Riverine transport of polycyclic aromatic hydrocarbons (PAHs) to coastal seas in China poses environmental threats. This study examined the spatial and temporal distribution of PAHs in coastal rivers in Yancheng City in Jiangsu Province of China, with the aim of identifying their likely sources, concentrations, and influencing factors. Surface sediments were taken from the Xinyanggang River (XYR) and the Sheyang River (SYR). The concentrations of Ʃ16PAHs in river sediments were measured on average 477.05 ng/g dry weight (dw), with values varying from 2.18 to 6351.42 ng/g, indicating a moderate pollution level, with a dominance of high molecular weight (HMW) PAHs. The XYR exhibited significantly higher PAHs concentrations compared to the SYR. The key sources of PAHs were vehicle emissions (47.87%), coal and natural gas combustion (35.07%). Geographically weighted regression and redundancy analysis linked PAHs pollution to distinct land use patterns and socioeconomic indicators, highlighting urban land as the major contributor, driven by high urbanization and industrialization (70.91%). In XYR, industrial activities and transport emissions were major contributors, while in SYR, agricultural activities predominantly influenced PAHs pollution. Urgent mitigation strategies are needed to reduce PAHs pollution in river sediments, mitigating ecological and human risks associated with these contaminants.

Biochars assisted phytoremediation of polycyclic aromatic hydrocarbons contaminated agricultural soil: Dynamic responses of functional genes and microbial community

A biochar-intensified phytoremediation experiment was designed to investigate the dynamic effects of different biochars on polycyclic aromatic hydrocarbon (PAH) removal in ryegrass rhizosphere contaminated soil. Maize and wheat straw biochar pyrolyzed at 300 °C and 500 °C were amended into PAH-contaminated soil, and then ryegrass (Lolium multiflorum L.) was planted for 90 days. Spearman's correlations among PAH removal, enzyme activity, abundance of PAH-ring hydroxylating dioxygenase (PAH-RHDα), and fungal and bacterial community structure were analyzed to elucidate the microbial degradation mechanisms during the combined remediation process. The results showed that 500 °C wheat straw biochar had higher surface area and more nutrients, and significantly accelerated the phytoremediation of PAHs (62.5 %), especially for high molecular weight PAH in contaminated soil. The activities of urease and dehydrogenase and the abundance of total and PAH-degrading bacteria, which improved with time by biochar and ryegrass, had a positive correlation with the removal rate of PAHs. Biochar enhanced the abundance of gram-negative (GN) PAH-RHDα genes. The GN PAH-degraders, Sphingomonas, bacteriap25, Haliangium, and Dongia may play vital roles in PAH degradation in biochar-amended rhizosphere soils. Principal coordinate analysis indicated that biochar led to significant differences in fungal community structures before 30 days, while the diversity of the bacterial community composition depended on planting ryegrass after 60 days. These findings imply that the structural reshaping of microbial communities results from incubation time and the selection of biochar and ryegrass in PAH-contaminated soils. Applying 500 °C wheat straw biochar could enhance the rhizoremediation of PAH-contaminated soil and benefit the soil microbial ecology.

Polycyclic Aromatic Hydrocarbons in Topsoils Along the Taipu River Banks in the Yangtze River Delta, China: Occurrence, Source and Risk Assessment

Taipu River is an important transboundary river and drinking water source in the Yangtze River Delta, China. This study collected 15 topsoil samples along the Taipu River banks and subsequently determined the polycyclic aromatic hydrocarbons (PAHs) concentrations, sources, and ecological and health risks. The sum of toxic 15 PAHs concentrations ranged from 83.13 to 28342.53 ng/g, with a mean of 2828.69 ng/g. High molecular weight (HMW) PAHs were the dominant components and Indene (1,2,3, -cd) benzopyrene (InP) accounted for the highest proportion in individuals. The average PAH concentration in residential land was the highest, followed by those in industrial and agricultural land. The PAH concentration was positively related to contents of total carbon, total nitrogen, ammonium nitrogen, and aminopeptidase activity in soils. The mixed combustion of biomass, coal, and petroleum and traffic emissions could be the primary PAH contributors. The total PAHs at over half of sampling points had relatively high risk quotients and incremental lifetime cancer risk (ILCR) values, posing potential or great ecological threats and health risks.

