The cadmium tolerance and bioaccumulation mechanism of Tetratostichococcus sp. P1: insight from transcriptomics analysis

Cadmium (Cd) has become a severe issue in relatively low concentration and attracts expert attention due to its toxicity, accumulation, and biomagnification in living organisms. Cd does not have a biological role and causes serious health issues. Therefore, Cd pollutants should be reduced and removed from the environment. Microalgae have great potential for Cd absorption for waste treatment since they are more environmentally friendly than existing treatment methods and have strong metal sorption selectivity. This study evaluated the tolerance and ability of the microalga Tetratostichococcus sp. P1 to remove Cd ions under acidic conditions and reveal mechanisms based on transcriptomics analysis. The results showed that Tetratostichococcus sp. P1 had a high Cd tolerance that survived under the presence of Cd up to 100 µM, and IC50, the half-maximal inhibitory concentration value, was 57.0 μM, calculated from the change in growth rate based on the chlorophyll content. Long-term Cd exposure affected the algal morphology and photosynthetic pigments of the alga. Tetratostichococcus sp. P1 removed Cd with a maximum uptake of 1.55 mg g-1 dry weight. Transcriptomic analysis revealed the upregulation of the expression of genes related to metal binding, such as metallothionein. Group A, Group B transporters and glutathione, were also found upregulated. While the downregulation of the genes were related to photosynthesis, mitochondria electron transport, ABC-2 transporter, polysaccharide metabolic process, and cell division. This research is the first study on heavy metal bioremediation using Tetratostichococcus sp. P1 and provides a new potential microalga strain for heavy metal removal in wastewater.[Figure: see text]Abbreviations:BP: Biological process; bZIP: Basic Leucine Zipper; CC: Cellular component; ccc1: Ca (II)-sensitive cross complementary 1; Cd: Cadmium; CDF: Cation diffusion facilitator; Chl: Chlorophyll; CTR: Cu TRansporter families; DAGs: Directed acyclic graphs; DEGs: Differentially expressed genes; DVR: Divinyl chlorophyllide, an 8-vinyl-reductase; FPN: FerroportinN; FTIR: Fourier transform infrared; FTR: Fe TRansporter; GO: Gene Ontology; IC50: Growth half maximal inhibitory concentration; ICP: Inductively coupled plasma; MF: molecular function; NRAMPs: Natural resistance-associated aacrophage proteins; OD: Optical density; RPKM: Reads Per Kilobase of Exon Per Million Reads Mapped; VIT1: Vacuolar iron transporter 1 families; ZIPs: Zrt-, Irt-like proteins.

Evaluating the productivity and bioremediation potential of two tropical marine algae in petroleum hydrocarbon polluted tropical marine water

Bioremediation using tropical marine algae provides cost effective and eco-friendly alternative mean of removing toxic and harmful substances from the environment. Bioremediation is an important tool in sustainable environmental management and protection. This study examined the productivity and bioremediation potential of Nannochloropsis oculata and Porphyridium cruentum in Water Soluble Fraction (WSF) of petroleum fuels by investigating the growth of Nannochloropsis oculata and Porphyridium cruentum at 0%, 10% 20% 30% 40% 50% 75% 100% of WSF of kerosene, diesel, and gasoline. Growth was monitored optically every two days for fourteen days using 721 Visible Spectrophotometer. Productivity was measured using prescribed procedure. Bioremediation potential of test algae were examined using standard method for the GC analysis of diesel range organics in 100% WSFs. The minimum growth for both species was recorded at 100% in all the fuels. The maximum growth of Porphyridium cruentum was obtained at 10% in all fuels, while the maximum growth of Nannochloropsis oculata was obtained at 30% in both kerosene and gasoline and at 50% in diesel. Whereas Porphyridium cruentum was greatly inhibited by all fuels, Nannochloropsis oculata was stimulated at lower concentration of the fuels. Nannochloropsis oculata proved more efficient for bioremediation of the petroleum fuels with 84.58%, 65.51% and 70.77% removal efficiency for kerosene, diesel and gasoline respectively, while Porphyridium cruentum was 58.94%, 46.64% and 56.67% respectively. Nannochloropsis oculata is a very strong and reliable candidate for bioremediation of petroleum hydrocarbons and should be subjected to further examination for sustainable and eco-friendly remediation of petroleum pollution.

Fluoranthene biotreatment using prominent freshwater microalgae: physiological responses of microalgae and artificial neural network modeling of the bioremoval process

Due to the intensified industrial activities and other anthropogenic actions, contamination of polycyclic aromatic hydrocarbons (PAHs) has been growing at an alarming rate, turning in to a serious environmental concern. Bioremediation, as an eco-friendly and sustainable removal technology, can be used by organisms to reduce the resulting contaminations. In the present study, the ability of Tetradesmus obliquus to remove of fluoranthene (FLA) was evaluated. It was confirmed that FLA removal efficiency was managed by various environmental parameters and pH was found to be one of the most important influencial factors. The reusability of the algae in long-term repetitive operations confirmed the occurrence of biodegradation along with other natural attenuation and 10 intermediate compounds were identified in the FLA biodegradation pathway by GC-MS. As a result of physiological assays, induced antioxidant enzymes activities and augmentation of phenol and flavonoids contents, after the treatment of the microalgae by a high concentration of FLA, confirmed the ability of the microalgae to upregulate its antioxidant defense system in response to the toxic effects of FLA. An artificial neural network (ANN) model was then developed to predict FLA biodegradation efficiency and the appropriate predictive performance of ANN was confirmed by comparing the experimental FLA removal efficiency with its predicted amounts (R2 = 0.99).

Plant extracts as an eco-friendly approach to remove paraquat from aqueous solution

Nowadays, water pollution by herbicides is known as a global concern. Paraquat (PQ) (1-1-methyl-4,4-bi-pyridinium-dichloride) is a chip with high performance, which is being widely used herbicide to remove weeds from agricultural and natural ecosystems. PQ can contaminate water sources due to its high solubility in water. Human death by poisoning effects of PQ has been reported in several countries. Therefore, the side effects of PQ are a global challenge. This study aimed to investigate the bioremediation of PQ by plant extracts, as a low-cost, nontoxic, and natural absorbent to remove PQ from aqueous solutions in different conditions. In this regard, the extracts of common purslane (portulaca oleracea), florist kalanchoe (kalanchoe blossfeldiana), and jade plant (crassula portulaca) were used as adsorbents. For this purpose, the effect of various parameters such as contact time, initial concentration of PQ solution, temperature, pH, and amount of extract was investigated. The results of present study showed that P. oleracea extract and C. portulaca extracts have higher adsorption efficiency than k. blossfeldiana extract. The highest PQ removal was obtained by P. oleracea extract (79.04%) and C. portulaca extract (78.72%) at pH = 11, the adsorbent content of 0.2 mg L-1, and the lowest absorption of PQ (50.6%) was obtained by K. blossfeldiana extract. The highest PQ removal by plant extract was observed at 30 min for P. oleracea and C. portulaca, and at 15 min for k. blossfeldiana extract. Moreover, surface absorption capacity increased with increasing plant extract concentration, decreasing PQ concentration and decreased with increasing temperature. Finally, it can be concluded that plant extract can help to remove PQ from the aqueous solution.

AK1 and AK9

PURPOSE

Present study deals with the role of gamma irradiation in modulating arsenic bioremediation of Pseudomonas sp. AK1 and AK9 strains.

MATERIALS AND METHODS

The bacterial strains AK1 and AK9 of Pseudomonas sp. were irradiated at different doses (5 Gy, 10 Gy, 15 Gy and 20 Gy) of gamma irradiation. The effect of γ-irradiation on the growth and arsenic modulating ability of AK1 and AK9 strains was determined in the presence and absence of arsenic along with non-irradiated strains. Further, a comparative study of non-irradiated and irradiated strains by protein profiling in absence and presence of arsenic was carried out to confirm of the increased expression ofarsenite oxidase.

