Insights in the regulation of the degradation of PAHs in Novosphingobium sp. HR1a and utilization of this regulatory system as a tool for the detection of PAHs

Experimental research on the transport-transformation of organic contaminants under the influence of multi-field coupling at a site scale

Organic-contaminated shallow aquifers have become a global concern of groundwater contamination, yet little is known about the coupled effects of hydrodynamic-thermal-chemical-microbial (HTCM) multi-field on organic contaminant transport and transformation over a short time in aquifers. Therefore, this study proposed a quick and efficient field experimental method for the transport-transformation of contaminants under multi-field coupling to explore the relationship between organic contaminants (total petroleum hydrocarbon (TPH), polycyclic aromatic hydrocarbons (PAHs), benzene-toluene-ethylbenzene-xylene (BTEX) and phthalates acid esters (PAEs)) and multi-field factors. The results showed that hydrodynamics (affecting pH, p < 0.001) and temperature (affecting dissolved oxygen, pH and HCO3-, p < 0.05) mainly affected the organic contaminants indirectly by influencing the hydrochemistry to regulate redox conditions in the aquifer. The main degradation reactions of the petroleum hydrocarbons (TPH, PAHs and BTEX) and PAEs in the aquifer were sulfate reduction and nitrate reduction, respectively. Furthermore, the organic contamination was directly influenced by microbial communities, whose spatial patterns were shaped by the combined effects of the spatial pattern of hydrochemistry (induced by the organic contamination pressure) and other multi-field factors. Overall, our findings imply that the spatiotemporal patterns of organic contaminants are synergistically regulated by HTCM, with distinct mechanisms for petroleum hydrocarbons and PAEs.

Activated DBP degradation and relevant signal transduction path via quorum sensing autoinducers in Streptomyces sp. SH5

Microbe-mediated DBP (dibutyl phthalate) mineralization is acknowledged to be affected by diverse extracellular factors. However, little is known about the regulatory effects from quorum sensing (QS) signals. In this study, extracellularly applied QS signals A-like (hydroxymethyl dihydrofuran) was discovered to significantly enhance DBP degradation efficiency in Streptomyces sp. SH5. Monobutyl phthalate, protocatechuic acid and beta-ketoadipate were discovered as degradation intermediates by HPLC-TOF-MS/MS. Multi-omics analysis revealed the up-regulation of multiple hydrolases, transferases and decarboxylases that potentially contributed to A-like accelerated DBP degradation. Transcription of Orf2708, an orthologue of global transcriptional activator, was significantly induced by A-like. Orf2708 was demonstrated to interact specifically with the promoter of hydrolase orf2879 gene by EMSA, and the overexpression of orf2879 led to an enhanced DBP degradation in SH5. Taken together with the molecular docking studies showing the stability of ligand-receptor complex of A-like and its potential receptor Orf3712, a hierarchical regulatory cascade underlying the QS signal mediated DBP degradation was proposed as A-like/Orf3712 duplex formation, enhanced orf2708 expression and the downstream specific activation of hydrolase Orf2879. Our study presents the first evidence of GBLs-type promoted DBP degradation among bacteria, and the elucidated signal transduction path indicates a universal application potential of this activation strategy.

Microbes and microbial strategies in carcinogenic polycyclic aromatic hydrocarbons remediation: a systematic review

Degradation, detoxification, or removal of the omnipresent polycyclic aromatic hydrocarbons (PAHs) from the ecosphere as well as their prevention from entering into food chain has never appeared simple. In this context, cost-effective, eco-friendly, and sustainable solutions like microbe-mediated strategies have been adopted worldwide. With this connection, measures have been taken by multifarious modes of microbial remedial strategies, i.e., enzymatic degradation, biofilm and biosurfactant production, application of biochar-immobilized microbes, lactic acid bacteria, rhizospheric-phyllospheric-endophytic microorganisms, genetically engineered microorganisms, and bioelectrochemical techniques like microbial fuel cell. In this review, a nine-way directional approach which is based on the microbial resources reported over the last couple of decades has been described. Fungi were found to be the most dominant taxa among the CPAH-degrading microbial community constituting 52.2%, while bacteria, algae, and yeasts occupied 37.4%, 9.1%, and 1.3%, respectively. In addition to these, category-wise CPAH degrading efficiencies of each microbial taxon, consortium-based applications, CPAH degradation-related molecular tools, and factors affecting CPAH degradation are the other important aspects of this review in light of their appropriate selection and application in the PAH-contaminated environment for better human-health management in order to achieve a sustainable ecosystem.

LuxR402 of Novosphingobium sp. HR1a regulates the correct configuration of cell envelopes

Although there is some evidence to suggest that LuxR-solo proteins participate in inter-species or even inter-kingdom communication, most of the LuxR-solo protein functions are unknown. We have characterized the LuxR402 regulator of Novosphingobium sp. HR1a, a bacterial strain with the ability to establish high numbers in the plant rhizosphere and able to degrade a wide range of polycyclic aromatic hydrocarbons. LuxR402 controls the aggregation state of the bacterial culture; cultures of a mutant strain lacking this regulator flocculate in less than 3 h without agitation. We have demonstrated that the bacterial surface of the mutant is highly hydrophobic and that the mutant cells assimilate sugars slower than the wild-type. The flocculation mechanism has been demonstrated to be involved in the survival of the strain under unfavorable conditions; the luxR402 gene is repressed and produces flocculation in the presence of salicylate, a substrate that, although being assimilated by Novosphingobium, is toxic to cells at high concentrations. The flocculation of cultures in industrial setups has mainly been achieved through the addition of chemicals; these studies open up the possibility of controlling the flocculation by regulating the level of expression of the luxR402 gene.

Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome

BACKGROUND

Keystone taxa are drivers of microbiome structure and functioning, which may play critical roles in microbiome-level responses to recalcitrant pollution and are a key to bioremediation. However, the characterization and manipulation of such taxa is a major challenge due to the complexity of microbial communities and rapid turnover in both time and space. Here, microcosms were set up with benzo[a]-pyrene (BaP) and/or nitrate based on C-rich, S-rich, and N-limited mangrove sediments as reductive experimental models to trigger and track the turnover of keystone taxa to address this challenge.