Effect of plant root exudate constituents on the degradation of phenanthrene by rhizobacterium Mycolicibacterium gilvum (Mycobacteriaceae, Actinobacteria)

The influence of the major components of plant root exudates, namely, carboxylic acids (succinic acid as an example) and secondary plant phenolic metabolites – flavonoids (rutin as an example), on the microbial degradation of the three-ring polycyclic aromatic hydrocarbon (PAH) phenanthrene by rhizobacterium Mycolicibacterium gilvum was studied. The destructive activity of this microorganism relative to PAH was studied by cultivating it in a liquid mineral medium containing phenanthrene (0.2 g/L), succinic acid (5 g/L), and rutin (0, 0.05, 0.1 or 0.2 mmol/L) at 30°C under aeration on a shaker (130 rpm) for 14 days. The stimulating effect of succinic acid and rutin on the microbial degradation of phenanthrene was revealed. It was found that carboxylate was utilized as the main growth substrate for the microorganism, while flavonol and PAH had little effect on bacterial growth. Rutin had no antimicrobial effect on the microorganisms studied; on the contrary, in combination with succinic acid, it significantly increased the biomass growth. At high concentrations (0.1 and 0.2 mmol/L), rutin inhibited the degradation of phenanthrene by 22 and 56%, respectively. However, at a concentration of 0.05 mmol/L rutin increased phenanthrene degradation by 10%. Thus, the results obtained showed the dependence of the PAH microbial degradation efficiency on the presence, combination, and concentration of the plant root exudate constituents.

Assessment for combined phytoremediation and biomass production on a moderately contaminated soil

Once previous industrial activity has ceased, brownfields are found in urban and suburban environments and managed in different ways ranging from being left untouched to total reconversion. These situations apply to large surface areas often impacted by residual diffuse pollution. Though significant and preventing any sensitive use, residual contamination does not necessarily require treatment. Moreover, conventional treatments show their technical and economic limits in these situations and gentle remediation options such as phytomanagement might appear more relevant to the management of those sites. Thus, these sites face up two major issues: managing moderate contamination levels and providing an alternative use of economic interest. This work proposes to assess a management strategy associating the phytoremediation of organic pollution along with the production of biomass for energy generation production. A 16-week controlled growth experiment was conducted on a soil substrate moderately impacted by multiple pollution (trace elements, mainly Zn and Pb, and hydrocarbons), by associating rhizodegradation with Medicago sativa or biomass production with Robinia pseudoacacia or Alnus incana in monocultures. The effect of a microbial inoculum amendment on the performances of these treatments was also evaluated. Results showed total hydrocarbons (TH), and to a lesser extent polycyclic aromatic hydrocarbons (PAH), concentrations decreased over time, whatever the plant cover. Good biomass production yields were achieved for both tree species in comparison with the control sample, even though R. pseudoacacia seemed to perform better. Furthermore, the quality of the biomass produced was in conformity with the thresholds set by the legislation concerning its use as a renewable energy source.

Variation in Bacterial Community Structures and Functions as Indicators of Response to the Restoration of Suaeda salsa: A Case Study of the Restoration in the Beidaihe Coastal Wetland

Microbes play an essential role in the restoration of degraded coastal wetlands. However, few studies have focused on the role of key bacteria in the restoration process. Here, Suaeda salsa was planted to recover the biodiversity in the degraded Beidaihe coastal wetland. We monitored omics and soil environmental factors to understand the complex relationship between the bacterial community and wetland health during the restoration period. After planting S. salsa in the degraded area, the soil quality was improved in the later stage of restoration (LPR). Bacterial α-diversity increased with restoration and was positively correlated with TOC. Proteobacteria is the dominant bacterial phylum during the restoration period, and Bacteroidetes, Planctomycetes, Gemmatimonadetes, and Acidobacteria were sensitive to the planting restoration. Random forest analysis picked 30 key OTUs, showing the key bacterial variation of successful restoration. The result indicated that the sum of the relative abundances of key bacterial OTUs was more than 2% in the health wetland. The β-diversity showed that the growth of S. salsa reshaped the soil bacterial community structure and function in the LPR, which recovered to the level in the control area. Putative biogeochemical functions showed that symbionts and aromatic compound degradation were dominant bacterial functions in the growth period of S. salsa. Our study proposed a new indicator to assess wetland health and the planting restoration of S. salsa increased bacteria groups with the ability of symbionts and aromatic compound degradation in the Beidaihe coastal wetland. This study expanded our knowledge of coastal wetland restoration and its ecological contributions.