RESULTS

Both strains were able to transform AsIII to AsV. Both strains AK1 and AK9 decrease the arsenic concentration by 626.68 ppb (13.36%) and 686.40 ppb (14.71%) after an incubation period of 96 h in presence of arsenic. Gamma irradiated AK9 strains showed doubled growth in presence of arsenic as compared to non-irradiated strains at 10 Gy treatment whereas no changes in growth was observed in irradiated AK1 strains. Gamma irradiated AK9 strain decrease 378.65 ppb (7.27%) more arsenic concentration from natural water sample supplemented with AsIII than non-irradiated AK9 strain. Further, in the protein profile, increased expression of arsenite oxidase (∼85 kDa) was observed in irradiated AK9 strains in presence of arsenic.

CONCLUSIONS

Overall, the results suggested that the gamma irradiated AK9 strain having potential for arsenic accumulation and increased arsenite tolerance may play a great role in the bioremediation of the arsenite at arsenic contaminated sites.

Influence of heavy Canadian crude oil on pristine freshwater boreal lake ecosystems in an experimental oil spill

The overall impact of a crude oil spill into a pristine freshwater environment in Canada is largely unknown. To evaluate the impact on the native microbial community, a large-scale in situ model experimental spill was conducted to assess the potential role of the natural community to attenuate hydrocarbons. A small volume of conventional heavy crude oil (CHV) was introduced within contained mesocosm enclosures deployed on the shoreline of a freshwater lake. The oil was left to interact with the shoreline for 72 h and then free-floating oil was recovered using common oil spill response methods (i.e. freshwater flushing and capture on oleophilic absorptive media). Residual PAH concentrations returned to near pre-oiling concentrations within 2 months, while the microbial community composition across the water, soil, and sediment matrices of the enclosed oligotrophic freshwater ecosystems did not shift significantly over this period. Metagenomic analysis revealed key polycyclic aromatic and alkane degradation mechanisms also did not change in their relative abundance over the monitoring period. These trends suggest that for small spills (<2 L of oil per 15 m2 of surface freshwater), physical oil recovery reduces PAH concentrations to levels tolerated by the native microbial community. Additionally, the native microbial community present in the monitored pristine freshwater ecosystem possesses the appropriate hydrocarbon degradation mechanisms without prior challenge by hydrocarbon substrates. This study corroborated trends found previously (Kharey et al. 2024) toward freshwater hydrocarbon degradation in an environmentally relevant scale and conditions on the tolerance of residual hydrocarbons in situ.

Native freshwater lake microbial community response to an in situ experimental dilbit spill

With the increase in crude oil transport throughout Canada, the potential for spills into freshwater ecosystems has increased and additional research is needed in these sensitive environments. Large enclosures erected in a lake were used as mesocosms for this controlled experimental dilbit (diluted bitumen) spill under ambient environmental conditions. The microbial response to dilbit, the efficacy of standard remediation protocols on different shoreline types commonly found in Canadian freshwater lakes, including a testing of a shoreline washing agent were all evaluated. We found that the native microbial community did not undergo any significant shifts in composition after exposure to dilbit or the ensuing remediation treatments. Regardless of the treatment, sample type (soil, sediment, or water), or type of associated shoreline, the community remained relatively consistent over a 3-month monitoring period. Following this, metagenomic analysis of polycyclic aromatic and alkane hydrocarbon degradation mechanisms also showed that while many key genes identified in PAH and alkane biodegradation were present, their abundance did not change significantly over the course of the experiment. These results showed that the native microbial community present in a pristine freshwater lake has the prerequisite mechanisms for hydrocarbon degradation in place, and combined with standard remediation practices in use in Canada, has the genetic potential and resilience to potentially undertake bioremediation.

Fe(II)Cl2 amendment suppresses pond methane emissions by stimulating iron-dependent anaerobic oxidation of methane

Aquatic ecosystems are large contributors to global methane (CH4) emissions. Eutrophication significantly enhances CH4-production as it stimulates methanogenesis. Mitigation measures aimed at reducing eutrophication, such as the addition of metal salts to immobilize phosphate (PO43-), are now common practice. However, the effects of such remedies on methanogenic and methanotrophic communities-and therefore on CH4-cycling-remain largely unexplored. Here, we demonstrate that Fe(II)Cl2 addition, used as PO43- binder, differentially affected microbial CH4 cycling-processes in field experiments and batch incubations. In the field experiments, carried out in enclosures in a eutrophic pond, Fe(II)Cl2 application lowered in-situ CH4 emissions by lowering net CH4-production, while sediment aerobic CH4-oxidation rates-as found in batch incubations of sediment from the enclosures-did not differ from control. In Fe(II)Cl2-treated sediments, a decrease in net CH4-production rates could be attributed to the stimulation of iron-dependent anaerobic CH4-oxidation (Fe-AOM). In batch incubations, anaerobic CH4-oxidation and Fe(II)-production started immediately after CH4 addition, indicating Fe-AOM, likely enabled by favorable indigenous iron cycling conditions and the present methanotroph community in the pond sediment. 16S rRNA sequencing data confirmed the presence of anaerobic CH4-oxidizing archaea and both iron-reducing and iron-oxidizing bacteria in the tested sediments. Thus, besides combatting eutrophication, Fe(II)Cl2 application can mitigate CH4 emissions by reducing microbial net CH4-production and stimulating Fe-AOM.

Continuous planting of euhalophyte Suaeda salsa enhances microbial diversity and multifunctionality of saline soil

Halophyte-based remediation emerges as a novel strategy for ameliorating saline soils, offering a sustainable alternative to conventional leaching methods. While bioremediation is recognized for its ability to energize soil fertility and structure, the complex interplays among plant traits, soil functions, and soil microbial diversity remain greatly unknown. Here, we conducted a 5-year field experiment involving the continuous cultivation of the annual halophyte Suaeda salsa in saline soils to explore soil microbial diversity and their relationships with plant traits and soil functions. Our findings demonstrate that a decline in soil salinity corresponded with increases in the biomass and seed yield of S. salsa, which sustained a consistent seed oil content of approximately 22% across various salinity levels. Significantly, prolonged cultivation of halophytes substantially augmented soil microbial diversity, particularly from the third year of cultivation. Moreover, we identified positive associations between soil multifunctionality, seed yield, and taxonomic richness within a pivotal microbial network module. Soils enriched with taxa from this module showed enhanced multifunctionality and greater seed yields, correlating with the presence of functional genes implicated in nitrogen fixation and nitrification. Genomic analysis suggests that these taxa have elevated gene copy numbers of crucial functional genes related to nutrient cycling. Overall, our study emphasizes that the continuous cultivation of S. salsa enhances soil microbial diversity and recovers soil multifunctionality, expanding the understanding of plant-soil-microbe feedback in bioremediation.IMPORTANCEThe restoration of saline soils utilizing euhalophytes offers a viable alternative to conventional irrigation techniques for salt abatement and soil quality enhancement. The ongoing cultivation of the annual Suaeda salsa and its associated plant traits, soil microbial diversity, and functionalities are, however, largely underexplored. Our investigation sheds light on these dynamics, revealing that cultivation of S. salsa sustains robust plant productivity while fostering soil microbial diversity and multifunctionality. Notably, the links between enhanced soil multifunctionality, increased seed yield, and network-dependent taxa were found, emphasizing the importance of key microbial taxa linked with functional genes vital to nitrogen fixation and nitrification. These findings introduce a novel understanding of the role of soil microbes in bioremediation and advance our knowledge of the ecological processes that are vital for the rehabilitation of saline environments.

