Diversity and distribution of 16S rRNA and phenol monooxygenase genes in the rhizosphere and endophytic bacteria isolated from PAH-contaminated sites

The Changes of the Endophytic Bacterial Community from Pepper Varieties with Different Capsaicinoids

Capsaicinoids, the key compounds responsible for pepper pungency, have significant commercial and health value, yet the role of endophytic bacteria in their biosynthesis remains unclear. This study investigated the relationship between endophytic bacterial communities and capsaicinoid content across 100 Capsicum annuum varieties. Two high-capsaicinoid (35.0 and 24.8 mg/g) and two low-capsaicinoid (0.8 and 0.9 mg/g) varieties were selected for 16S rRNA sequencing and microbial analysis. High-capsaicinoid varieties exhibited greater bacterial richness and diversity compared to low-capsaicinoid varieties. Taxonomic profiling revealed distinct community compositions: Enterobacter, Bacteroides, and Escherichia_Shigella were enriched in high-capsaicinoid fruits and positively correlated with capsaicinoid levels, while Chujaibacter and Brochothrix dominated the low-capsaicinoid varieties. Functional annotation highlighted nitrogen-fixing bacteria as more abundant in high-capsaicinoid varieties. Inoculating peppers with isolated Enterobacter strains significantly increased capsaicinoid content, confirming its role in biosynthesis. These findings demonstrate that the pepper genotype shapes endophytic bacterial communities, which in turn influence capsaicinoid production through metabolic- and nitrogen-associated pathways. This study provides foundational insights into microbiome-mediated enhancement of pepper pungency, offering potential strategies for agricultural and industrial applications.

Potential mechanisms of synthetic endophytic bacterial community to reduce PAHs accumulation in vegetables

The functional endophytic bacterial community can effectively degrade polycyclic aromatic hydrocarbons (PAHs), thereby reducing their accumulation in vegetables grown on contaminated sites. However, the biological mechanisms underlying this reduction remain unclear. In this study, we analyzed the efficacy of different colonization methods of the functional endophytic bacterial community m5 in reducing PAHs in vegetables, with a particular focus on the leaf painting method. The results demonstrated that various colonization methods effectively reduced PAHs in vegetables, with leaf painting proving to be a cost-effective and efficient approach. Compared to the non-inoculated control, PAH content in the edible parts of amaranth was reduced by 40.63 % using the leaf painting method. High-throughput sequencing and quantitative PCR revealed that leaf painting altered the bacterial community structure and key components of the bacterial network, enhancing bacterial cooperation. After 20 days of colonization, the abundance of phe and nidA genes in vegetables increased significantly, by tens to hundreds of times, compared to uninoculated controls, thereby promoting the degradation of PAHs in vegetables. This study enhances our understanding of the biological mechanisms by which endophytic bacterial communities reduce PAHs in vegetables.

Radial Oxygen Loss from the Roots of Mangrove Seedlings Enhances the Removal of Polycyclic Aromatic Hydrocarbons

The presence of polycyclic aromatic hydrocarbons (PAHs) in soil poses a significant global environmental concern, particularly in coastal wetlands. Mangrove ecosystems exhibit enormous potential in environmental purification; however, the underlying mechanisms involved in the degradation of pollutants (e.g., PAHs) remain ambiguous. In the present investigation, a soil pot experiment was conducted with the addition of pyrene to evaluate the effect of radial oxygen loss (ROL) from roots on PAH degradation using three mangrove seedlings (Rhizophora stylosa, Aegiceras corniculatum, and Avicennia marina). The results showed that mangrove plantation can significantly promote the efficiency of pyrene removal. As for the three mangrove species studied, the greatest removal rate (90.75%) was observed in the soils associated with A. marina, followed by A. corniculatum (83.83%) and R. stylosa (77.15%). The higher PAH removal efficiency of A. marina can be partially attributed to its distinctive root anatomical structure, characterized by a thin exodermis and high porosity, which facilitates ROL from the roots. The results from qPCR further demonstrate that ROL is beneficial for promoting the abundance of PAH-ring hydroxylating dioxygenase gene, leading to a higher removal efficiency. Additionally, Rhizobiales, Defferrisomatales, and Ardenticatenales may also play important roles in the process of pyrene degradation. In summary, this study provides evidence for elucidating the mechanism of PAH removal from the perspective of ROL, thereby contributing valuable insights for species selection during mangrove restoration and remediation.