Potential ability of tobacco (Nicotiana tabacum L.) to phytomanage an urban brownfield soil

The ability of tobacco (Nicotiana tabacum L. cv. Badischer Geudertheimer) for phytomanaging and remediating soil ecological functions at a contaminated site was assessed with a potted soil series made by fading an uncontaminated sandy soil with a contaminated sandy soil from the Borifer brownfield site, Bordeaux, SW France, at the 0%, 25%, 50%, 75%, and 100% addition rates. Activities of sandblasting and painting with metal-based paints occurred for decades at this urban brownfield, polluting the soil with metal(loid)s and organic contaminants, e.g., polycyclic aromatic hydrocarbons, in addition to past backfilling. Total topsoil metal(loid)s (e.g., 54,700 mg Zn and 5060 mg Cu kg-1) exceeded by seven- to tenfold the background values for French sandy soils, but the soil pH was 7.9, and overall, the 1M NH4NO3 extractable soil fractions of metals were relatively low. Leaf area, water content of shoots, and total chlorophyll (Chl) progressively decreased with the soil contamination, but the Chl fluorescence remained constant near its optimum value. Foliar Cu and Zn concentrations varied from 17.8 ± 4.2 (0%) to 27 ± 5 mg Cu kg-1 (100%) and from 60 ± 15 (0%) to 454 ± 53 mg Zn kg-1 (100%), respectively. Foliar Cd concentration peaked up to 1.74 ± 0.09 mg Cd kg-1, and its bioconcentration factor had the highest value (0.2) among those of the metal(loid)s. Few nutrient concentrations in the aboveground plant parts decreased with the soil contamination, e.g., foliar P concentration from 5972 ± 1026 (0%) to 2861 ± 334 mg kg-1 (100%). Vulnerability to drought-induced embolism (P50) did not differ for the tobacco stems across the soil series, whereas their hydraulic efficiency (Ks) declined significantly with increasing soil contamination. Overall, this tobacco cultivar grew relatively well even in the Borifer soil (100%), keeping its photosynthetic system healthy under stress, and contaminant exposure did not increase the vulnerability of the vascular system to drought. This tobacco had a relevant potential to annually phytoextract a part of the bioavailable soil Zn and Cd, i.e., shoot removals representing here 8.8% for Zn and 43.3% for Cd of their 1M NH4NO3 extractable amount in the potted Borifer soil.

The effect of combined pollution by PAHs and heavy metals on the topsoil microbial communities of Spolic Technosols of the lake Atamanskoe, Southern Russia

The contamination with organic and inorganic pollutants changes significantly soil microbial community structure. These shifts indicate anthropogenic pressure and help to discover new possibilities for soil remediation. In this study, the microbial community structure of Spolic Technosols formed at the territory of a former industrial sludge reservoir near the Kamensk-Shakhtinsky (Southern Russia) was studied using a metagenomics approach. The studied soils contain high concentrations of heavy metals (HM) (up to 72,900 mg kg^-1) and 16 priority polycyclic aromatic hydrocarbons (PAHs) (up to 6670 mg kg^-1). Its microbial communities demonstrate an excellent adaptability level reflected in their complexity and diversity. As shown by the high values of alpha diversity indices (Shannon values up to 10.1, Chao1 values from 1430 to 4273), instead of decreasing quantitatively and qualitatively on the systemic level, microbial communities tend to undergo complex redistribution. Regardless of contamination level, the share of Actinobacteria and Proteobacteria was consistently high and varied from 20 to 50%. Following the results of the Mann-Whitney U test, there were significant changes of less abundant phyla. The abundance of oligotrophic bacteria from Gemmatimonadetes and Verrucomicrobia phyla and autotrophic bacteria (e.g., Nitrospira) decreased due to the high PAH's level. And abundance of Firmicutes and amoebae-associated bacteria such as TM6 and soil Chlamydia increased in highly contaminated plots. In the Spolic Technosols studied, the influence of factors on the microbial community composition decreased from PAHs concentration to soil characteristics (organic carbon content) and phylum-phylum interactions. The high concentrations of HMs influenced weakly on the microbial community composition.