Vermicomposting technology as a dynamic strategy to mitigate environmental crisis: a bibliometric study of last three decades

Efficient recycling of resources forms the cornerstone of sustainable development. Among multiple options in stock for waste recycling, vermicomposting technology is regarded as a futuristic strategy, being tested in every part of the globe due to easy accessibility. Hence, a bibliometric study was planned to set a sight on global scientific trends encompassing vermicomposting research in last three decades. The data were retrieved from Google Scholar, Scopus and PubMed. Publications from different search engines were filtered out and 2064 unique documents were collected and illustrated in MS Excel and Vos-viewer. Inferences were drawn on significant aspects, such as publication growth trend, journal analysis and co-occurrence of keywords. The study revealed that the number of publications increased from 3 in 1992 to 166 in 2021. The number of citations also increased and peaked at 4314 in 2015. Following this, we clustered keywords using principle component analysis and worked out links between domains of vermicomposting. Vermicomposting conjoined to words substrate manipulation, quality improvement, heavy metal adsorption, and yield parameters. This implies that vermicompost is being explored for many alternate uses in addition to its use as a fertiliser. We concluded that vermicomposting is one of the promising technologies for waste recycling. It modulates plant growth and subdues stress in plants. Additionally, being an efficient adsorbent, it serves bioremediation of contaminated sites. Therefore, the future of this technology lies in synthesising nano-formulations, integrating into biosensor technology, simulating for predicting timelines under different conditions and making efforts to improve their adsorption.

Enhancement of benzo[a]pyrene mineralization: symbiotic biodegradation by Acinetobacter sp. strain HAP1 in Association with Cyanobacteriota sp. S66

The ability of Acinetobacter sp. strain HAP1, isolated from petroleum refinery effluent, to eliminate different concentrations (20, 40, 60, 80 and 100 mg/L) of Benzo[a]Pyrene degradation (BaP) was studied. A test to improve this degradation capacity was carried out by culturing the bacterial strain in association with a cyanobacteria. The results show a highly significant effect of the concentration of (BaP) and a very highly significant effect of the symbiosis between the bacterial strain and the cyanobacteria. This combination was able to significantly improve the (BaP) degradation rate by up to 18%. This degradation and especially in association leads to a complete mineralization of (BaP) and there is a difference in yield that can go up to 15%. Through molecular identification based on 16S rRNA gene sequence analysis, strains HAP1 and S66 were recognized as Acinetobacter sp. strain HAP1 and Cyanobacteriota sp. S66, respectively. Comparison of the retrieved sequences with the NCBI GenBank database was done, and the closest matches were found to be Acinetobacter pittii strain JD-10 for bacteria and Pseudochroococcus couteii strain PMC 885.14 for cyanobacteria.

Complete genome sequence of Paraburkholderia sp. strain 22B1P capable of utilizing 3-chlorobenzoate as a carbon source

Paraburkholderia sp. strain 22B1P utilizes 3-chlorobenzoate as a carbon source. Complete genome sequencing of strain 22B1P revealed two chromosomes and two plasmids. The genes involved in the conversion of 3-chlorobenzoate to 3-chlorocatechol and those involved in the conversion of 3-chlorocatechol to 3-oxoadipate were located on chromosomes 2 and 1, respectively.

Acetylene Tunes Microbial Growth During Aerobic Cometabolism of Trichloroethene

Microbial aerobic cometabolism is a possible treatment approach for large, dilute trichloroethene (TCE) plumes at groundwater contaminated sites. Rapid microbial growth and bioclogging pose a persistent problem in bioremediation schemes. Bioclogging reduces soil porosity and permeability, which negatively affects substrate distribution and contaminant treatment efficacy while also increasing the operation and maintenance costs of bioremediation. In this study, we evaluated the ability of acetylene, an oxygenase enzyme-specific inhibitor, to decrease biomass production while maintaining aerobic TCE cometabolism capacity upon removal of acetylene. We first exposed propane-metabolizing cultures (pure and mixed) to 5% acetylene (v v-1) for 1, 2, 4, and 8 d and we then verified TCE aerobic cometabolic activity. Exposure to acetylene overall decreased biomass production and TCE degradation rates while retaining the TCE degradation capacity. In the mixed culture, exposure to acetylene for 1-8 d showed minimal effects on the composition and relative abundance of TCE cometabolizing bacterial taxa. TCE aerobic cometabolism and incubation conditions exerted more notable effects on microbial ecology than did acetylene. Acetylene appears to be a viable approach to control biomass production that may lessen the likelihood of bioclogging during TCE cometabolism. The findings from this study may lead to advancements in aerobic cometabolism remediation technologies for dilute plumes.

Improved, reference quality genome sequence of the plastic-degrading greater wax moth, Galleria mellonella

Galleria mellonella is a pest of honeybees in many countries because its larvae feed on beeswax. However, G. mellonella larvae can also eat various plastics, including polyethylene, polystyrene and polypropylene, so the species is garnering increasing interest as a tool for plastic biodegradation research. This paper presents an improved genome (99.3% completed lepidoptera_odb10 BUSCO; genome mode) for G. mellonella. This 472 Mb genome is in 221 contigs with an N50 of 6.4 MB and contains 13,604 protein-coding genes. Genes that code for known and putative polyethylene-degrading enzymes and their similarity to proteins found in other Lepidoptera are highlighted. An analysis of secretory proteins more likely to be involved in the plastic catabolic process has also been carried out.

Toxicity and bioremediation of the lead: a critical review

Lead is a naturally occurring, bluish-gray metal that is found in small quantities in the earth's crust. The existing literature demonstrates that non-biodegradable character and continuous use results in accumulation of lead concentration in the environment and causes various ill effects such as neurotoxicity, change in psychological and behavioral development of different organisms. Nowadays the most effective technique in the revival of the environment is bioremediation and it is environmentally friendly and cost-effective. Bacterial strains such as Oceanobacillus profundus and Lactobacillus acidophilus ATCC4356 have the ability to reduce lead 97% and 73.9%, respectively. Similarly some species of algae and fungal strains also showed lead removal efficiency as 74% (spirulina), 97.1% (Chlorella kessleri), 95.5% (Penicillium janthinillum) and 86% (Aspergillus flavus). Biodegradation of lead by various microbes would be the most efficient and sustainable approach. This review focuses on toxicity, fate of lead in the environment and its microbial degradation.

In silico and in vitro assays suggests Congo red dye degradation by a Lentinus sp. laccase enzyme

Laccase is a superfamily of ligninolytic enzymes known to degrade a wide variety of xenobiotics, including synthetic dyes. Congo Red (CR) has a diazo dye function, carcinogenic and mutagenic potential, and is currently applied in clinical analysis. The objective of this work was to produce and characterize the crude extract of Lentinus sp. in semi-solid fermentation (FSS) and perform in vitro and in silico studies to assess the potential of the crude extract to discolor the CR dye. Laccase activity was determined using ABTS as substrate and characterized. The in vitro discoloration was carried out using experimental design 22 at room temperature and monitored at 340 nm for 24h. Molecular docking and molecular dynamics simulations were performed between laccase and CR. The maximum laccase activity production was 29.63 U L-1 with six days of FSS. The optimal temperature and pH were 50 °C and 3.0, respectively. Discoloration of the CR dye was obtained only in tests containing CuSO4. Laccase formed stable complexes with the dye, presenting negative binding energy values ranging from -70.94 to -63.16 kcal mol-1 and the occurrence of seven hydrogen bonds. Molecular dynamics results showed the stability of the system (RMSD ranging from 1.0 to 2.5 Ä) and protein-ligand interaction along simulation. RMSF values pointed residues at the end of chains A (residues 300 to 305, 480 to 500) and B (residues 650 to 655 and 950 to 1000) as the most flexible regions of the laccase. This study highlighted the enzymatic action in the bioremediation of CR in vitro in agreement with the in silico simulations that demonstrate the enzyme potential.Communicated by Ramaswamy H. Sarma.