RESULTS

Based on microbial co-occurrence network analysis, two keystone taxa, Sulfurovum and Sulfurimonas, were found to exhibit significant role transitions in different microcosms, where these two taxa played nonkeystone roles with neutral relationships in in situ mangrove sediments. However, Sulfurimonas transitioned to be keystone taxa in nitrate-replenished microcosms and formed a keystone guild with Thioalkalispira. Sulfurovum stood out in BaP-added microcosms and mutualized in a densely polycyclic aromatic hydrocarbon (PAH)-degrader-centric keystone guild with Novosphingobium and Robiginitalea, where 63.25% of added BaP was removed. Under the occurrence of nitrate and BaP, they simultaneously played roles as keystone taxa in their respective guilds but exhibited significant competition. Comparative genomics and metagenome-assembled genome (MAG) analysis was then performed to reveal the metabolic potential of those keystone taxa and to empirically deduce their functional role in keystone guilds. Sulfurimonas possesses a better sense system and motility, indicative of its aggressive role in nitrate acquisition and conversion; Sulfurovum exhibited a better ability for oxidation resistance and transporting nutrients and electrons. High-efficiency thermal asymmetric interlaced polymerase reaction (hiTAIL-PCR) and enhanced green fluorescent protein (eGFP)-labeling approaches were employed to capture and label the BaP key degrader to further experimentally verify the roles of keystone taxa Sulfurovum in the keystone guilds. Observations of the enhancement in reactive oxygen species (ROS) removal, cell growth, and degradation efficiency by co-culture of isolated keystone taxa strains experimentally demonstrated that Sulfurovum contributes to the BaP degradative microbiome against BaP toxicity.

CONCLUSIONS

Our findings suggest that the combined use of co-occurrence network analysis, comparative genomics, and co-culture of captured keystone taxa (3C-strategy) in microbial communities whose structure is strongly shaped by changing environmental factors can characterize keystone taxa roles in keystone guilds and may provide targets for manipulation to improve the function of the microbiome. Video Abstract.

Biotransformation of benzo[a]pyrene by Pannonibacter sp. JPA3 and the degradation mechanism through the initially oxidized benzo[a]pyrene-4,5-dihydrodiol to downstream metabolites

Owing to its adverse effects on the environment and human health, benzo[a]pyrene (BaP) has attracted considerable attention and has been used as a model compound in ecotoxicology. In this study, Pannonibacter sp. JPA3 as a BaP-degrading strain was isolated from the production water of an oil well. The strain could remove 80% of BaP at an initial concentration of 100 mg L^-1 after 35 d culture. The BaP-4,5-dihydrodiol, BaP-4,5-epoxide, 5-hydroxychrysene, and 2-hydroxy-1-naphthoic acid metabolites were identified in the biodegradation process. Simultaneously, the gene sequence coding for dioxygenase in the strain was amplified and a dioxygenase model was built by homology modeling. Combined with the identification of the metabolites, the interaction mechanism of BaP with dioxygenase was investigated using molecular docking. It was assumed that BaP was initially oxidized at the C₄-C₅ positions in the active cavity of dioxygenase. Moreover, a hypothesis for the progressive degradation mechanism of BaP by this strain was proposed via the identification of the downstream metabolites. In conclusion, our study provided an efficient BaP degrader and a comprehensive reference for the study of the degradation mechanism in terms of the degrading metabolites and theoretical research at the molecular level.

A FadR-Type Regulator Activates the Biodegradation of Polycyclic Aromatic Hydrocarbons by Mediating Quorum Sensing in Croceicoccus naphthovorans Strain PQ-2

Bacteria employ multiple transcriptional regulators to orchestrate cellular responses to adapt to constantly varying environments. The bacterial biodegradation of polycyclic aromatic hydrocarbons (PAHs) has been extensively described, and yet, the PAH-related transcriptional regulators remain elusive. In this report, we identified an FadR-type transcriptional regulator that controls phenanthrene biodegradation in Croceicoccus naphthovorans strain PQ-2. The expression of fadR in C. naphthovorans PQ-2 was induced by phenanthrene, and its deletion significantly impaired both the biodegradation of phenanthrene and the synthesis of acyl-homoserine lactones (AHLs). In the fadR deletion strain, the biodegradation of phenanthrene could be recovered by supplying either AHLs or fatty acids. Notably, FadR simultaneously activated the fatty acid biosynthesis pathway and repressed the fatty acid degradation pathway. As intracellular AHLs are synthesized with fatty acids as substrates, boosting the fatty acid supply could enhance AHL synthesis. Collectively, these findings demonstrate that FadR in C. naphthovorans PQ-2 positively regulates PAH biodegradation by controlling the formation of AHLs, which is mediated by the metabolism of fatty acids. IMPORTANCE Master transcriptional regulation of carbon catabolites is extremely important for the survival of bacteria that face changes in carbon sources. Polycyclic aromatic hydrocarbons (PAHs) can be utilized as carbon sources by some bacteria. FadR is a well-known transcriptional regulator involved in fatty acid metabolism; however, the connection between FadR regulation and PAH utilization in bacteria remains unknown. This study revealed that a FadR-type regulator in Croceicoccus naphthovorans PQ-2 stimulated PAH biodegradation by controlling the biosynthesis of the acyl-homoserine lactone quorum-sensing signals that belong to fatty acid-derived compounds. These results provide a unique perspective for understanding bacterial adaptation to PAH-containing environments.

Enrichment and response of iron-metabolizing microorganisms and metabolic genes in the contaminated area of stratified stacking coal gangue dumps, Northern China

In the Xishan coalfield of northern China, the stratified stacking of soil and gangue was applied to limit the acid pollution from high-sulfur coal gangue. In this study, we found that stratified stacking can effectively neutralize the acidity, with the pH value of gangue-leaching water being 6.02-8.13. In contrast to the acidic contaminated area, most of the microorganisms in the study area sediment were neutrophilic, with the main genera being Arthrobacter, Pseudorhodobacter, Pseudomonas, and Rhodoferax. A variety of iron- and sulfur-metabolizing bacteria was discovered in the gangue-leaching sediment, with the total relative abundance ranging from 4.20 to 23.75%, of which the iron-reducing bacteria (FeRB) accounted for the highest percentage. The distributions of these functional microorganisms in the samples were significantly influenced by Fe and S. The co-occurrence network analysis revealed a significant positive correlation between the iron- and sulfur-metabolizing bacteria in the sediment (93.75%), indicating a strong reciprocal symbiotic relationship between these bacteria. The iron and sulfur metabolism genes in the sediment were predicted and compared based on the Tax4Fun functional prediction method. Results showed that functional genes related to iron metabolism were highly expressed in the gangue-leaching sediment. This study enhances the understanding of iron and sulfur metabolism in gangue-leaching contaminated areas.

Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach

BACKGROUND

Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation genes have been reported. However, a comprehensive PAH-degrading gene database is still lacking, hindering a deep understanding of PAH degraders in the era of big data. Furthermore, the relationships between the PAH-catabolic genotype and phenotype remain unclear.

RESULTS

Here, we established a bacterial PAH-degrading gene database and explored PAH biodegradation capability via a genome-function relationship approach. The investigation of functional genes in the experimentally verified PAH degraders indicated that genes encoding hydratase-aldolase could serve as a biomarker for preliminarily identifying potential degraders. Additionally, a genome-centric interpretation of PAH-degrading genes was performed in the public genome database, demonstrating that they were ubiquitous in Proteobacteria and Actinobacteria. Meanwhile, the global phylogenetic distribution was generally consistent with the culture-based evidence. Notably, a few strains affiliated with the genera without any previously known PAH degraders (Hyphomonas, Hoeflea, Henriciella, Saccharomonospora, Sciscionella, Tepidiphilus, and Xenophilus) also bore a complete PAH-catabolic gene cluster, implying their potential of PAH biodegradation. Moreover, a random forest analysis was applied to predict the PAH-degrading trait in the complete genome database, revealing 28 newly predicted PAH degraders, of which nine strains encoded a complete PAH-catabolic pathway.