In situ and ex situ bioassays with Cantareus aspersus for environmental risk assessment of metal(loid) and PAH-contaminated soils

Environmental risk assessment of contaminated soils requires bioindicators that allow the assessment of bioavailability and toxicity of chemicals. Although many bioassays can determine the ecotoxicity of soil samples in the laboratory, few are available and standardized for on-site application. Bioassays based on specific threshold values that assess the in situ and ex situ bioavailability and risk of metal(loid)s and polycyclic aromatic hydrocarbons (PAHs) in soils to the land snail Cantareus aspersus have never been simultaneously applied to the same soils. The aims of this study were to compare the results provided by in situ and ex situ bioassays and to determine their respective importance for environmental risk assessment. The feasibility and reproducibility of the in situ bioassay were assessed using an international ring test. This study used five plots located at a former industrial site and six laboratories participated in the ring test. The results revealed the impact of environmental parameters on the bioavailability of metal(loid)s and PAHs to snails exposed in the field to structured soils and vegetation compared to those exposed under laboratory conditions to soil collected from the same field site (excavated soils). The risk coefficients were generally higher ex situ than in situ, with some exceptions (mainly due to Cd and Mo), which might be explained by the in situ contribution of plants and humus layer as sources of exposure of snails to contaminants and by climatic parameters. The ring test showed good agreement among laboratories, which determined the same levels of risk in most of the plots. Comparison of the bioavailability to land snails and the subsequent risk estimated in situ or ex situ highlighted the complementarity between both approaches in the environmental risk assessment of contaminated soils, namely, to guide decisions on the fate and future use of the sites (e.g., excavation, embankments, and land restoration). Integr Environ Assess Manag 2022;18:539-554. © 2021 SETAC.

Mycolicibacterium sp. strain PAM1, an alfalfa rhizosphere dweller, catabolizes PAHs and promotes partner-plant growth

This research was focused on the isolation and characterization of a PAH-catabolizing mycobacterial strain from the petroleum hydrocarbon-contaminated rhizosphere of alfalfa, as well as on revealing some points of interaction between the microorganism and the plant. Mycolicibacterium sp. PAM1, a pyrene degrader isolated from the niche of interest to us, can catabolize fluoranthene, anthracene, fluorene, and phenanthrene. On the basis of curves of PAM1 growth with different PAHs as the sole carbon sources and on the basis of PAH-degradation rates, we found that pollutant availability to the strain decreased in the sequence phenanthrene > fluorene > fluoranthene ∼ pyrene > anthracene. For each PAH, the catabolic products were identified. PAM1 was found to have the functional genes nidA and nidB. New data modeling the 2D and 3D structures, intrinsic structural disorder, and molecular dynamics of the nidA and nidB gene products were obtained. The identified genes and intermediates of pyrene degradation indicate that PAM1 has a PAH catabolic pathway that is peculiar to known mycobacterial pyrene degraders. PAM1 utilized some components of alfalfa root exudates as nutrients and promoted plant growth. The use of mycobacterial partners of alfalfa is attractive for enhancing the phytoremediation of PAH-contaminated soils.

Field study on the soil bacterial associations to combined contamination with heavy metals and organic contaminants