Bacteriophage Engineering for Improved Copper Ion Binding

In this study, fd viruses are genetically modified to display seven cropped versions (H, HG, HGF, HGFA, HGFAN, HGFANV and HGFANVA) of the previously identified Cu(II) specific peptide (HGFANVA). Atomic force microscopy (AFM) imaging reveals the typical filamentous structures of recombinant phages with thicknesses of ≈2-5 nm in dry state. Scanning electron microscopy (SEM) imaging shows that HGFANVA viruses form larger elongated assemblies than H viruses that are deposited with a mineral layer after Cu(II) treatment. C and N peaks are detected for virus samples through Energy dispersive X-ray spectroscopy (EDX) analyses confirming the presence of phage organic material. Cu peak is only detected for engineered viruses after Cu(II) exposure. Enzyme-linked immunosorbent assay (ELISA) analyses show the selective Cu(II) binding of engineered phages. Agarose gel electrophoresis (AGE) and zeta potential analyses reveal negative surface charges of engineered viral constructs. Positively charged Cytopore beads are coated with bacteriophages and used for Cu(II) ion sorption studies. ICP-MS analyses clearly show the improved Cu(II) binding of engineered viruses with respect to wild-type fd phages. Such bottom-up constructed, genetically engineered virus-based biomaterials may be applied in bioremediation studies targeting metal species from environmental samples.

Microbial metabolism of caffeine and potential applications in bioremediation

With increasing global consumption of caffeine-rich products, such as coffee, tea, and energy drinks, there is also an increase in urban and processing waste full of residual caffeine with limited disposal options. This waste caffeine has been found to leach into the surrounding environment where it poses a threat to microorganisms, insects, small animals, and entire ecosystems. Growing interest in harnessing this environmental contaminant has led to the discovery of 79 bacterial strains, eight yeast strains, and 32 fungal strains capable of metabolizing caffeine by N-demethylation and/or C-8 oxidation. Recently observed promiscuity of caffeine-degrading enzymes in vivo has opened up the possibility of engineering bacterial strains capable of producing a wide variety of caffeine derivatives from a renewable resource. These engineered strains can be used to reduce the negative environmental impact of leached caffeine-rich waste through bioremediation efforts supplemented by our increasing understanding of new techniques such as cell immobilization. Here, we compile all of the known caffeine-degrading microbial strains, discuss their metabolism and related enzymology, and investigate their potential application in bioremediation.

Enhanced Strontium Removal through Microbially Induced Carbonate Precipitation by Indigenous Ureolytic Bacteria

Microbial ureolysis offers the potential to remove metals including Sr2+ as carbonate minerals via the generation of alkalinity coupled to NH4+ and HCO3- production. Here, we investigated the potential for bacteria, indigenous to sediments representative of the U.K. Sellafield nuclear site where 90Sr is present as a groundwater contaminant, to utilize urea in order to target Sr2+-associated (Ca)CO3 formation in sediment microcosm studies. Strontium removal was enhanced in most sediments in the presence of urea only, coinciding with a significant pH increase. Adding the biostimulation agents acetate/lactate, Fe(III), and yeast extract to further enhance microbial metabolism, including ureolysis, enhanced ureolysis and increased Sr and Ca removal. Environmental scanning electron microscopy analyses suggested that coprecipitation of Ca and Sr occurred, with evidence of Sr associated with calcium carbonate polymorphs. Sr K-edge X-ray absorption spectroscopy analysis was conducted on authentic Sellafield sediments stimulated with Fe(III) and quarry outcrop sediments amended with yeast extract. Spectra from the treated Sellafield and quarry sediments showed Sr2+ local coordination environments indicative of incorporation into calcite and vaterite crystal structures, respectively. 16S rRNA gene analysis identified ureolytic bacteria of the genus Sporosarcina in these incubations, suggesting they have a key role in enhancing strontium removal. The onset of ureolysis also appeared to enhance the microbial reduction of Fe(III), potentially via a tight coupling between Fe(III) and NH4+ as an electron donor for metal reduction. This suggests ureolysis may support the immobilization of 90Sr via coprecipitation with insoluble calcium carbonate and cofacilitate reductive precipitation of certain redox active radionuclides, e.g., uranium.

Exploiting the role of plant growth promoting rhizobacteria in reducing heavy metal toxicity of pepper (Capsicum annuum L.)

Microorganisms are cost-effective and eco-friendly alternative methods for removing heavy metals (HM) from contaminated agricultural soils. Therefore, this study aims to identify and characterize HM-tolerant (HMT) plant growth-promoting rhizobacteria (PGPR) isolated from industry-contaminated soils to determine their impact as bioremediators on HM-stressed pepper plants. Four isolates [Pseudomonas azotoformans (Pa), Serratia rubidaea (Sr), Paenibacillus pabuli (Pp) and Bacillus velezensis (Bv)] were identified based on their remarkable levels of HM tolerance in vitro. Field studies were conducted to evaluate the growth promotion and tolerance to HM toxicity of pepper plants grown in HM-polluted soils. Plants exposed to HM stress showed improved growth, physio-biochemistry, and antioxidant defense system components when treated with any of the individual isolates, in contrast to the control group that did not receive PGPR. The combined treatment of the tested HMT PGPR was, however, relatively superior to other treatments. Compared to no or single PGPR treatment, the consortia (Pa+Sr+Pp+Bv) increased the photosynthetic pigment contents, relative water content, and membrane stability index but lowered the electrolyte leakage and contents of malondialdehyde and hydrogen peroxide by suppressing the (non) enzymatic antioxidants in plant tissues. In pepper, Cd, Cu, Pb, and Ni contents decreased by 88.0-88.5, 63.8-66.5, 66.2-67.0, and 90.2-90.9% in leaves, and 87.2-88.1, 69.4-70.0%, 80.0-81.3, and 92.3%% in fruits, respectively. Thus, these PGPR are highly effective at immobilizing HM and reducing translocation in planta. These findings indicate that the application of HMT PGPR could be a promising "bioremediation" strategy to enhance growth and productivity of crops cultivated in soils contaminated with HM for sustainable agricultural practices.

Exploring biodegradative efficiency: a systematic review on the main microplastic-degrading bacteria

Introduction

Microplastics (MPs) are widely distributed in the environment, causing damage to biota and human health. Due to their physicochemical characteristics, they become resistant particles to environmental degradation, leading to their accumulation in large quantities in the terrestrial ecosystem. Thus, there is an urgent need for measures to mitigate such pollution, with biological degradation being a viable alternative, where bacteria play a crucial role, demonstrating high efficiency in degrading various types of MPs. Therefore, the study aimed to identify bacteria with the potential for MP biodegradation and the enzymes produced during the process.

Methods

The methodology used followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol.

Results and Discussion

The research yielded 68 eligible studies, highlighting bacteria from the genera Bacillus, Pseudomonas, Stenotrophomonas, and Rhodococcus as the main organisms involved in MP biodegradation. Additionally, enzymes such as hydrolases and alkane hydroxylases were emphasized for their involvement in this process. Thus, the potential of bacterial biodegradation is emphasized as a promising pathway to mitigate the environmental impact of MPs, highlighting the relevance of identifying bacteria with biotechnological potential for large-scale applications in reducing MP pollution.