Variations of different PAH fractions and bacterial communities during the biological self-purification in the soil vertical profile

Wild PAH-contaminated sites struggle to provide continuous and stable monitoring, resulting in the potential risks of contaminated soil utilization could not be evaluated effectively. This work provided a 9-months laboratory simulation which was close to the natural ecological process. These results believed that PAH-degrading bacteria (PDB) preferred to degrade organic extracted PAH (PAH_OS) and fresh bound-PAH (79.36-99.97%). The formation and migration efficiency of PAH binding with HA humic acid (HA) (PAH_HA) was lower than that of PAH binding with fulvic acid (FA) and humin (HM) (PAH_FA and PAH_HM), leading to PAH_HA had more persistent retention and influenced bacterial communities in shallow soils. Besides, phylum Proteobacteria gradually dominated the bacterial community and decreased 12.05-20.48% diversity at all depths during the biological self-purification process. Although the effect of this process enhanced the abundance of 28 genes 16 s rRNA and three PAH-degrading genes (PDGs) by 5.91-2047.34 times (phe, nahAc and nidA), the top 30 genera maintained their ecological characteristics. This study provided insights into the important influencing factor and mechanism of the biological self-purification processes and discerned the linkages between bacterial communities and environmental variables in the vertical profile, which is important to the isolation and application of PDB and ecological risk assessment.

Assessment of bioremediation potential of petroleum-contaminated soils from the shanbei oilfield of China revealed by qPCR and high throughput sequencing

With the crude oil exploration activities in the Shanbei oilfield of China, the risk of soil contamination with crude oil spills has become a major concern. This study aimed at assessing the bioremediation potential of the petroleum polluted soils by investigating the expression of key functional genes decoding alkane and aromatic component degradation using an array of primers and real-time quantitative PCR (qPCR), and the functional microbiomes were determined using a combination of substrate-induced metabolic responses and high throughput sequencing. The results showed that the species that were more inclined to degrade aliphatic fraction of crude oil included Acinetobacter, Stenotrophomonas, Neorhizobium and Olivebacter. And Pseudomonas genus was a highly specific keystone species with the potential to degrade PAH fraction. Both aliphatic and PAH-degrading genes were upregulated when the soil petroleum contents were less than 10,000 mg/kg but downregulated when the oil contents were over 10,000 mg/kg. Bioremediation potential could be feasible for medium pollution with petroleum contents of less than 10,000 mg/kg. Optimization of the niche of Acinetobacter, Stenotrophomonas, Pseudomonas, Neorhizobium and Olivebacter species was beneficial to the biodegradation of refractory hydrocarbon components in the Shanbei plateau oilfield.

Root-Associated Endophytic Bacterial Community Composition of Asparagus officinalis of Three Different Varieties

Asparagus (Asparagus officinalis L) is an economically important crop, rich in nutrients, and is also conducive to solving ecological and environmental problems. Plants may acquire benefits from root-associated endophytic bacteria. However, the composition of the endophytic bacterial community associated with the roots of asparagus is poorly elucidated. In this study, the nine root samples of asparagus from three different varieties including Asparagus officinalis var. Grande (GLD), A. officinalis var. Jinglvlu3 (JL3) and A. officinalis var. Jingzilu2 (JZL) were investigated by high-throughput sequencing technology of the 16S rDNA V5-V7 hypervariable region of endophytic bacteria. A total of 16 phyla, 29 classes, 90 orders, 171 families, and 312 genera were identified. Endophytic bacteria diversity and bacteria structure was different among the three varieties and was influenced by rhizosphere soil properties and varieties. In the GLD variety, the main phyla were Proteobacteria, Actinobacteria, and Firmicutes. The main phylum in JL3 and JZL varieties was Proteobacteria. The observations showed that GLD had the highest diversity of endophytes as indicated by the Shannon index (GLD > JZL > JL3). The order of the endophytes richness was GLD > JL3 > JZL. The PCA and PCoA analysis revealed the microbial communities were different between three different asparagus varieties, and the microbial composition of GLD and JZL was more similar. This report provides an important reference for the study of endophytic microorganisms of asparagus.