CONCLUSIONS

Our results established a comprehensive PAH-degrading gene database and a genome-function relationship approach, which revealed several potential novel PAH-degrader lineages. Importantly, this genome-centric and function-oriented approach can overcome the bottleneck of conventional cultivation-based biodegradation research and substantially expand our current knowledge on the potential degraders of environmental pollutants.

Succession Patterns of Microbial Composition and Activity following the Diesel Spill in an Urban River

Diesel spills in freshwater systems have adverse impacts on the water quality and the shore wetland. Microbial degradation is the major and ultimate natural mechanism that can clean the diesel from the environment. However, which, and how fast, diesel-degrading microorganisms could degrade spilled diesel has not been well-documented in river water. Using a combination of 14C-/3H--based radiotracer assays, analytical chemistry, MiSeq sequencing, and simulation-based microcosm incubation approaches, we demonstrated succession patterns of microbial diesel-degrading activities, and bacterial and fungal community compositions. The biodegradation activities of alkanes and polycyclic aromatic hydrocarbons (PAHs) were induced within 24 h after diesel addition, and reached their maximum after incubation for 7 days. Potential diesel-degrading bacteria Perlucidibaca, Acinetobacter, Pseudomonas, Acidovorax, and Aquabacterium dominated the community initially (day 3 and day 7), but later community structure (day 21) was dominated by bacteria Ralstonia and Planctomyces. The key early fungi responders were Aspergillus, Mortierella, and Phaeoacremonium by day 7, whereas Bullera and Basidiobolus dominated the fungal community at day 21. These results directly characterize the rapid response of microbial community to diesel spills, and suggest that the progression of diesel microbial degradation is performed by the cooperative system of the versatile obligate diesel-degrading and some general heterotrophic microorganisms in river diesel spills.

Transcriptome analysis reveals phenanthrene degradation strategy of Pseudomonas stutzeri LH-42

Toxic polycyclic aromatic hydrocarbons (PAHs) are often released into the environment during the combustion and processing of fossil fuels and are capable of causing significant pollution to people and the environment. One of the representative substances of PAHs is phenanthrene, which is often studied as a model compound for PAHs treatment. In this study, we compared the results of transcriptome analysis of Pseudomonas stutzeri LH-42 in two different culture conditions under phenanthrene-induced culture (test group) and glucose-induced culture (control group), and analysed the key enzymatic mechanisms of Pseudomonas stutzeri LH-42 in the biodegradation of phenanthrene. In our experiments, the transcriptome results showed that a total of 380 genes were more than twofold differentially expressed in the test group, of which 187 genes were significantly up-regulated in expression under Phenanthrene induction. Among the 380 differentially expressed genes, 90 genes were involved in Phenanthrene biodegradation, mainly including genes involved in biometabolism, cellular chemotaxis, substrate transport, signal induction and other related processes. Based on the transcriptome sequence analysis of Pseudomonas stutzeri LH-42 at the time of phenanthrene induction, a total of 25 dioxygenase genes were identified, and the related genes were mainly concentrated in two relatively concentrated clusters of PAHs biodegradation genes. The transcriptome analysis resulted in a complete set of enzyme genes related to the phenanthrene biodegradation pathway. The analysis of key enzymes led to the inference of a possible phenanthrene biodegradation pathway: the salicylic acid degradation pathway. The results of this study provide a theoretical basis for in situ remediation of PAHs-contaminated environments using Pseudomonas stutzeri LH-42.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03473-7.

Effect of Novosphingobium sp. CuT1 inoculation on the rhizoremediation of heavy metal- and diesel-contaminated soil planted with tall fescue

Rhizoremediation is a promising method based on the synergism between plant and rhizobacteria to remediate soil co-contaminated with heavy metals and total petroleum hydrocarbons (TPHs). A plant growth-promoting (PGP) rhizobacterium with diesel-degrading capacity and heavy metal tolerance was isolated from the rhizosphere of tall fescue (Festuca arundinacea L.), after which the effects of its inoculation on rhizoremediation performance were evaluated in heavy metal- and diesel-contaminated soil planted with tall fescue. The bacterial isolate (Novosphingobium sp. CuT1) was characterized by its indole-3-acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, and siderophore productivity as PGP traits. CuT1 was able to grow on 1/10 LB-agar plates containing 5 mM of Cu or 5 mM of Pb. To evaluate the remediation effect of heavy metal- and diesel-contaminated soil by CuT1 inoculation, the experimental conditions were prepared as follows. The soil was artificially contaminated with heavy metals (Cu and Pb) at a final concentration of 500 ppm. The soil was then further contaminated with diesel at final concentrations of 0, 10,000, and 30,000 ppm. Finally, all plots were planted with tall fescue, a representative hyperaccumulating plant. Compared to the rhizoremediation performance of the co-contaminated soil (Cu + Pb + diesel) without inoculation, the bioavailable Cu concentrations in the soil and the tall fescue biomass were significantly increased in CuT1 inoculation. Additionally, the root growth of tall fescue was also promoted in CuT1 inoculation. Correlation analysis showed that Cu bioavailability and bioconcentration factor were positively correlated with CuT1 inoculation. The diesel removal efficiency showed a positive correlation with CuT1 inoculation, although the diesel removal was below 30%. CuT1 inoculation was positively correlated with IAA and dehydrogenase activity in the soil. Moreover, the dry biomass of the tall fescue's roots was highly associated with CuT1 inoculation. Collectively, our findings suggest that Novosphingobium sp. CuT1 can be utilized as an applicable bioresource to enhance rhizoremediation performance in heavy metal- and TPH-contaminated soils.