Draft Genome Sequence of Pantoea sp. Strain MHSD4, a Bacterial Endophyte With Bioremediation Potential

Pantoea sp. strain MHSD4 is a bacterial endophyte isolated from the leaves of the medicinal plant Pellaea calomelanos. Here, we report on strain MHSD4 draft whole genome sequence and annotation. The draft genome size of Pantoea sp. strain MHSD4 is 4 647 677 bp with a G+C content of 54.2% and 41 contigs. The National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline tool predicted a total of 4395 genes inclusive of 4235 protein-coding genes, 87 total RNA genes, 14 non-coding (nc) RNAs and 70 tRNAs, and 73 pseudogenes. Biosynthesis pathways for naphthalene and anthracene degradation were identified. Putative genes involved in bioremediation such as copA, copD, cueO, cueR, glnGm, and trxC were identified. Putative genes involved in copper homeostasis and tolerance were identified which may suggest that Pantoea sp. strain MHSD4 has biotechnological potential for bioremediation of heavy metals.

Draft genome sequence of Exiguobacterium sp. strain MMG028 isolated from a salt marsh

Here, we report the draft genome sequence of Exiguobacterium sp. strain MMG028, isolated from Rose Creek, San Diego, CA, USA, assembled and analyzed by undergraduate students participating in a marine microbial genomics course. A genomic comparison suggests that MMG028 is a novel species, providing a resource for future microbiology and biotechnology investigations.

Preparation of microbial agent immobilized composites for Cr(VI) removal from wastewater

Because of its extreme toxicity and health risks, hexavalent chromium [Cr(VI)] has been identified as a major environmental contaminant. Bioreduction is considered as one of effective techniques for cleaning up Cr(VI)-contaminated sites, but the remediation efficiency needs to be enhanced. Here, a novel immobilized microbial agent was produced by immobilizing Bacillus cereus ZY-2009 with sodium alginate (SA) using polyvinyl alcohol (PVA) and activated carbon (AC). To evaluate the decrease of Cr(VI) by immobilized bacterial agents, batch tests were conducted with varying immobilization conditions, immobilization carriers, and dosages of medication. The removal of Cr(VI) by the agent prepared by the composite immobilization method was better than that by the adsorption and encapsulation methods. The optimal preparation conditions were the fraction of magnetic PVA was 5.00%, the fraction of SA was 4.00%, the fraction of CaCl2 was 4.00%, and the calcification time was 12 h. The experimental results indicated that PVA/SA/AC agents accelerated the reduction rate of Cr(VI). The removal rate of Cr(VI) by immobilized cells (90.5%) under ideal conditions was substantially higher than that of free cells (11.0%). This novel agent had a large specific surface area and a rich pore structure, accounting for its high reduction rate. The results suggest that the PVA/SA/AC immobilized Bacillus cereus ZY-2009 agent has great potential to remove Cr(VI) from wastewater treatment systems.

Molecular and metabolic characterization of petroleum hydrocarbons degrading Bacillus cereus

Hydrocarbon constituents of petroleum are persistent, bioaccumulated, and bio-magnified in living tissues, transported to longer distances, and exert hazardous effects on human health and the ecosystem. Bioaugmentation with microorganisms like bacteria is an emerging approach that can mitigate the toxins from environmental sources. The present study was initiated to target the petroleum-contaminated soil of gasoline stations situated in Lahore. Petroleum degrading bacteria were isolated by serial dilution method followed by growth analysis, biochemical and molecular characterization, removal efficiency estimation, metabolites extraction, and GC-MS of the metabolites. Molecular analysis identified the bacterium as Bacillus cereus, which exhibited maximum growth at 72 hours and removed 75% petroleum. Biochemical characterization via the Remel RapID™ ONE panel system showed positive results for arginine dehydrolase (ADH), ornithine decarboxylase (ODC), lysine decarboxylase (LDC), o-nitrophenyl-β-D-galactosidase (ONPG), p-nitrophenyl-β-D-glucosidase (βGLU), p-nitrophenyl-N-acetyl-β-D-glucosaminidase (NAG), malonate (MAL), adonitol fermentation (ADON), and tryptophane utilization (IND). GC-MS-based metabolic profiling identified alcohols (methyl alcohol, o-, p- and m-cresols, catechol, and 3-methyl catechol), aldehydes (methanone, acetaldehyde, and m-tolualdehyde), carboxylic acid (methanoic acid, cis,cis-muconic acid, cyclohexane carboxylic acid and benzoic acid), conjugate bases of carboxylic acids (benzoate, cis,cis-muconate, 4-hydroxybenzoate, and pyruvate) and cycloalkane (cyclohexene). It suggested the presence of methane, methylcyclohexane, toluene, xylene, and benzene degradation pathways in B. cereus.

The critical roles of propanethiol oxidoreductase and sulfide-quinone oxidoreductase in the propanethiol catabolism pathway in Pseudomonas putida S-1

Propanethiol (PT) is a hazardous pollutant that poses risks to both the environment and human well-being. Pseudomonas putida S-1 has been identified as a microorganism capable of utilizing PT as its sole carbon source. However, the metabolic pathway responsible for PT degradation in P. putida S-1 has remained poorly understood, impeding its optimization and practical application. In this study, we investigated the catabolic network involved in PT desulfurization with P. putida S-1 and identified key gene modules crucial to this process. Notably, propanethiol oxidoreductase (PTO) catalyzes the initial degradation of PT, a pivotal step for P. putida S-1's survival on PT. PTO facilitates the oxidation of PT, resulting H2S, H2O2, and propionaldehyde (PA). Catalase-peroxidase catalyzes the conversion of H2O2 to oxygen and water, while PA undergoes gradual conversion to Succinyl-CoA, which is subsequently utilized in the tricarboxylic acid cycle. H2S is digested in a comprehensive desulfurization network where sulfide-quinone oxidoreductase (SQOR) predominantly converts it to sulfane sulfur. The transcriptome analysis suggests that sulfur can be finally converted to sulfite or sulfate and exported out of the cell. The PT degradation capacity of P. putida S-1 was enhanced by increasing the transcription level of PTO and SQOR genes in vivo.IMPORTANCEThis work investigated the PT catabolism pathway in Pseudomonas putida S-1, a microorganism capable of utilizing PT as the sole carbon source. Critical genes that control the initiation of PT degradation were identified and characterized, such as pto and sqor. By increasing the transcription level of pto and sqor genes in vivo, we have successfully enhanced the PT degradation efficiency and growth rate of P. putida S-1. This work does not only reveal a unique PT degradation pathway but also highlights the potential of enhancing the microbial desulfurization process in the bioremediation of thiol-contaminated environment.

Purification Effect of Water Eutrophication Using the Mosaic System of Submerged-Emerged Plants and Growth Response

Aquatic plants play a crucial role in the sustainable management of eutrophic water bodies, serving as a valuable tool for water purification. However, the effectiveness of using aquatic plants for improving water quality is influenced by landscape considerations. In practical applications, challenges arise concerning low purification efficiency and compromised aesthetic appeal when utilizing plants for water purification. To address these issues, this study aimed to examine the impact of aquatic plants on the purification of simulated landscape water bodies, specifically focusing on the effectiveness of the mosaic system of submerged-emerged plants in remediating eutrophic water bodies. Our findings indicated that individual aquatic plants exhibited limited efficacy in pollutant (total nitrogen, total phosphorus, ammonia nitrogen, and chemical oxygen demand) removal. However, when combined in appropriate proportions, submerged plants could enhance species growth and improve the purification efficiency of polluted water bodies. Notably, the mosaic system of submerged-emerged plants neither significantly promoted nor inhibited the growth of each other, but it effectively removed pollutants from the simulated water bodies and inhibited turbidity increase. The comprehensive evaluation ranked the purification capacity as Canna indica-submerged plants combination (C + S) > Thalia dealbata-submerged plants combination (T + S) > Iris pseudacorus-submerged plants combination (I + S) > Lythrum salicaria-submerged plants combination (L + S). Both C + S and T + S configurations effectively mitigated the rise of water turbidity and offered appealing landscape benefits, making them viable options for practical applications in urban landscape water bodies. Our study highlights that a submerged-emerged mosaic combination is a means of water purification that combines landscape aesthetics and purification efficiency.

