Bacilli-Mediated Degradation of Xenobiotic Compounds and Heavy Metals

Advancements in bacterial chemotaxis: Utilizing the navigational intelligence of bacteria and its practical applications

The fascinating world of microscopic life unveils a captivating spectacle as bacteria effortlessly maneuver through their surroundings with astonishing accuracy, guided by the intricate mechanism of chemotaxis. This review explores the complex mechanisms behind this behavior, analyzing the flagellum as the driving force and unraveling the intricate signaling pathways that govern its movement. We delve into the hidden costs and benefits of this intricate skill, analyzing its potential to propagate antibiotic resistance gene while shedding light on its vital role in plant colonization and beneficial symbiosis. We explore the realm of human intervention, considering strategies to manipulate bacterial chemotaxis for various applications, including nutrient cycling, algal bloom and biofilm formation. This review explores the wide range of applications for bacterial capabilities, from targeted drug delivery in medicine to bioremediation and disease control in the environment. Ultimately, through unraveling the intricacies of bacterial movement, we can enhance our comprehension of the intricate web of life on our planet. This knowledge opens up avenues for progress in fields such as medicine, agriculture, and environmental conservation.

Effect of toluene on siloxane biodegradation and microbial communities in biofilters

The removal of volatile methyl siloxanes (VMS) from landfill biogas is crucial for clean energy utilization. VMS are usually found together with aromatic compounds in landfill biogas of which toluene is the major representative. In the present study, two biofilters (BFs) packed with either woodchips and compost (WC) or perlite (PER) were used to study the (co-) removal of octamethyltrisiloxane (L3) and octamethylcyclotetrasiloxane (D4) from gas in presence and absence of toluene, used as a representative aromatic compound. The presence of low inlet toluene concentrations (315 ± 19 - 635 ± 80 mg toluene m-3) enhanced the VMS elimination capacity (EC) in both BFs by a factor of 1.8 to 12.6. The highest removal efficiencies for D4 (57.1 ± 1.1 %; EC = 0.12 ± 0.01 gD4 m-3 h-1) and L3 (52.0 ± 0.6 %; EC = 0.23 ± 0.01 gL3 m-3 h-1) were observed in the BF packed with WC. The first section of the BFs (EBRT = 9 min), where toluene was (almost) completely removed, accounted for the majority (87.7 ± 0.6 %) of the total VMS removal. Microbial analysis revealed the impact of VMS and toluene in the activated sludge, showing a clear selection for certain genera in samples influenced by VMS in the presence (X2) or absence (X1) of toluene, such as Pseudomonas (X1 = 0.91 and X2 = 12.0 %), Sphingobium (X1 = 0.09 and X2 = 4.04 %), Rhodococcus (X1 = 0.42 and X2 = 3.91 %), and Bacillus (X1 = 7.15 and X2 = 3.84 %). The significant maximum EC values obtained by the BFs (0.58 gVMS m-3 h-1) hold notable significance in a combined system framework as they could enhance the longevity of traditional physicochemical methods to remove VMS like activated carbon in diverse environmental scenarios.

How to deal with xenobiotic compounds through environment friendly approach?

Every year, a huge amount of lethal compounds, such as synthetic dyes, pesticides, pharmaceuticals, hydrocarbons, etc. are mass produced worldwide, which negatively affect soil, air, and water quality. At present, pesticides are used very frequently to meet the requirements of modernized agriculture. The Food and Agriculture Organization of the United Nations (FAO) estimates that food production will increase by 80% by 2050 to keep up with the growing population, consequently pesticides will continue to play a role in agriculture. However, improper handling of these highly persistent chemicals leads to pollution of the environment and accumulation in food chain. These effects necessitate the development of technologies to eliminate or degrade these pollutants. Degradation of these compounds by physical and chemical processes is expensive and usually results in secondary compounds with higher toxicity. The biological strategies proposed for the degradation of these compounds are both cost-effective and eco-friendly. Microbes play an imperative role in the degradation of xenobiotic compounds that have toxic effects on the environment. This review on the fate of xenobiotic compounds in the environment presents cutting-edge insights and novel contributions in different fields. Microbial community dynamics in water bodies, genetic modification for enhanced pesticide degradation and the use of fungi for pharmaceutical removal, white-rot fungi's versatile ligninolytic enzymes and biodegradation potential are highlighted. Here we emphasize the factors influencing bioremediation, such as microbial interactions and carbon catabolism repression, along with a nuanced view of challenges and limitations. Overall, this review provides a comprehensive perspective on the bioremediation strategies.

Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects

Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.

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.

Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments

Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.

Biofilm formation in xenobiotic-degrading microorganisms

The increased presence of xenobiotics affects living organisms and the environment at large on a global scale. Microbial degradation is effective for the removal of xenobiotics from the ecosystem. In natural habitats, biofilms are formed by single or multiple populations attached to biotic/abiotic surfaces and interfaces. The attachment of microbial cells to these surfaces is possible via the matrix of extracellular polymeric substances (EPSs). However, the molecular machinery underlying the development of biofilms differs depending on the microbial species. Biofilms act as biocatalysts and degrade xenobiotic compounds, thereby removing them from the environment. Quorum sensing (QS) helps with biofilm formation and is linked to the development of biofilms in natural contaminated sites. To date, scant information is available about the biofilm-mediated degradation of toxic chemicals from the environment. Therefore, we review novel insights into the impact of microbial biofilms in xenobiotic contamination remediation, the regulation of biofilms in contaminated sites, and the implications for large-scale xenobiotic compound treatment.