Ganga River sediments of India predominate with aerobic and chemo-heterotrophic bacteria majorly engaged in the degradation of xenobiotic compounds

Sediment provides a stagnant habitat to microbes that accumulate organic matter and other industrial pollutants from the upper layer of the water. The sediment of the Ganga River of India is overlooked for exploring the bacterial diversity despite their taxon richness over the water counterpart. To enrich the limited information on the bacterial diversity of the Ganga River sediment, the present study was planned that relies on amplicon-based bacterial diversity of the Ganga River sediment by using bacterial-specific 16S hypervariable region (V₃-V₄). The Illumina MiSeq2500 platform generated 1,769,226 raw reads from the metagenomes of various samples obtained from ten sites in five major cities of Uttar Pradesh and Uttarakhand regions traversing the Ganga River. Taxonomy level analysis assigned 58 phyla, 366 order, and 715 genera of bacterial type. The high values of various diversity indices (Chao1, Shannon, and Simpson) in Kanpur sediment indicate the high bacterial richness compared to the Rishikesh sediment. However, several other ecological parameters (Shannon index, Simpson index, enspie _vector, and Faith_pd) were comparatively higher in Rishikesh sediment which is a comparatively less disturbed region by human activities over the other sediments samples studied here. Ganga River sediment dominates with Gram-negative, chemo-heterotrophic, and aerobic bacteria that chiefly belong to Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidota. The abundance of Nitrospira, Hydrogenophaga, Thauera, Vicinamibacteraceae, and Latescibacterota in the Ganga River sediment could be considered as the ecological indicators that find a significant role in the degradation of xenobiotic compounds. The PICRUSt-based analysis showed that ~ 35% of genes were involved in benzoate and aminobenzoate degradation where a significant portion of genes belong to nitrotoluene degradation (14%). Thus, the study uncovers a new perspective in the lineage of bacterial communities and their functional characterization of the Ganga River sediment.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

Novosphingobium percolationis sp. nov. and Novosphingobium huizhouense sp. nov., isolated from landfill leachate of a domestic waste treatment plant

Two strains designated as c1T and c7T, were isolated from the landfill leachate of a domestic waste treatment plant in Huizhou City, Guangdong Province, PR China. The cells of both strains were aerobic, rod-shaped, non-motile and formed yellow colonies on Reasoner’s 2A agar plates. Strain c1T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 7.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Strain c7T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 6.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Phylogenetic analyses revealed that strains c1T and c7T belong to the genus Novosphingobium . The 16S rRNA gene sequence similarities of strains c1T and c7T to the type strains of Novosphingobium species were 94.5–98.2 % and 94.3–99.1 %, respectively. The calculated pairwise average nucleotide identity values among strains c1T, c7T and the reference strains were in the range of 75.2–85.9 % and the calculated pairwise average amino acid identity values among strains c1T, c7T and reference strains were in the range of 72.0–88.3 %. Their major respiratory quinone was Q-10, and the major cellular fatty acids were C18 : 1  ω7c, C18 : 0, C16 : 1  ω7c, C16 : 0 and C14 : 0 2OH. The major polar lipids of strains c1T and c7T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, unidentified lipids and unidentified phospholipid. Based on phenotypic, chemotaxonomic, phylogenetic and genomic results from this study, strains c1T and c7T should represent two independent novel species of Novosphingobium , for which the names Novosphingobium percolationis sp. nov. (type strain c1T=GDMCC 1.2555T=KCTC 82826T) and Novosphingobium huizhouense sp. nov. (type strain c7T=GDMCC 1.2556T=KCTC 82827T) are proposed. The gene function annotation results of strains c1T and c7T suggest that they could play an important role in the degradation of organic pollutants.

Negative correlations between cultivable and active-yet-uncultivable pyrene degraders explain the postponed bioaugmentation

Bioaugmentation is an effective approach to remediate soils contaminated by polycyclic aromatic hydrocarbons (PAHs), but suffers from unsatisfactory performance in engineering practices, which is hypothetically explained by the complicated interactions between indigenous microbes and introduced degraders. This study isolated a cultivable pyrene degrader (Sphingomonas sp. YT1005) and an active pyrene degrading consortium (Gp16, Streptomyces, Pseudonocardia, Panacagrimonas, Methylotenera and Nitrospira) by magnetic-nanoparticle mediated isolation (MMI) from soils. Pyrene biodegradation was postponed in bioaugmentation with Sphingomonas sp. YT1005, whilst increased by 30.17% by the active pyrene degrading consortium. Pyrene dioxygenase encoding genes (nidA, nidA3 and PAH-RHDα-GP) were enriched in MMI isolates and positively correlated with pyrene degradation efficiency. Pyrene degradation by Sphingomonas sp. YT1005 only followed the phthalate pathway, whereas both phthalate and salicylate pathways were observed in the active pyrene degrading consortium. The results indicated that the uncultivable pyrene degraders were suitable for bioaugmentation, rather than cultivable Sphingomonas sp. YT1005. The negative correlations between Sphingomonas sp. YT1005 and the active-yet-uncultivable pyrene degraders were the underlying mechanisms of bioaugmentation postpone in engineering practices.

Biodegradation and metabolic pathway of phenanthrene by a newly isolated bacterium Gordonia sp. SCSIO19801

The bacterium Gordonia sp. SCSIO19801, which could effectively utilize phenanthrene as the sole carbon source, was isolated from the seawater of the South China Sea. Its biodegradation characteristics, whole genome sequence, and biodegradation pathway were investigated. The phenanthrene biodegradation process of Gordonia sp. SCSIO19801 was estimated to be a first-order kinetic model with a k value of 0.26/day. Based on the identification of metabolites, utilization of probable intermediates, and genomics analysis of related genes, the degradation of phenanthrene by Gordonia sp. SCSIO19801 was proposed to occur via the salicylate metabolic pathway. This is the first report of a phenanthrene degradation pathway in Gordonia species. In addition, the Gordonia sp. SCSIO19801 could use other aromatic compounds as the sole source of carbon and energy. These characteristics indicate that Gordonia sp. SCSIO19801 can be utilized for developing effective methods for the biodegradation of petroleum hydrocarbons in marine environments.

Impacts of bio-stimulants on pyrene degradation, prokaryotic community compositions, and functions

Bio-stimulation of the indigenous microbial community is considered as an effective strategy for the bioremediation of polluted environments. This examination explored the near effects of various bio-stimulants on pyrene degradation, prokaryotic community compositions, and functions using 16S rRNA amplicon sequencing and qPCR. At first, the results displayed significant differences (p < 0.05) between the prokaryotic community structures of the control group, PYR (contains pyrene only), and bio-stimulants amended groups. Among the bio-stimulants, biochar, oxalic acid, salicylate, NPK, and ammonium sulfate augmented the pyrene degradation potential of microbial communities. Moreover, the higher abundance of genera, such as Flavobacterium, Hydrogenophaga, Mycobacterium, Rhodococcus, Flavihumibacter, Pseudomonas, Novosphingobium, etc., across the treatments indicated that these genera play a vital role in pyrene metabolism. Based on the higher abundance of GP-RHD and nidA genes, we speculated that Gram-positive prokaryotic communities are more competent in pyrene dissipation than Gram-negative. Furthermore, the marked abundance of nifH, and pqqC genes in the NPK and SA treatments, respectively, suggested that different bio-stimulants might enrich certain bacterial assemblages. Besides, the significant distinctions (p < 0.05) between the bacterial consortia of HA (humic acid) and SA (sodium acetate) groups from NPK, OX (oxalic acid), UR (urea), NH4, and SC (salicylate) groups also suggested that different bio-stimulants might induce distinct ecological impacts influencing the succession of prokaryotic communities in distinct directions. This work provides new insight into the bacterial degradation of pyrene using the bio-stimulation technique. It suggests that it is equally important to investigate the community structure and functions along with studying their impacts on degradation when devising a bio-stimulation technology.