Probiotic Cities: microbiome-integrated design for healthy urban ecosystems

Combining microbiome science and biointegrated design offers opportunities to help address the intertwined challenges of urban ecosystem degradation and human disease. Biointegrated materials have the potential to combat superbugs and remediate pollution while inoculating landscape materials with microbiota can promote human immunoregulation and biodiverse green infrastructure, contributing to 'probiotic cities'.

Removal of Chromium (III) and Reduction in Toxicity in a Primary Tannery Effluent Using Two Floating Macrophytes

Trivalent chromium (Cr(III)) is a contaminant with toxic activity. Its presence in waters and soils is usually related to industrial activities such as tanneries. The aim of this study was to compare the removal of Cr(III) in hydroponic solutions and tannery effluents using two floating macrophytes: Salvinia auriculata and Eichhornia crassipes. First, to determine the chromium removal capacity in solution and the bioaccumulation factor (BAF) in tissues of each plant, experiments were set up with contaminated solutions with Cr(III) concentrations of 2, 5, 10, 20, and 40 mg/L. Subsequently, both plant species were exposed to a primary tannery effluent contaminated with 12 mg/L of Cr(III) in order to study the removal capacity of organic and inorganic matter, as well as the acute toxicity in the water flea (Daphnia magna) and genotoxicity in zebrafish (Danio rerio). Tests carried out on nutrient solutions revealed that both plants have a high capacity for removing Cr(III) in solution. The BAF in tissues was higher in E. crassipes compared to S. auriculata. In the experiments with a tannery effluent, both species presented low nutrient and organic matter removal efficiency, but they showed good Cr(III) removal capacity, with average reduction values of 57% for S. auriculata and 54% for E. crassipes after 72 h of exposure. E. crassipes contributed most to the reduction in acute toxicity in D. magna, while S. auriculata did not show a similar effect. However, both plant species managed to reduce the genotoxicity marker in D. rerio when compared with the initial effluent and the control.

Draft genome sequence of Priestia megaterium AB-S79 strain isolated from active gold mine

We screened and isolated Priestia megaterium strain AB-S79 from active gold mine soil, then sequenced its genome to unravel its biosynthetic traits. The isolate with a 5.7-Mb genome can be utilized as a reference in genome-guided strain selection for metabolic engineering and other biotechnological operations.

Harnessing Fermentation May Enhance the Performance of Biological Sulfate-Reducing Bioreactors

Biological sulfate reduction (BSR) represents a promising strategy for bioremediation of sulfate-rich waste streams, yet the impact of metabolic interactions on performance is largely unexplored. Here, genome-resolved metagenomics was used to characterize 17 microbial communities in reactors treating synthetic sulfate-contaminated solutions. Reactors were supplemented with lactate or acetate and a small amount of fermentable substrate. Of the 163 genomes representing all the abundant bacteria, 130 encode 321 NiFe and FeFe hydrogenases and all genomes of the 22 sulfate-reducing microorganisms (SRM) encode genes for H2 uptake. We observed lactate oxidation solely in the first packed bed reactor zone, with propionate and acetate oxidation in the middle and predominantly acetate oxidation in the effluent zone. The energetics of these reactions are very different, yet sulfate reduction kinetics were unaffected by the type of electron donor available. We hypothesize that the comparable rates, despite the typically slow growth of SRM on acetate, are a result of the consumption of H2 generated by fermentation. This is supported by the sustained performance of a predominantly acetate-supplemented stirred tank reactor dominated by diverse fermentative bacteria encoding FeFe hydrogenase genes and SRM capable of acetate and hydrogen consumption and CO2 assimilation. Thus, addition of fermentable substrates to stimulate syntrophic relationships may improve the performance of BSR reactors supplemented with inexpensive acetate.

Differences in soil bacterial community structure during the remediation of Cd-polluted cotton fields by biochar and biofertilizer in Xinjiang, China

Introduction

Heavy metal pollution is a major worldwide environmental problem. Many remediation techniques have been developed, these techniques have different performance in different environments.

Methods

In this study, soil sampling was conducted in multiple cotton fields in Xinjiang, China, and found that cadmium (Cd) was the most abundant soil heavy metal. Then, to find the most suitable technique for the remediation of Cd pollution in cotton fields, a two-year study was conducted to explore the effects of cotton straw-derived biochar (BC, 3%) and Bacillus-based biofertilizer (BF, 1.5%) on cotton Cd uptake and transport and soil microbial community structure under Cd exposure conditions (soil Cd contents: 1, 2, and 4 mg·kg-1).

Results

The results showed that the bioaccumulation coefficients (Cd content of cotton organs / soil available Cd content) of cotton roots, stems, leaves, and buds/bolls reduced by 15.93%, 14.41%, 23.53%, and 20.68%, respectively after the application of BC, and reduced by 16.83%, 17.15%, 22.21%, and 26.25%, respectively after the application of BF, compared with the control (no BC and BF). Besides, the application of BC and BF reduced the transport of Cd from soil to root system, and enhanced the diversity of soil bacterial communities (dominant species: Alphaproteobacteria and Actinobacteria) and the metabolic functions related to amino acid synthesis. It was worth noting that the differential species for BF group vs BC group including Alphaproteobacteria, Gemmatimonadetes, Bacilli, and Vicinamibacteria were associated with the enrichment and transport of Cd, especially the transport of Cd from cotton roots to stems.

Discussion

Therefore, the application of BC and BF changed the soil bacterial diversity in Cd-polluted cotton field, and then promoted the transport of Cd in cotton, ultimately improving soil quality. This study will provide a reference for the selection of soil heavy metal pollution remediation techniques in Xinjiang, China.

Bottom-up construction and screening of algae-bacteria consortia for pollutant biodegradation

Microbial communities have been used as important biological tools for a variety of purposes associated with agriculture, the food industry and human health. Artificial engineering of microbial communities is an emerging field of research motivated by finding stable and efficient microbial systems. However, the successful design of microbial communities with desirable functions not only requires profound understanding of microbial activities, but also needs efficient approaches to piece together the known microbial traits to give rise to more complex systems. This study demonstrates the bottom-up integration of environmentally isolated phototrophic microalgae and chemotrophic bacteria as artificial consortia to bio-degrade selected volatile organic compounds (VOCs). A high throughput screening method based on 96-well plate format was developed for discovering consortia with bioremediation potential. Screened exemplar consortia were verified for VOCs degradation performance, among these, certain robust consortia were estimated to have achieved efficiencies of 95.72% and 92.70% and near 100% removal (7 days) of benzene, toluene, and phenol, respectively, with initial concentrations of 100 mg/L. VOCs degradation by consortia was mainly attributed to certain bacteria including Rhodococcus erythropolis, and Cupriavidus metallidurans, and directly contributed to the growth of microalgae Coelastrella terrestris (R = 0.82, p < 0.001). This work revealed the potential of converting VOCs waste into algal biomass by algae-bacteria consortia constructed through a bottom-up approach. The screening method enables rapid shortlisting of consortia combinatorial scenarios without prior knowledge about the individual strains or the need for interpreting complex microbial interactions.