Effect of Lyoprotective Agents on the Preservation of Survival of a Bacillus cereus Strain PBG in the Freeze-Drying Process

Lyophilization is a widely employed long-term preservation method in which the bacterial survival rate largely depends on the cryoprotectant used. Bacillus cereus strain PBC was selected for its ability to thrive in environments contaminated with arsenic, lead, and cadmium, tolerate 500 ppm of free cyanide, and the presence of genes such as ars, cad, ppa, dap, among others, associated with the bioremediation of toxic compounds and enterotoxins (nheA, nheB, nheC). Following lyophilization, the survival rates for Mannitol 2.5%, Mannitol 10%, and Glucose 1% were 98.02%, 97.12%, and 96.30%, respectively, with the rates being lower than 95% for other sugars. However, during storage, for the same sugars, the survival rates were 78.71%, 97.12%, and 99.97%, respectively. In the cake morphology, it was found that the lyophilized morphology showed no relationship with bacterial survival rate. The best cryoprotectant for the PBC strain was 1% glucose since it maintained constant and elevated bacterial growth rates during storage, ensuring that the unique characteristics of the bacterium were preserved over time. These findings hold significant implications for research as they report a new Bacillus cereus strain with the potential to be utilized in bioremediation processes.

New roles for Bacillus thuringiensis in the removal of environmental pollutants

For a long time, the well-known Gram-positive bacterium Bacillus thuringiensis (Bt) has been extensively studied and developed as a biological insecticide for Lepidoptera and Coleoptera pests due to its ability to secrete a large number of specific insecticidal proteins. In recent years, studies have found that Bt strains can also potentially biodegrade residual pollutants in the environment. Many researchers have isolated Bt strains from multiple sites polluted by exogenous compounds and characterized and identified their xenobiotic-degrading potential. Furthermore, its pathway for degradation was also investigated at molecular level, and a number of major genes/enzymes responsible for degradation have been explored. At present, a variety of xenobiotics involved in degradation in Bt have been reported, including inorganic pollutants (used in the field of heavy metal biosorption and recovery and precious metal recovery and regeneration), pesticides (chlorpyrifos, cypermethrin, 2,2-dichloropropionic acid, etc.), organic tin, petroleum and polycyclic aromatic hydrocarbons, reactive dyes (congo red, methyl orange, methyl blue, etc.), and ibuprofen, among others. In this paper, the biodegrading ability of Bt is reviewed according to the categories of related pollutants, so as to emphasize that Bt is a powerful agent for removing environmental pollutants.

Current trends in bioremediation and bio-integrated treatment of petroleum hydrocarbons

Petroleum hydrocarbons and their derivatives constitute the leading group of environmental pollutants worldwide. In the present global scenario, petroleum and natural gas production, exploration, petroleum refining, and other anthropogenic activities produce huge amounts of hazardous petroleum wastes that accumulate in the terrestrial and marine environment. Due to their carcinogenic, neurotoxic, and mutagenic characteristics, petroleum pollutants pose severe risks to human health and exert ecotoxicological effects on the ecosystems. To mitigate petroleum hydrocarbons (PHs) contamination, implementing "green technologies" for effective cleanup and restoration of an affected environment is considered as a pragmatic approach. This review provides a comprehensive outline of newly emerging bioremediation technologies, for instance; nanobioremediation, electrokinetic bioremediation, vermiremediation, multifunctional and sustainably implemented on-site applied biotechnologies such as; natural attenuation, biostimulation, bioaugmentation, bioventing, phytoremediation and multi-process hybrid technologies. Additionally, the scope of the effectiveness and limitations of individual technologies in treating the petroleum hydrocarbon polluted sites are also evaluated.

Biodegradation of phenanthrene by piezotolerant Bacillus subtilis EB1 and genomic insights for bioremediation

A marine strain B. subtilis EB1, isolated from Equator water, showed excellent degradation towards a wide range of hydrocarbons. Degradation studies revealed dense growth with 93 % and 83 % removal of phenanthrene within 72 h at 0.1 and 20 MPa, respectively. The identification of phenanthrene degradation metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 3,983,989 bp with 4331 annotated genes. The genome provided the genetic compartments, which includes monooxygenase, dioxygenase, dehydrogenase, biosurfactant synthesis catabolic genes for the biodegradation of aromatic compounds. Detailed COG and KEGG pathway analysis confirmed the genes involved in the oxygenation reaction of hydrocarbons, piezotolerance, siderophores, chemotaxis and transporter systems which were specific to adaptation for survival in extreme marine habitat. The results of this study will be a key to design an optimal bioremediation strategy for oil contaminated extreme marine environment.