An Intracellular Sensing and Signal Transduction System That Regulates the Metabolism of Polycyclic Aromatic Hydrocarbons in Bacteria

Many bacteria utilize polycyclic aromatic hydrocarbon (PAH) as carbon and energy sources for growth. These bacteria play an important role in the amelioration of PAH pollution in various environments. However, it is unclear how bacteria sense PAHs and how PAH degradation pathways are regulated via signal transduction. Here, we investigated these mechanisms in Cycloclasticus, a ubiquitous PAH-degrading bacterium in marine environments. We identified the key genes involved in intracellular PAH sensing, signal transduction, and the differential regulation of degradation pathways for each PAH examined. Our results showed that PAHs bind specifically to a diguanylate cyclase PdgC, leading to the generation of cyclic dimeric GMP (c-di-GMP), which subsequently binds to two CRP/FNR family regulators, DPR-1 and DPR-2. c-di-GMP activates the transcription of DPR-1 and DPR-2 to positively regulate degradation pathways specific to pyrene and phenanthrene/naphthalene, respectively. This is the first report of an intracellular signal transduction pathway associated with PAH degradation in bacteria. Our results improve our understanding of the intracellular responses to PAHs. The existence of the identified genes in other bacteria indicates that the strategy described here is widely used by other PAH-degrading bacteria. IMPORTANCE Polycyclic aromatic hydrocarbons (PAHs) are widely distributed and have been found indoors, in the atmosphere, in terrestrial soils, in marine waters and sediments, and even in outer space. Bacteria degrade PAHs via degradation pathways. PAH signal sensing and transduction, as well as the regulation of PAH degradation pathways, are crucial for bacterial PAH biodegradation. However, prior to this study, these processes were poorly known. This study employed multiple molecular approaches to better understand the regulatory networks controlling PAH metabolism in bacteria. This report illustrates, for the first time, PAH-specific intracellular sensing, signal transduction, and metabolic regulatory pathways. Our results will help to increase our understanding of the hydrocarbon-metabolism regulatory network as well as the regulatory intricacies that control microbial biodegradation of organic matter. These key data should be considered to improve the rational design and efficiency of recombinant biodegradable, bacterial biosensors, and biocatalysts in modern green chemistry.

Genetically engineered microbial remediation of soils co-contaminated by heavy metals and polycyclic aromatic hydrocarbons: Advances and ecological risk assessment

Soils contaminated with heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have been becoming a worldwide concerned environmental problem because of threatening public healthy via food chain exposure. Thus soils polluted by HMs and PAHs need to be remediated urgently. Physical and chemical remediation methods usually have some disadvantages, e.g., cost-expensiveness and incomplete removal, easily causing secondary pollution, which are hence not environmental-friendly. Conventional microbial approaches are mostly used to treat a single contaminant in soils and lack high efficiency and specificity for combined contaminants. Genetically engineered microorganisms (GEMs) have emerged as a desired requirement of higher bioremediation efficiency for soils polluted with HMs and PAHs and environmental sustainability, which can provide a more eco-friendly and cost-effective strategy in comparison with some conventional techniques. This review comments the recent advances about successful bioremediation techniques and approaches for soil contaminated with HMs and/or PAHs by GEMs, and discusses some challenges in the simultaneous removal of HMs and PAHs from soil by designing multi-functional genetic engineering microorganisms (MFGEMs), such as improvement of higher efficiency, strict environmental conditions, and possible ecological risks. Also, the modern biotechnological techniques and approaches in improving the ability of microbial enzymes to effectively degrade combined contaminants at a faster rate are introduced, such as reasonable gene editing, metabolic pathway modification, and protoplast fusion. Although MFGEMs are more potent than the native microbes and can quickly adapt to combined contaminants in soils, the ecological risk of MFGEMs needs to be evaluated under a regulatory, safety, or costs benefit-driving system in a way of stratified regulation. Nevertheless, the innovation of genetic engineering to produce MFGEMs should be inspired for the welfare of successful bioremediation for soils contaminated with HMs and PAHs but it must be supervised by the public, authorities, and laws.

Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation

Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.

PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influences its survival in soil and rhizospheres

Novosphingobium sp. HR1a is a good biodegrader of PAHs and aromatic compounds, and also a good colonizer of rhizospheric environments. It was previously demonstrated that this microbe is able to co-metabolize nutrients existing in root exudates together with the PAHs. We have revealed here that PahT, a regulator of the IclR-family, regulates the central carbon fluxes favouring the degradation of PAHs and mono-aromatic compounds, the ethanol and acetate metabolism and the uptake, phosphorylation and further degradation of mono- and oligo-saccharides through a phosphoenolpyruvate transferase system (PTS). As final products of these fluxes, pyruvate and acetyl-CoA are obtained. The pahT gene is located within a genomic region containing two putative transposons that carry all the genes for PAH catabolism; PahT also regulates these genes. Furthermore, encoded in this genomic region, there are genes that are involved in the recycling of phosphoenolpyruvate, from the obtained pyruvate, which is the motor molecule involved in the saccharide uptake by the PTS system. The co-metabolism of PAHs with different carbon sources, together with the activation of the thiosulfate utilization and an alternative cytochrome oxidase system, also regulated by PahT, represents an advantage for Novosphingobium sp. HR1a to survive in rhizospheric environments.

A new global regulator that facilitates the co-metabolization of polyaromatic hydrocarbons and other nutrients in Novosphingobium

In an article in this issue of Environmental Microbiology, Segura et al. report the identification of an unusual global regulator in Novosphingobium sp. HR1a, a metabolically versatile bacterial strain isolated from the rhizosphere able to assimilate a wide range of polyaromatic hydrocarbons (PAHs). Physiological and transcriptomic assays suggest that this regulator, named PahT, activates the expression of genes involved in the assimilation of PAHs, and of compounds such as sugars and acetate, facilitating their co-metabolism. This effect is the opposite to the carbon catabolite repression strategy that allows metabolically versatile bacteria to favour the use of some compounds over others. PahT was found to stimulate sugar uptake and metabolization in the presence and absence of PAHs and to facilitate microaerobic respiration if PAHs were present. A survey of the genomes of several Sphingomonadaceae members showed that PahT is not present in all strains of this family, but that it is strongly associated with PAH degradation genes. Since not all PAH-degrading strains contain pahT, it seems that PahT is not essential for PAH degradation but likely provides a selective advantage to PAH-degrading strains in environments such as the rhizosphere where other potential carbon sources are available.