Biodegradation of used engine oil by lead-resistant bacteria Acinetobacter sp.HAR20 newly isolated from harbour seawater (Oran, Algeria)

This paper focuses on the degrading capacity of various hydrocarbon fractions of used engine oils (UEO) by marine microorganisms, as well as the biosorption of heavy metals. A bacterial strain with a significant capability to grow on UEO as a sole source of carbon and energy was isolated from harbour seawater samples (Oran, Algeria). The molecular identification by sequencing the 16S rDNA gene revealed that the bacterium matched Acinetobacter baumanii with 96.84% homology similarity. Thus, strain HAR20 was named Acinetobacter sp.HAR20. The degradation rate of UEO (at 1%, v/v) obtained after 15 days of incubation was about 53.4 ± 4.2%. The results of GC-MS analysis of the biodegraded residual motor oil indicate that strain Acinetobacter sp.HAR20 degrades alkanes with chain lengths ranging from C4 to C48 completely or to shorter fractions. The bacterium was also able to degrade all aromatic compounds of UEO, including polycyclic aromatic hydrocarbons (alkylated and no alkylated naphthalene, alkylated phenanthrene, and fluorene). The strain Acinetobacter sp.HAR20 exhibited different degrees of resistance to the heavy metals tested (Cd, Zn, Ni, Cu, Fe, and Pb). The highest tolerance was obtained for Pb (600 mg.l-1). The study of lead biosorption at a concentration of 300 mg.l-1 revealed that the bacterium displayed a removal rate of 57.47 ± 7.5%. The strain Acinetobacter sp.HAR20 has shown an interesting biodegradation potential; therefore, it could be proposed as a choice for the bioremediation of contaminated seawater by used engine oils.

Metabolic Synergy of Dehalococcoides Populations Leading to Greater Reductive Dechlorination of Polychlorinated Biphenyls

Polychlorinated biphenyls (PCBs) are dioxin-like pollutants that cause persistent harm to life. Organohalide-respiring bacteria (OHRB) can detoxify PCBs via reductive dechlorination, but individual OHRB are potent in dechlorinating only specific PCB congeners, restricting the extent of PCB dechlorination. Moreover, the low biomass of OHRB frequently leads to the slow natural attenuation of PCBs at contaminated sites. Here we constructed defined microbial consortia comprising various combinations of PCB-dechlorinating Dehalococcoides strains (CG1, CG4, and CG5) to successfully enhance PCB dechlorination. Specifically, the defined consortia consisting of strains CG1 and CG4 removed 0.28-0.44 and 0.23-0.25 more chlorine per PCB from Aroclor1260 and Aroclor1254, respectively, compared to individual strains, which was attributed to the emergence of new PCB dechlorination pathways in defined consortia. Notably, different Dehalococcoides populations exhibited similar growth when cocultivated, but temporal differences in the expression of PCB reductive dehalogenase genes indicated their metabolic synergy. Bioaugmentation with individual strains (CG1, CG4, and CG5) or defined consortia led to greater PCB dechlorination in wetland sediments, and augmentation with the consortium comprising strains CG1 and CG4 resulted in the greatest PCB dechlorination. These findings collectively suggest that simultaneous application of multiple Dehalococcoides strains, which catalyze complementary dechlorination pathways, is an effective strategy to accelerate PCB dechlorination.

Degradation of a mixture of 13 polycyclic aromatic hydrocarbons by commercial effective microorganisms

The study focused on the contribution of effective microorganisms (EM) and their consortia, used in commercial biological preparations and formulations for soil revitalization, to the degradation of a mixture of 13 polycyclic aromatic hydrocarbons (PAHs) commonly found in the soil environment. PAHs, diverse forms of which are present in the environment, never occur individually but always as a part of a chemical mixture. Therefore, the research presented in this article, focusing on the EM impact on the mixture of PAHs, reflects the conditions most similar to natural ones. On Day 35 of the experiment, PAH levels decreased by 75.5-95.5%. The highest PAHs degradation efficiency was achieved for fluorene, with a preparation containing eight bacteria strains from the Bacillus genus: B. coagulans, B. amyloliquefaciens, B. laterosporus, B. licheniformis, B. mucilaginosus, B. megaterium, B. polymyxa, and B. pumilus. All tested preparations containing bacterial consortia and a preparation with the yeast S. cerevisiae intensified the PAHs degradation more effectively than formulations including only the yeast Yarrowia lipolytica or a mixture of Debaryomyces hansenii and Bacillus. The designed and proposed research will contribute to the development of biotechnological methods - bioremediation by microorganisms that are safe for the human and environment health.

Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400

Introduction

Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress.

Methods

By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400.

Results

Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern.

Discussions

This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.

Acidified groundnut cake for enhanced bio adsorption of anionic textile dye Reactive Red 195

This study focuses on the improvement of bioremediation of textile dye Reactive Red 195 using agro-industrial waste, groundnut oil cake (GNOC) obtained after oil-pressing. The treatment of GNOC with 1 N H2SO4 had resulted in physiochemical changes on the insoluble porous adsorbent, which improved their adsorption efficiency. The dye removal efficiency increased from 55% to 94% on acidification of GNOC. The raw groundnut oil cake (RGNOC) and acid-treated groundnut oil cake (AGNOC) were characterized using Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), X-ray diffraction, and zeta potential. The rate and efficiency of dye adsorption were examined using adsorption kinetics and isotherm models. The results confirm that acid-treated GNOC eliminates impurities, alter the surface functional groups, and significantly increase porous surface areas of RGNOC. The investigation of key factors such as contact time, initial concentration of dye, static/agitation impact, particle size, and adsorbent dose had significantly influenced adsorption capacity of GNOC. Adsorption of dye fits best into the Langmuir model and equilibrium data of dye on AGNOC was explained by psuedo-second-order reaction with maximum adsorption capacity of 12.65 mg/g. This emphasis AGNOC has a very excellent potential to remove the textile dye Reactive Red dye from industrial effluent.

Microbially Induced Calcium Carbonate Precipitation as a Bioremediation Technique for Mining Waste

Mining waste represents a global issue due to its potential of generating acidic or alkaline leachate with high concentrations of metals and metalloids (metal(loid)s). Microbial-induced calcium carbonate precipitation (MICP) is an engineering tool used for remediation. MICP, induced via biological activity, aims to precipitate calcium carbonate (CaCO3) or co-precipitate other metal carbonates (MCO3). MICP is a bio-geochemical remediation method that aims to immobilize or remove metal(loid)s via enzyme, redox, or photosynthetic metabolic pathways. Contaminants are removed directly through immobilization as mineral precipitates (CaCO3 or MCO3), or indirectly (via sorption, complexes, or inclusion into the crystal structure). Further, CaCO3 precipitates deposited on the surface or within the pore spaces of a solid matrix create a clogging effect to reduce contaminant leachate. Experimental research on MICP has shown its promise as a bioremediation technique for mining waste. Additional research is required to evaluate the long-term feasibility and potential by-products of MICP-treated/stabilized waste.

A Review about the Mycoremediation of Soil Impacted by War-like Activities: Challenges and Gaps

(1) Background: The frequency and intensity of war-like activities (war, military training, and shooting ranges) worldwide cause soil pollution by metals, metalloids, explosives, radionuclides, and herbicides. Despite this environmentally worrying scenario, soil decontamination in former war zones almost always involves incineration. Nevertheless, this practice is expensive, and its efficiency is suitable only for organic pollutants. Therefore, treating soils polluted by wars requires efficient and economically viable alternatives. In this sense, this manuscript reviews the status and knowledge gaps of mycoremediation. (2) Methods: The literature review consisted of searches on ScienceDirect and Web of Science for articles (1980 to 2023) on the mycoremediation of soils containing pollutants derived from war-like activities. (3) Results: This review highlighted that mycoremediation has many successful applications for removing all pollutants of war-like activities. However, the mycoremediation of soils in former war zones and those impacted by military training and shooting ranges is still very incipient, with most applications emphasizing explosives. (4) Conclusion: The mycoremediation of soils from conflict zones is an entirely open field of research, and the main challenge is to optimize experimental conditions on a field scale.