The understanding of soil microbial associations to combined contamination would substantially benefit the restoration of damaged ecosystems, which is currently limited at the field scale. In this study, we investigated the soil bacterial associations to combined contamination with metals (Cd, Cu, Hg, Pb, and Zn), polyaromatic hydrocarbons (PAHs), and polybrominated diphenyl ethers (PBDEs). Samples were collected from field sites under five land-use patterns with electronic waste recycling. Results showed that the contents of Cd (0.22-12.86 mg/kg), Cu (17-14,136 mg/kg), Pb (4.6-77,014 mg/kg), Hg (0.28-22 mg/kg), Zn (26-42,495 mg/kg), PAHs (4.6-1753 μg/kg), and PBDEs (1.9-1079 μg/kg) varied significantly across sites. We observed positive correlations between catalase activity and heavy metals, indicative of a resistance response to the oxidative stress induced by metals. Furthermore, the bacterial community diversity was found to be determined primarily by PBDEs, whereas acenaphthylene, available phosphorus, and 2,2',3,3',4,5,6-heptabrominated diphenyl ether (BDE-183) were the three major drivers affecting community composition. The co-occurrence network constructed for bacterial communities exposed to combined contamination was non-random with scale-free, small-world and modularity features. We further proposed functional roles of the modules including stress resistance, hydrocarbon degradation, and nutrient cycling. Overall, the findings of redundancy analysis, variation partition analysis and the co-occurrence network indicated that soil bacterial community under combined contamination cooperated to survive. Members including Rhodoplanes and Nitrospira were capable of degrading PAHs and PBDEs in various pathways, while others, including Acinetobacter, Citrobacter, and Pseudomonas, reduced the metal toxicity to the community. Our findings provide new insights into the responses of soil bacteria, particularly in terms of inter-specific relationships, under combined contamination at the field scale.

DNA-based stable isotope probing identifies triclosan degraders in nitrification systems under different surfactants

Three widely-used surfactants, rhamnolipid (RL), sophorolipid (SL) and sodium dodecyl benzene sulfonate (SDBS), were chosen to investigate their effects on the nitrification systems treating step-wised triclosan (TCS). Surfactants had little effects on nitrification. Surfactants could promote the desorption of TCS and enhance the TCS biodegradation in nitrification systems. And TCS biodegradation efficiencies obtained with RL, SL and SDBS were 1.25, 1.23 and 1.14 times higher than the control with 9.0 mg/L TCS, respectively. Illumina MiSeq sequencing showed that Amaricoccus could be resistant to TCS. And Amaricoccus, detected with RL, SL and SDBS, were more abundant than the control. DNA-based stable isotope probing assays revealed Amaricoccus was the major TCS degrader. And the addition of surfactants could obviously increase the diversity of active TCS degraders, especially for biosurfactants. It seems that the addition of surfactants showed positive effects for the nitrification systems treating TCS wastewater.

Single-step transfer of biosynthetic operons endows a non-magnetotactic Magnetospirillum strain from wetland with magnetosome biosynthesis

The magnetotactic lifestyle represents one of the most complex traits found in many bacteria from aquatic environments and depends on magnetic organelles, the magnetosomes. Genetic transfer of magnetosome biosynthesis operons to a non-magnetotactic bacterium has only been reported once so far, but it is unclear whether this may also occur in other recipients. Besides magnetotactic species from freshwater, the genus Magnetospirillum of the Alphaproteobacteria also comprises a number of strains lacking magnetosomes, which are abundant in diverse microbial communities. Their close phylogenetic interrelationships raise the question whether the non-magnetotactic magnetospirilla may have the potential to (re)gain a magnetotactic lifestyle upon acquisition of magnetosome gene clusters. Here, we studied the transfer of magnetosome gene operons into several non-magnetotactic environmental magnetospirilla. Single-step transfer of a compact vector harbouring >30 major magnetosome genes from M. gryphiswaldense induced magnetosome biosynthesis in a Magnetospirillum strain from a constructed wetland. However, the resulting magnetic cellular alignment was insufficient for efficient magnetotaxis under conditions mimicking the weak geomagnetic field. Our work provides insights into possible evolutionary scenarios and potential limitations for the dissemination of magnetotaxis by horizontal gene transfer and expands the range of foreign recipients that can be genetically magnetized.

Comparison of PAH content, potential risk in vegetation, and bare soil near Daqing oil well and evaluating the effects of soil properties on PAHs