Bacterial community response to petroleum contamination in brackish tidal marsh sediments in the Yangtze River Estuary, China

The brackish tidal marsh in the Baimaosha area of the Yangtze River Estuary was severely contaminated by 400 tons of heavy crude petroleum from a tanker that sank in December 2012. The spill accident led to severe environmental damage owing to its high toxicity, persistence and wide distribution. Microbial communities play vital roles in petroleum degradation in marsh sediments. Therefore, taxonomic analysis, high-throughput sequencing and 16S rRNA functional prediction were used to analyze the structure and function of microbial communities among uncontaminated (CK), lightly polluted (LP), heavily polluted (HP), and treated (TD) sediments. The bacterial communities responded with increased richness and decreased diversity when exposed to petroleum contamination. The dominant class changed from Deltaproteobacteria to Gammaproteobacteria after petroleum contamination. The phylum Firmicutes increased dramatically in oil-enriched sediment by 75.78%, 346.19% and 267.26% in LP, HP and TD, respectively. One of the suspected oil-degrading genera, Dechloromonas, increased the most in oil-contaminated sediment, by 540.54%, 711.27% and 656.78% in LP, HP and TD, respectively. Spore protease, quinate dehydrogenase (quinone) and glutathione-independent formaldehyde dehydrogenase, three types of identified enzymes, increased enormously with the increasing petroleum concentration. In conclusion, petroleum contamination altered the community composition and microorganism structure, and promoted some bacteria to produce the corresponding degrading enzymes. Additionally, the suspected petroleum-degrading genera should be considered when restoring oil-contaminated sediment.

A high-efficiency phenanthrene-degrading Diaphorobacter sp. isolated from PAH-contaminated river sediment

Polycyclic aromatic hydrocarbons (PAHs) are typical persistent organic pollutants that accumulate in the environment, mainly from anthropogenic activities. Microbial degradation is the main pathway of PAHs degradation in the natural environment. Therefore, the widen of the available bank of microbial resources and exploration of the molecular degradation mechanisms of PAHs are crucial to the proper management of PAHs-polluted sites. In this work, a bacterial strain, YM-6, which has a high ability to utilize phenanthrene (PHE) as its sole source of carbon and energy, was isolated from sediment contaminated with PAHs. The strain YM-6 was found to degrade 96.3% of 100 mg/L of PHE in liquid cultures within 52 h. The strain was identified as Diaphorobacter sp. by 16S rDNA sequencing. The optimum growth conditions of the YM-6 strain were studied, and the results indicated that the optimum growth temperature of the strain was 30 °C, and the optimum growth pH was 7. The stain is well-suited for high-temperature stress (40 °C), and it could withstand 400 mg/L of PHE. The strain's PHE metabolism was assayed using GC-MS analyses. The results revealed that the YM-6 strain metabolized PHE via the phthalic acid pathway because the intermediates, such as phthalic acid, diethyl ester and phthalaldehydic acid, methyl ester, were detected. The use of this strain may be an attractive alternative for the bioremediation of polycyclic aromatic hydrocarbons in an aquatic environment.

Coupling of Fe-C and aerobic granular sludge to treat refractory wastewater from a membrane manufacturer in a pilot-scale system

A novel pilot-scale system based on aerobic granular sludge (AGS) as a biological treatment step was proposed to treat refractory wastewater from a membrane manufacturer. The components of the system included a microelectrolysis Fe-C filter, a hydrolysis acidification bioreactor (HA), sequence batch reactor 1 (AGS SBR1), sequence batch reactor 2 (AGS SBR2), and a membrane bioreactor (MBR). The Fe-C filter effectively improved the biodegradability of the wastewater components and introduced some byproducts (such as Fe²⁺, Fe³⁺, and Fe minerals) that are beneficial for the cultivation and stability of the AGS. Ideal conditions for aerobic granulation were maintained in the SBR, such as alternating feast and famine conditions. A selection pressure, including a hydraulic shear force and settling time, was also created therein. The results showed that the AGS was formed successfully in both SBR1 and SBR2, the sludge volume index after 30 min (SVI₃₀) and mean particle size reached 34.2 mL/g and 720 µm, and 36.7 mL/g and 610 µm, respectively, and a satisfactory nutrient removal capacity was achieved in the system. During the entire experimental period, the microbial community changed significantly; enrichment of microbes with the secretion of extracellular polymeric substances (EPS), granule stabilization functions in the AGS, and the differentiation of microbes corresponding to the function of each unit were observed. The use of Fe-C, application of SBRs, and use of dewatered sludge as an inoculant played key roles in the cultivation and stability of the AGS.

Secretion dynamics of soyasaponins in soybean roots and effects to modify the bacterial composition

Soyasaponins are triterpenoid saponins widely found in legume plants. These compounds have drawn considerable attention because they have various activities beneficial for human health, and their biosynthesis has been actively studied. In our previous study, we found that legume plants including soybean secrete soyasaponins from the roots in hydroponic culture throughout the growth period, but the physiological roles of soyasaponins in the rhizosphere and their fate in soil after exudation have remained unknown. This study demonstrates that soyasaponins are secreted from the roots of field-grown soybean, and soyasaponin Bb is the major soyasaponin detected in the rhizosphere. In vitro analysis of the distribution coefficient suggested that soyasaponin Bb can diffuse over longer distances in the soil in comparison with daidzein, which is a typical isoflavone secreted from soybean roots. The degradation rate of soyasaponin Bb in soil was slightly faster than that of daidzein, whereas no soyasaponin Bb degradation was observed in autoclaved soil, suggesting that microbes utilize soyasaponins in the rhizosphere. Bacterial community composition was clearly influenced by soyasaponin Bb, and potential plant growth-promoting rhizobacteria such as Novosphingobium were significantly enriched in both soyasaponin Bb-treated soil and the soybean rhizosphere. These results strongly suggest that soyasaponin Bb plays an important role in the enrichment of certain microbes in the soybean rhizosphere.

The LuxI/LuxR-Type Quorum Sensing System Regulates Degradation of Polycyclic Aromatic Hydrocarbons via Two Mechanisms

Members of the Sphingomonadales are renowned for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). However, little is known about the regulatory mechanisms of the degradative pathway. Using cross-feeding bioassay, a functional LuxI/LuxR-type acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) system was identified from Croceicoccus naphthovorans PQ-2, a member of the order Sphingomonadales. Inactivation of the QS system resulted in a significant decrease in PAHs degradation. The QS system positively controlled the expression of three PAH-degrading genes (ahdA1e, xylE and xylG) and a regulatory gene ardR, which are located on the large plasmid. Interestingly, the transcription levels of these three PAH-degrading genes were significantly down-regulated in the ardR mutant. In addition, bacterial cell surface hydrophobicity and cell morphology were altered in the QS-deficient mutant. Therefore, the QS system in strain PQ-2 positively regulates PAH degradation via two mechanisms: (i) by induction of PAH-degrading genes directly and/or indirectly; and (ii) by an increase of bacterial cell surface hydrophobicity. The findings of this study improve our understanding of how the QS system influences the degradation of PAHs, therefore facilitating the development of new strategies for the bioremediation of PAHs.