Arsenic Contamination of Groundwater Is Determined by Complex Interactions between Various Chemical and Biological Processes

At a great many locations worldwide, the safety of drinking water is not assured due to pollution with arsenic. Arsenic toxicity is a matter of both systems chemistry and systems biology: it is determined by complex and intertwined networks of chemical reactions in the inanimate environment, in microbes in that environment, and in the human body. We here review what is known about these networks and their interconnections. We then discuss how consideration of the systems aspects of arsenic levels in groundwater may open up new avenues towards the realization of safer drinking water. Along such avenues, both geochemical and microbiological conditions can optimize groundwater microbial ecology vis-à-vis reduced arsenic toxicity.

Environmentally Friendly Degradation and Detoxification of Rifampicin by a Bacterial Laccase and Hydrogen Peroxide

Antibiotics are micropollutants accumulating in our rivers and wastewaters, potentially leading to bacterial antibiotic resistance, a worldwide problem to which there is no current solution. Here, we have developed an environmentally friendly two-step process to transform the antibiotic rifampicin (RIF) into non-antimicrobial compounds. The process involves an enzymatic oxidation step by the bacterial CotA-laccase and a hydrogen peroxide bleaching step. NMR identified rifampicin quinone as the main product of the enzymatic oxidation. Growth of Escherichia coli strains in the presence of final degradation products (FP) and minimum inhibitory concentration (MIC) measurements confirmed that FP are non-anti-microbial compounds, and bioassays suggest that FP is not toxic to eukaryotic organisms. Moreover, competitive fitness assays between susceptible and RIF-resistant bacteria show that susceptible bacteria is strongly favoured in the presence of FP. Our results show that we have developed a robust and environmentally friendly process to effectively remediate rifampicin from antibiotic contaminated environments.

Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates

IMPORTANCE

Polycyclic aromatic hydrocarbon (PAH) pollution is widespread throughout marine environments and significantly affects native flora and fauna. Investigating microbes responsible for degrading PAHs in these environments provides a greater understanding of natural attenuation in these systems. In addition, the use of culture-based approaches to inform bioinformatic and omics-based approaches is useful in identifying novel mechanisms of PAH degradation that elude genetic biomarker-based investigations. Furthermore, culture-based approaches allow for the study of PAH co-metabolism, which increasingly appears to be a prominent mechanism for PAH degradation in marine microbes.

Phytochemicals, Probiotics, Recombinant Proteins: Enzymatic Remedies to Pesticide Poisonings in Bees

The ongoing global decline of bees threatens biodiversity and food safety as both wild plants and crops rely on bee pollination to produce viable progeny or high-quality products in high yields. Pesticide exposure is a major driving force for the decline, yet pesticide use remains unreconciled with bee conservation since studies demonstrate that bees continue to be heavily exposed to and threatened by pesticides in crops and natural habitats. Pharmaceutical methods, including the administration of phytochemicals, probiotics (beneficial bacteria), and recombinant proteins (enzymes) with detoxification functions, show promise as potential solutions to mitigate pesticide poisonings. We discuss how these new methods can be appropriately developed and applied in agriculture from bee biology and ecotoxicology perspectives. As countless phytochemicals, probiotics, and recombinant proteins exist, this Perspective will provide suggestive guidance to accelerate the development of new techniques by directing research and resources toward promising candidates. Furthermore, we discuss practical limitations of the new methods mentioned above in realistic field applications and propose recommendations to overcome these limitations. This Perspective builds a framework to allow researchers to use new detoxification techniques more efficiently in order to mitigate the harmful impacts of pesticides on bees.

Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals

Organic pollutants are an increasing threat for wildlife and humans. Managing their removal is however complicated by the difficulties in predicting degradation rates. In this work, we demonstrate that the complexity of the pollutant profile, the set of co-existing contaminants, is a major driver of biodegradation in wastewater. We built representative assemblages out of one to five common pharmaceuticals (caffeine, atenolol, paracetamol, ibuprofen, and enalapril) selected along a gradient of biodegradability. We followed their individual removal by wastewater microbial communities. The presence of multichemical background pollution was essential for the removal of recalcitrant molecules such as ibuprofen. High-order interactions between multiple pollutants drove removal efficiency. We explain these interactions by shifts in the microbiome, with degradable molecules such as paracetamol enriching species and pathways involved in the removal of several organic pollutants. We conclude that pollutants should be treated as part of a complex system, with emerging pollutants potentially showing cascading effects and offering leverage to promote bioremediation.

Draft genome analysis for Enterobacter kobei, a promising lead bioremediation bacterium

Lead pollution of the environment poses a major global threat to the ecosystem. Bacterial bioremediation offers a promising alternative to traditional methods for removing these pollutants, that are often hindered by various limitations. Our research focused on isolating lead-resistant bacteria from industrial wastewater generated by heavily lead-containing industries. Eight lead-resistant strains were successfully isolated, and subsequently identified through molecular analysis. Among these, Enterobacter kobei FACU6 emerged as a particularly promising candidate, demonstrating an efficient lead removal rate of 83.4% and a remarkable lead absorption capacity of 571.9 mg/g dry weight. Furthermore, E. kobei FACU6 displayed a remarkable a maximum tolerance concentration (MTC) for lead reaching 3,000 mg/L. To further investigate the morphological changes in E. kobei FACU6 in response to lead exposure, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed. These analyses revealed significant lead adsorption and intracellular accumulation in treated bacteria in contrast to the control bacterium. Whole-genome sequencing was performed to gain deeper insights into E. kobei's lead resistance mechanisms. Structural annotation revealed a genome size of 4,856,454 bp, with a G + C content of 55.06%. The genome encodes 4,655 coding sequences (CDS), 75 tRNA genes, and 4 rRNA genes. Notably, genes associated with heavy metal resistance and their corresponding regulatory elements were identified within the genome. Furthermore, the expression levels of four specific heavy metal resistance genes were evaluated. Our findings revealed a statistically significant upregulation in gene expression under specific environmental conditions, including pH 7, temperature of 30°C, and high concentrations of heavy metals. The outstanding potential of E. kobei FACU6 as a source of diverse genes related to heavy metal resistance and plant growth promotion makes it a valuable candidate for developing safe and effective strategies for heavy metal disposal.

A systematic study on the characteristics and applications of laccases produced by fungi: insights on their potential for biotechnologies

Laccases are polyphenol oxidase enzymes and form the enzyme complex known for their role in wood decomposition and lignin degradation. The present study aimed to systematically review the state-of-the-art trends in scientific publications on laccase enzymes of the last 10 years. The main aspects checked included the laccase-producing fungal genera, the conditions of fungal growth and laccase production, the methods of immobilization, and potential applications of laccase. After applying the systematic search method 177 articles were selected to compound the final database. Although various fungi produce laccase, most studies were Trametes and Pleurotus genera. The submerged fermentation (SmF) has been the most used, however, the use of solid-state fermentation (SSF) appeared as a promising technique to produce laccase when using agro-industrial residues as substrates. Studies on laccase immobilization showed the covalent bonding and entrapment methods were the most used, showing greater efficiency of immobilization and a high number of enzyme reuses. The main use of the laccase was in bioremediation, especially in the discoloration of dyes from the textile industry and the degradation of pharmaceutical waste. Implications and consequences of all these findings in biotechnology and environment, as well as the trends and gaps of laccase research were discussed.