As the largest oil field in China, Daqing oil field has been developed in the past six decades. The objectives of this study were to measure the levels of polycyclic aromatic hydrocarbons (PAHs) and assess their ecological risk of PAHs in vegetation soil and bare soil near oil well in Daqing and surrounding soil. Ten sites were selected from two types of soil in grassland: vegetation soil (VS, n = 5) and bare soil (BS, n = 5). The mean concentration of 16 PAHs (∑₁₆ PAHs) was 2240.2 μg/kg. The mean concentrations of eight carcinogenic PAHs (∑_8c PAHs) was 1312.3 μg/kg which accounts for 59% of ∑₁₆ PAHs. The sampling sites had higher proportions of high weight molecular ringed PAHs with higher proportions of benzo (a) pyren (BaP) and benzo (k) fluoranthene (BkF). The main source of PAHs was petroleum, coal/biomass combustion, and vehicular emission in these sampling sites. According to Canadian soil quality guidelines, 60% sites had a significant risk to human health. Moreover, 50% sites had high ecological risk and 30% sites were close to this critical value. Notably, PAH levels were significantly higher in VS than BS; moreover, VS had higher organic matter (OM) content, soil dehydrogenase (sDHA) activity, and lower pH and salt content. A structural equation model was established to explore the effects of soil properties on PAH concentration in VS. The result revealed that OM and sDHA were meaningful to enhance the adsorption and biological fixation of PAHs. This study will provide basic information on PAH level and potential application for phytoremediation.

Changes in endophytic bacterial communities during different growth stages of cucumber (Cucumis sativus L.)

Endophytic bacterial diversity in plants presents the level of interaction between culturable and non-culturable endophytic bacteria, thereby providing an appropriate insight into the endophytic environment. This study was conducted to determine the trend of culturable and non-culturable endophytic bacteria at two different sites encompassing four consecutive growth stages. For culturable endophytic bacteria, isolation was carried out using the dilution plate technique, and the obtained colonies were compared using PCR-restriction fragment length polymorphism (RFLP). Different RFLP-types were identified to their nearest neighbour using 16S rRNA sequencing. The non-culturable endophytic bacterial diversity was obtained by next generation sequencing. Results suggested a similar trend among the culturable and non-culturable bacteria for observed operational taxonomic units and diversity indices. It is noticeable that the endophytic bacteria inhabiting in stage 1 disappeared, and instead, different endophytic bacteria appeared. Moreover, the temporal persistence of certain culturable and non-culturable bacteria was also observed. In conclusion, the endophytic bacterial diversity in cucumber initially increased with the plant growth and then decreased at a later stage. Furthermore, it was suggested that plants regulate the number and diversity of endophytes throughout the lifecycle of plants.

Effect of plants and their root exudate on bacterial activities during rhizobacterium-plant remediation of phenol from water

We investigated remediation of phenol from water using microbe-plant partnerships. Co-introduction of maize seedlings, Pseudomonas fluorescens rifampicin-resistant P13 and P. stutzeri P7 carrying self-transmissible TOL-like plasmids reduced phenol content in water at lower phenol concentrations (25, 50, and 75 mg/L), similar to individual introduction of the bacteria. Co-introduction of plants and bacteria significantly reduced phenol content in water at higher phenol concentrations (100, 125, and 150 mg/L) compared to using individual introduction of the bacteria. Moreover, TOL-like plasmids were transferred from P7 to P13. Addition of plants promoted the growth of both strains, leading to increased plasmid transfer. At higher phenol concentrations, addition of plants resulted in increases of catechol 2, 3-dioxygenase (C23O) activity and reduction in level of reactive oxygen species (ROS) of bacteria in the degradation experiments. Increased plasmid transfer and C23O activity and reduction in ROS level might be the major reasons why plants promote bacterial degradation of phenol at higher phenol concentrations. Furthermore, root exudate of maize seedlings and artificial root exudate (ARE) constructed using major components of the root exudate had the same effects on bacterial activities. Unlike the ARE, deletion of glucose, arabinose, or fructose or all the monosaccharides from ARE resulted in no increase in numbers of both strains and in plasmid transfer. At the higher phenol concentrations, deletion of glutamic acid, aspartic acid, alanine, or glycine or all the amino acids did not stimulate bacterial C23O activity. Deletion of fumaric, oxaloacetic or citric acids still reduced bacterial ROS level as ARE did, but, deletion of all the organic acids or DIMBOA, a hydroxamic acid, did not reduce bacterial ROS level as ARE did. The data showed that each monosaccharide might be important for sufficient numbers of plant-associated bacteria and increased plasmid transfer while each amino acid might be important for maintaining bacterial C23O activity and that DIMBOA might be responsible for the decrease in ROS levels. These results are the basis for efficient remediation of phenol from water by microbe-plant partnerships and further studies on the mechanism of rhizobacterium-plant interaction.