Microcystin-LR-induced changes of hepatopancreatic transcriptome, intestinal microbiota, and histopathology of freshwater crayfish (Procambarus clarkii)

As a hepatotoxin, microcystin-LR (MC-LR) poses a great threat to aquatic organisms. In this research, the hepatopancreatic transcriptome, intestinal microbiota, and histopathology of Procambarus clarkii (P. clarkii) in response to acute MC-LR exposure were studied. RNA-seq analysis of hepatopancreas identified 372 and 781 differentially expressed genes (DEGs) after treatment with 10 and 40 μg/L MC-LR, respectively. Among the DEGs, 23 genes were immune-related and 21 genes were redox-related. GO functional enrichment analysis revealed that MC-LR could impact nuclear-transcribed mRNA catabolic process, cobalamin- and heme-related processes, and sirohydrochlorin cobaltochelatase activity of P. clarkii. In addition, the only significantly enriched KEGG pathway induced by MC-LR was galactose metabolism pathway. Meanwhile, sequencing of the bacterial 16S rRNA gene demonstrated that MC-LR decreased bacterial richness and diversity, and altered the intestinal microbiota composition. At the phylum level, after 96 h, the abundance of Verrucomicrobia decreased after treatment with 10 and 40 μg/L MC-LR, while Firmicutes increased in the 40 μg/L MC-LR-treated group. At the genus level, the abundances of 15 genera were significantly altered after exposure to MC-LR. Our research demonstrated that MC-LR exposure caused histological alterations such as structural damage of hepatopancreas and intestines. This research provides an insight into the mechanisms associated with MC-LR toxicity in aquatic crustaceans.

The versatility of Pseudomonas putida in the rhizosphere environment

This article addresses the lifestyle of Pseudomonas and focuses on how Pseudomonas putida can be used as a model system for biotechnological processes in agriculture, and in the removal of pollutants from soils. In this chapter we aim to show how a deep analysis using genetic information and experimental tests has helped to reveal insights into the lifestyle of Pseudomonads. Pseudomonas putida is a Plant Growth Promoting Rhizobacteria (PGPR) that establishes commensal relationships with plants. The interaction involves a series of functions encoded by core genes which favor nutrient mobilization, prevention of pathogen development and efficient niche colonization. Certain Pseudomonas putida strains harbor accessory genes that confer specific biodegradative properties and because these microorganisms can thrive on the roots of plants they can be exploited to remove pollutants via rhizoremediation, making the consortium plant/Pseudomonas a useful tool to combat pollution.

Enhanced anaerobic degradation of quinoline, pyriding, and indole with polyurethane (PU), Fe3O4@PU, powdered activated carbon (PAC), Fe(OH)3@PAC, biochar, and Fe(OH)3@biochar and analysis of microbial succession in different reactors

The study was to explore the feasibility of polyurethane (PU), Fe₃O₄@PU, powdered activated carbon (PAC), Fe(OH)₃@PAC, biochar, and Fe(OH)₃@biochar as biological carriers in strengthening anaerobic degradation of quinoline, pyridine, and indole. When the concentrations of pollutants were 25 mg/L and 50 mg/L, reactors based on PAC and Fe(OH)₃@PAC had higher degradation ratios than the other reactors. However, when the concentrations of pollutants were 75 mg/L and 100 mg/L, with the addition of PU and Fe₃O₄@PU, reactors began to show their superiority in the degradation of the selected NHCs. Among these, the reactor based on Fe₃O₄@PU had the optimal degradation ratio on quinoline, pyridine, and indole. PU, PAC, Fe(OH)₃@PAC, biochar, and Fe(OH)₃@biochar benefited the enrichment of Acinetobacter, Comamonas, Levilinea, Longilinea, and Desulfomicrobium. The reactor with the carrier of Fe₃O₄@PU had some specificity, which benefited the enrichment of Zoogloea, Thiobacillus, Anaeromyxobacter, Sphingobium, Terrimonas, Parcubacteria genera incertae sedis, Bdellovibrio, Rhizobium, and Acidovorax.

Combining electrokinetic transport and bioremediation for enhanced removal of crude oil from contaminated marine sediments: Results of a long-term, mesocosm-scale experiment

Marine sediments represent an important sink of harmful petroleum hydrocarbons after an accidental oil spill. Electrobioremediation techniques, which combine electrokinetic transport and biodegradation processes, represent an emerging technological platform for a sustainable remediation of contaminated sediments. Here, we describe the results of a long-term mesocosm-scale electrobioremediation experiment for the treatment of marine sediments contaminated by crude oil. A dimensionally stable anode and a stainless-steel mesh cathode were employed to drive seawater electrolysis at a fixed current density of 11 A/m². This approach allowed establishing conditions conducive to contaminants biodegradation, as confirmed by the enrichment of Alcanivorax borkumensis cells harboring the alkB-gene and other aerobic hydrocarbonoclastic bacteria. Oil chemistry analyses indicated that aromatic hydrocarbons were primarily removed from the sediment via electroosmosis and low molecular weight alkanes (nC₆ to nC₁₀) via biodegradation.

Co-metabolic degradation of the antibiotic ciprofloxacin by the enriched bacterial consortium XG and its bacterial community composition

Ciprofloxacin is a broad spectral and highly refractory antibiotic. It is an emerging pollutant. This study aimed to utilise co-metabolism as a means to degrade ciprofloxacin by a bacterial consortium. The stable bacterial consortium XG capable of efficiently degrading ciprofloxacin was successfully established through successive acclimation of indigenous microorganisms. The consortium XG was primarily consisted of Achromobacter, Bacillus, Lactococcus, Ochrobactrum, and Enterococcus as well as at least other five minor genera. A novel strain YJ17 with CIP-degrading ability was isolated from the consortium and identified as Ochrobactrum sp. The consortium XG utilised amino acids, carbohydrates, and carboxylic acids at a rate approximately 16.6-243-fold greater than the other carbon substrates, but only slow utilisation of ciprofloxacin as a sole carbon source. Ciprofloxacin can be co-metabolized along with many carbon sources, attaining degradation rates up to 63%. Glycyl-l-glutamic acid, d-cellobiose, and itaconic acid are among the substrates most favourable for co-metabolism. The metabolites of ciprofloxacin were identified by LC-QTOF-MS. Co-metabolic degradation of ciprofloxacin by consortium XG led to the removal of essential functional groups from parent compound, thus resulting in formation of metabolites with less bioactive potency. Finally, a possible biochemical pathway for the degradation of ciprofloxacin was proposed. Consortium XG possesses high potential for bioremediation of ciprofloxacin-contaminated environments in the presence of a co-substrate.

A Low-Cost Approach Using Diatomaceous Earth Biosorbent as Alternative SPME Coating for the Determination of PAHs in Water Samples by GC-MS

In this study, the use of recycled diatomaceous earth as the extraction phase in solid phase microextraction (SPME) technique for the determination of polycyclic aromatic hydrocarbons (PAHs) in river water samples, with separation/detection performed by gas chromatography-mass spectrometry (GC-MS), is proposed. The optimized extraction conditions are extraction time 70 min at 80 °C with no addition of salt. The limits of quantification were close to 0.5 μg L−1 with RSD values lower than 25% (n = 3). The linear working range was 0.5 μg L−1 to 25 μg L−1 for all analytes. The method was applied to samples collected from the Itajaí River (Santa Catarina, Brazil) and the RSD values for repeatability and reproducibility were lower than 15% and 17%, respectively. The efficiency of the recycled diatomaceous earth fiber was compared with that of commercial fibers and good results were obtained, confirming that this is a promising option to use as the extraction phase in SPME.

Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1

Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by CycloclasticusCycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in CycloclasticusIMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.

Salt stress alleviation in citrus plants by plant growth-promoting rhizobacteria Pseudomonas putida and Novosphingobium sp

This work reveals the protective role of two rhizobacteria, Pseudomonas putida and Novosphingobium sp., on citrus plants subjected to salt stress conditions. Detrimental salt stress effects on crops are likely to increase due to climate change reducing the quality of irrigation water. Plant growth-promoting rhizobacteria (PGPRs) can mitigate stress-induced damage in plants cultivated under high salinity conditions. In this work, Citrus macrophylla (alemow) plants inoculated with the rhizobacteria Pseudomonas putida KT2440 or Novosphingobium sp. HR1a were subjected to salt stress for 30 days. Results showed that in absence of salt stress, Novosphingobium sp. HR1a induced a decrease of transpiration (E) and stomatal conductance (g_s). Both rhizobacteria reduced salt stress-induced damage. Levels of abscisic acid (ABA) and salicylic acid (SA) were lower in inoculated plants under salt stress conditions. Similarly, under stress conditions maximum efficiency of photosystem II (F_v/F_m) in inoculated plants decreased to a lower extent than in non-inoculated ones. In stressed plants, Novosphingobium sp. HR1a also induced leaf accumulation of 3-indole acetic acid (IAA) and a delay in the decrease of quantum yield (ΦPSII). P. putida KT2440 inhibited root chloride and proline accumulation in response to salt stress. Although both bacterial species had beneficial effects on salt-stressed citrus plants, Novosphingobium sp. HR1a induced a better plant performance. Therefore, both strains could be candidates to be used as PGPRs in programs of inoculation for citrus protection against salt stress.

Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1

Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by Cycloclasticus Cycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in Cycloclasticus IMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.

Effects of secondary carbon supplement on biofilm-mediated biodegradation of naphthalene by mutated naphthalene 1, 2-dioxygenase encoded by Pseudomonas putida strain KD9

Polycyclic aromatic hydrocarbons (PAHs) belong to a diverse group of environmental pollutants distributed ubiquitously in the environment. The carcinogenic properties of PAHs are the main causes of harm to human health. The green technology, biodegradation have become convenient options to address the environmental pollution. In this study, we analyzed the biodegradation potential of naphthalene with secondary carbon supplements (SCSs) in carbon deficient media (CSM) by Pseudomonas putida strain KD9 isolated from oil refinerary waste. The rigid-flexible molecular docking method revealed that the mutated naphthalene 1,2-dioxygenase had lower affinity for naphthalene than that found in wild type strain. Moreover, analytical methods (HPLC, qRT-PCR) and soft agar chemotaxis suggest sucrose (0.5 wt%) to be the best chemo-attractant and it unequivocally caused enhanced biodegradation of naphthalene (500 mg L^-1) in both biofilm-mediated and shake-flask biodegradation methods. In addition, the morphological analysis detected from microscopy clearly showed KD9 to change its size and shape (rod to pointed) during biodegradation of naphthalene in CSM as sole source of carbon and energy. The forward versus side light scatter plot of the singlet cells obtained from flow cytometry suggests smaller cell size in CSM and lower florescence intensity of the total DNA content of cells. This study concludes that sucrose may be used as potential bio-stimulation agent.

Root exudates from citrus plants subjected to abiotic stress conditions have a positive effect on rhizobacteria

Plants are constantly releasing root exudates to the rhizosphere. These compounds are responsible for different (positive or negative) interactions with other organisms, including plants, fungi or bacteria. In this work, the effect of root exudates obtained from in vitro cultured citrus plants on two rhizobacteria (Pseudomonas putida KT2440 and Novosphingobium sp. HR1a) was evaluated. Root exudates were obtained from two citrus genotypes differing in their sensitivity to salt and heat stress and differentially affected the growth of both rhizobacteria. Root exudates from salt-stressed plants of C. macrophylla (salt tolerant) induced an increase in bacterial growth higher than that obtained from Carrizo citrange exudates (salt sensitive). Root exudates from heat-stressed plants also had a positive effect on bacterial growth, which was more evident in the heat-sensitive C. macrophylla. These results reveal that the growth of these rhizobacteria can be modulated through citrus root exudates and can change depending on both the stress conditions as well as the genotype. Biosensors P. putida KT2442 (pMIS5) and Novosphingobium sp. HR1a (pPAH) were used to test the presence of proline and salicylates in root exudates by measuring β-galactosidase activity. This activity increased in the presence of root exudates obtained from stressed plants to a higher extent in the case of exudates obtained from the genotype resistant to each particular stress, indicating that those root exudates contain larger quantities of proline and salicylates, as it has been described previously. Our data reveals that both P. putida KT2442 (pMIS5) and Novosphingobium sp. HR1a (pPAH), could be used as biosensors of plant stress.

Citrus plants exude proline and phytohormones under abiotic stress conditions

This article describes the root exudation of proline and phytohormones in citrus and their involvement in salt- and heat-stress responses. Plants are constantly releasing several compounds to the rhizosphere through their roots, including primary and secondary metabolites. Root exudation can be affected by growth conditions, including pH, nutrient availability, soil salinity, or temperature. In vitro-cultured plants of two citrus genotypes with contrasting tolerance to salt- and heat-stress conditions were used as plant material. Proline and phytohormone contents in root exudates from plants subjected to salt or high-temperature conditions were evaluated. In addition, tissue damage and lipid peroxidation together with endogenous levels of chloride, proline, and phytohormones were determined in roots and shoots. Proline was released in larger quantities to the rhizosphere when plants were subjected to salt or heat stress. In each stress condition, the concentration of this amino acid was higher in the exudates obtained from plants tolerant to this particular stress condition. On the other hand, root exudation of phytohormones salicylic acid, indole acetic acid, abscisic acid, and jasmonic acid generally increased under both adverse conditions. Results confirm a phytohormone exudation in citrus plants, which had not been described previously and can have an important role in the rhizosphere communication. Moreover, stress conditions and the different tolerance of each genotype to the particular stress significantly modify the exudation pattern both quantitatively and qualitatively.

Complete Genome Sequence of Acinetobacter calcoaceticus CA16, a Bacterium Capable of Degrading Diesel and Lignin

We report here the complete assembled genome sequence of Acinetobacter calcoaceticus CA16, which is capable of utilizing diesel and lignin as a sole carbon source. CA16 contains a 4,110,074-bp chromosome and a 5,920-bp plasmid. The assembled sequences will help elucidate potential metabolic pathways and mechanisms responsible for CA16’s hydrocarbon degradation ability.