Supplementary information

The online version contains supplementary material available at (10.1007/s12088-021-00926-6) contains supplementary material, which is available to authorized users.

Rhizosphere effect on removal and bioavailability of PAHs in contaminated agricultural soil

The rhizosphere effect of ryegrass (Lolium perenne L.) on polycyclic aromatic hydrocarbons (PAHs) dissipation, bioavailability and the structure change of microbial community was investigated using a compartmented device-rhizobox. The PAHs removal efficiency, bioavailability and the change in structure of the microbial community were ascertained using HPLC, Tenax-TA extraction and PCR-DGGE, respectively. The results showed that in the root area (R1) and bulk soil (CK), the removal of 3-ring PAHs were 97.72 ± 0.34% and 95.51 ± 0.75%, 4-ring PAHs were 89.01 ± 1.61% and 78.65 ± 0.47%, 5-ring PAHs were 77.64 ± 4.05% and 48.63 ± 3.19%, 6-ring PAHs were 68.69 ± 3.68% and 36.09 ± 1.78%, respectively. The average removal efficiency of the total PAHs after 80 days followed the order: R1M (91.1%) > CKM (84.9%) > CK (77.6%), indicating that planted soil with inoculation of Mycobacterium sp. as well as non-planted soil inoculated with Mycobacterium sp. could both significantly accelerate the removal of PAHs compared to control soil. The bioavailability ratio of PAHs with 3 and 4 rings tended to decrease (from 59.9% to 14.8% for 3-ring and 7.61% to 5.08% for 4-ring, respectively in R1) while those with 5 rings increased significantly (from 2.41% to 33.78% in R1) during the last 40 days, indicating that bioavailability alteration varies with the number of rings in the PAHs. In addition, PAH bioavailability generally did not show a significant difference between treated soil and control soil. These results suggest that ryegrass rhizosphere effect as well as inoculation of Mycobacterium sp. can accelerate PAH removal in polluted soil. The bacteria community structure demonstrated a complex interplay of soil, bacteria and ryegrass root, and potential PAH degraders were present in abundance. This study provides the exploring data of rhizosphere and bioaugmentation effect on PAH dissipation in agricultural soil, as well as the change of bioavailability and microbial composition thereof.

Simple methods to remove microbes from leaf surfaces

Endophytes have been defined as microorganisms living inside plant tissues without causing negative effects on their hosts. Endophytic microbes have been extensively studied for their plant growth-promoting traits. However, analyses of endophytes require complete removal of epiphytic microorganisms. We found that the established tests to evaluate surface sterility, polymerase chain reaction, and leaf imprints, are unreliable. Therefore, we used scanning electron microscopy (SEM) as an additional assessment of epiphyte removal. We used a diverse suite of sterilization protocols to remove epiphytic microorganisms from the leaves of a gymnosperm and an angiosperm tree to test the influence of leaf morphology on the efficacy of these methods. Additionally, leaf tissue damage was also evaluated by SEM, as damaging the leaves might have an impact on endophytes and could lead to inaccurate assessment of endophytic communities. Our study indicates, that complete removal of the leaf cuticle by the sterilization technique assures loss of epiphytic microbes, and that leaves of different tree species may require different sterilization protocols. Furthermore, our study demonstrates the importance of choosing the appropriate sterilization protocol to prevent erroneous interpretation of host-endophyte interactions. Moreover, it shows the utility of SEM for evaluating the effectiveness of surface sterilization methods and their impact on leaf tissue integrity.

Joint response of chemistry and functional microbial community to oxygenation of the reductive confined aquifer

Oxygen can enter into reductive aquifer through natural and artificial processes. However, the joint response of groundwater chemistry and functional microbial communities to oxygenation is not well understood due to the gap between taxonomic and functional microbial composition. Here, two wells named CZK15 and CZK22 at the second confined aquifer in Central China were in situ aerated, and the chemical parameters of groundwater and microbial communities in bio-trapping sand sediment were analysed during aeration. The microbial metabolic functions related to C, N, S, Fe transformation were predicted by Functional Annotation of Prokaryotic Taxa (FAPROTAX) approach and some key functional genes, such as phe, nah, narG, and soxB were verified by the real-time quantitative Polymerase Chain Reaction (qPCR) method. The biomass was promoted, microbial diversity fluctuated, and microbial composition changed remarkably with aeration mainly constrained by reduction-oxidation (redox) variation and SO₄^2- concentration. Among functional microbes, aerobic chemoheterotrophs including aromatic compound degraders (also especially for relative abundance of phe and some nah gene) and methylotrophs are dramatically enriched interpreting dissolved oxygen (DO) consumption and total organic carbon (TOC) decomposing in sediment. Whilst fermenters and methanogen expectedly decreased during aeration. Denitrifying microbes and narG gene relative abundance increased corresponding to the NO₃^- increase after aeration, while microbes for N₂ fixation, ammonification, and nitrification decreased relating to the source of NH₄⁺. The sulfide oxidation causing increased SO₄^2- was reflected by the blooming of sulfur-oxidizing microbes and soxB gene. Some sulfate reducers persisted in sediment after aeration due to sufficient SO₄^2- as substrate. Fe(II) was mainly chemically oxidized as iron-oxidizing microbes were of low abundance and tended to decrease with aeration. The iron-reducing bacteria Geobacteraceae increased with aeration corresponding to the increased Fe(III) oxides formation. The findings of this study could have important implications in understanding the biogeochemical behaviours with cyclic redox conditions.

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

PAH biodegradation in plant rhizosphere has been investigated in many studies, but the timescale of degradation and degrading bacteria activity was rarely considered. We explored the impact of plants on the temporal variability of PAH degradation, microbial abundance, activity, and bacterial community structure in a rhizotron experiment. A historically contaminated soil was spiked with PAHs, planted or not with alfalfa, over 22 days with sampling once a week. In both conditions, most of the spiked PAHs were dissipated during the first week, conducting to polar polycyclic aromatic compound production and to decreased richness and diversity of bacterial communities. We showed a rapid impact of the rhizosphere on PAH degradation via the increased activity of PAH-degrading bacteria. After 12 days, PAH degradation was significantly higher in the planted (100% degradation) than in unplanted (70%) soil. Gram-negative (Proteobacteria) PAH-dioxygenase genes and transcripts were higher in planted than unplanted soil and were correlated to the spiked PAH degradation. Conversely, Gram-positive (Actinobacteria) PAH-dioxygenase gene transcription was constant over time in both conditions. At 12 days, plant growth favored the activity of many Gammaproteobacteria (Pseudomonadaceae, Stenotrophomonas, and Acinetobacter) while in unplanted soil Alphaproteobacteria (Sphingomonadaceae, Sphingobium, and Magnetospirillum) and Actinobacteria (Iamia, Geodermatophilaceae, and Solirubrobacterales) were more active.

Characterisation of the phenanthrene degradation-related genes and degrading ability of a newly isolated copper-tolerant bacterium

A copper-tolerant phenanthrene (PHE)-degrading bacterium, strain Sphingobium sp. PHE-1, was newly isolated from the activated sludge in a wastewater treatment plant. Two key genes, ahdA1b-1 encoding polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHDɑ) and xyLE encoding catechol-2,3-dioxygenase (C23O), involved in the PHE metabolism by strain PHE-1 were identified. The PAH-RHD gene cluster showed 96% identity with the same cluster of Sphingomonas sp. P2. Our results indicated the induced transcription of xylE and ahdA1b-1 genes by PHE, simultaneously promoted by Cu(II). For the first time, high concentration of Cu(II) is found to encourage the expression of PAH-RHDɑ and C23O genes during PHE degradation. Applying Sphingomonas PHE-1 in PHE-contaminated soils for bioaugmentation, the abundance of xylE gene was increased by the planting of ryegrass and the presence of Cu(II), which, in turn, benefited ryegrass growth. The best performance of PHE degradation and the highest abundance of xylE genes occurred in PHE-copper co-contaminated soils planted with ryegrass.

Comparative Investigation of Bacterial, Fungal, and Archaeal Community Structures in Soils in a Typical Oilfield in Jianghan, China

Agricultural soils in oilfields have high risk for polycyclic aromatic hydrocarbon (PAH) pollution. In this study, from the Jianghan Oilfield (Hubei Province, China) with a history of >50 years, 7 soil samples (OS-1 to OS-7) were collected. Subsequently, the bacterial, archaeal, and fungal community structures were investigated by Illumina MiSeq sequencing, and the relationship between microbial community structure and soil PAH content was analyzed. The results indicated that bacterial and archaeal Chao 1 indices showed a significantly negative relationship with soil PAH content, and only the bacterial Shannon index had a significantly negative relationship with soil PAH content. Moreover, the community structure of bacteria (r ² = 0.9001, p = 0.013) showed a stronger correlation with PAH content than that of fungi (r ² = 0.7357, p = 0.045), and no significant relationship was found between archaeal community structure (r ² = 0.4553, p = 0.262) and soil PAH content. In addition, the relative greater abundances of some bacterial genus belonging to Actinobacteria (Mycobacterium and Micromonospora) and Proteobacteria (Pseudomonas, Lysobacter, Idiomarina, Oxalobacteraceae, and Massilia), fungal genus belonging to Ascomycota (Sordariales and Pleosporales), and archaeal phylum (Euryarchaeota) were detected in the soil samples (OS-3 and OS-5) with greater PAH content. In summary, soil PAHs showed an obvious influence and selectivity on the soil microbiota. Furthermore, compared with fungi and archaea, bacteria was more sensitive to soil PAH pollution, and the diversity indices and community structure of bacteria both might be suitable indicators for assessment of soil PAH stress on the soil ecosystem.

Plant powder teabags: a novel and practical approach to resolve culturability and diversity of rhizobacteria

We have developed teabags packed with dehydrated plant powders, without any supplements, for preparation of plant infusions necessary to develop media for culturing rhizobacteria. These bacteria are efficiently cultivated on such plant teabag culture media, with better progressive in situ recoverability compared to standard chemically synthetic culture media. Combining various plant-based culture media and incubation conditions enabled us to resolve unique denaturing gradient gel electrophoresis (DGGE) bands that were not resolved by tested standard culture media. Based on polymerase chain reaction PCR-DGGE of 16S rDNA fingerprints and sequencing, the plant teabag culture media supported higher diversity and significant increases in the richness of endo-rhizobacteria, namely Gammaproteobacteria (Enterobacteriaceae) and predominantly Alphaproteobacteria (Rhizobiaceae). This culminated in greater retrieval of the rhizobacteria taxa associated with the plant roots. We conclude that the plant teabag culture medium by itself, without any nutritional supplements, is sufficient and efficient for recovering and mirroring the complex and diverse communities of rhizobacteria. Our message to fellow microbial ecologists is: simply dehydrate your plant canopy, teabag it and soak it to prepare your culture media, with no need for any additional supplementary nutrients.

Exogenous IAA treatment enhances phytoremediation of soil contaminated with phenanthrene by promoting soil enzyme activity and increasing microbial biomass

In this study, we aimed to confirm that indole-3-acetic acid promotes plant uptake of phenanthrene (PHE), stimulates the activity of soil enzymes or microflora, and thereby accelerates the dissipation of PHE in soil. Four treatments were evaluated: PHE-contaminated soil planted with (1) ryegrass (T0), (2) ryegrass and supplemented with 1 mg kg(-1) indole-3-acetic acid (IAA) (T1), (3) ryegrass and supplemented with 5 mg kg(-1) IAA (T5), and (4) ryegrass and supplemented with 10 mg kg(-1) IAA (T10). After 30 days, PHE concentrations were lower for all treatments and the removal rate was 70.19, 89.17, 91.26, and 97.07 % for T0, T1, T5, and T10, respectively. PHE was only detected in the roots and not in the shoots. IAA facilitated the accumulation of PHE in the roots, and plants subjected to the T10 treatment had the highest levels. Exogenous IAA stimulated soil peroxidase activity in a dose-dependent manner, whereas soil polyphenoloxidase activity was not significantly increased, except in T10. Soil microbial biomass also increased in response to IAA treatment, particularly in T10. Furthermore, phospholipid fatty acid analysis showed that IAA treatment increased microbial biomass and alleviated environmental stress. Gram-positive bacteria are largely responsible for polycyclic aromatic hydrocarbon degradation, and we found that the ratio of gram-positive to gram-negative bacteria in the soil significantly increased as the IAA concentrations increased (P < 0.05). Correlation analysis indicated that the increase in soil microbial biomass, enzyme activity, and plant uptake of PHE promotes removal of PHE from the soil.