Distribution, Sources, and Risk Assessment of Organochlorine Pesticides in Water from Beiluo River, Loess Plateau, China

The Loess Plateau has been a focus of public discussion and environmental concerns over the past three decades. In this study, in order to investigate the effect of OCP pollution in water of the Beiluo River, concentrations of 25 OCPs at 17 locations in the water were examined. The results showed that the concentration of ∑OCPs in the water ranged from 1.76 to 32.57 ng L^-1, with an average concentration of 7.23 ng L^-1. Compared with other basins in China and abroad, the OCP content in the Beiluo River was at a medium level. Hexachlorocyclohexane (HCH) pollution in the Beiluo River was mainly from the mixed input of lindane and technical HCHs. Dichlorodiphenyltrichloroethane (DDT) pollution was mainly from the mixed input of technical DDTs and dicofol. Most of the OCP pollution came from historical residues. The risk assessment results showed that hexachlorobenzene (HCB) and endosulfan had high ecological risks in the middle and lower reaches of the Beiluo River. Most residual OCPs were not sufficient to pose carcinogenic and non-carcinogenic health risks to humans. The results of this study can provide a reference for OCP prevention and control and watershed environmental management.

Revealing the role of microalgae-bacteria niche for boosting wastewater treatment and energy reclamation in response to temperature

Conventional biological treatment usually cannot achieve the same high water quality as advanced treatment when conducted under varied temperatures. Here, satisfactory wastewater treatment efficiency was observed in a microalgae-bacteria consortia (MBC) over a wide temperature range because of the predominance of microalgae. Microalgae contributed more toward wastewater treatment at low temperature because of the unsatisfactory performance of the accompanying bacteria, which experienced cold stress (e.g., bacterial abundance below 3000 sequences) and executed defensive strategies (e.g., enrichment of cold-shock proteins). A low abundance of amoA-C and hao indicated that conventional nitrogen removal was replaced through the involvement of microalgae. Diverse heterotrophic bacteria for nitrogen removal were identified at medium and high temperatures, implying this microbial niche treatment contained diverse flexible consortia with temperature variation. Additionally, pathogenic bacteria were eliminated through microalgal photosynthesis. After fitting the neutral community model and calculating the ecological niche, microalgae achieved a maximum niche breadth of 5.21 and the lowest niche overlap of 0.38, while the accompanying bacterial community in the consortia were shaped through deterministic processes. Finally, the maximum energy yield of 87.4 kJ L^-1 and lipid production of 1.9 g L^-1 were achieved at medium temperature. Altogether, this study demonstrates that advanced treatment and energy reclamation can be achieved through microalgae-bacteria niche strategies.

Elucidating molecular characterization of chlorpyrifos and profenofos degrading distinct bacterial strains for enhancing seed germination potential of Gossypium arboreum L

Chlorpyrifos (CP) and profenofos (PF) are organophosphate pesticides (OPs) widely used in agriculture and are noxious to both fauna and flora. The presented work was designed to attenuate the toxicity of both pesticides in the growth parameters of a cotton crop by applying plant growth-promoting rhizobacteria (PGPR), namely Pseudomonas aeruginosa PM36 and Bacillus sp. PM37. The multifarious biological activities of both strains include plant growth-promoting traits, including phosphate solubilization; indole-3-acetic acid (IAA), siderophore, and HCN production; nitrogen fixation; and enzymatic activity such as cellulase, protease, amylase, and catalase. Furthermore, the molecular profiling of multi-stress-responsive genes, including acdS, ituC, czcD, nifH, and sfp, also confirmed the plant growth regulation and abiotic stress tolerance potential of PM36 and PM37. Both strains (PM36 and PM37) revealed 92% and 89% of CP degradation at 50 ppm and 87% and 81% at 150 ppm within 7 days. Simultaneously 94% and 98% PF degradation was observed at 50 ppm and 90% and 92% at 150 ppm within 7 days at 35 °C and pH 7. Biodegradation was analyzed using HPLC and FTIR. The strains exhibited first-order reaction kinetics, indicating their reliance on CP and PF as energy and carbon sources. The presence of opd, mpd, and opdA genes in both strains also supported the CP and PF degradation potential of both strains. Inoculation of strains under normal and OP stress conditions resulted in a significant increase in seed germination, plant biomass, and chlorophyll contents of the cotton seedling. Our findings indicate that the strains PM36 and PM37 have abilities as biodegraders and plant growth promoters, with potential applications in crop sciences and bioremediation studies. These strains could serve as an environmentally friendly, sustainable, and socially acceptable solution to manage OP-contaminated sites.

Continuous bioreactors enable high-level bioremediation of diesel-contaminated seawater at low and mesophilic temperatures using Antarctic bacterial consortia: Pollutant analysis and microbial community composition

In 2020, more than 21,000 tons of diesel oil were released accidently into the environment with most of it contaminating water bodies. There is an urgent need for sustainable technologies to clean up rivers and oceans to protect wildlife and human health. One solution is harnessing the power of bacterial consortia; however isolated microbes from different environments have shown low diesel bioremediation rates in seawater thus far. An outstanding question is whether Antarctic microorganisms that thrive in environments polluted with hydrocarbons exhibit better diesel degrading activities when propagated at higher temperatures than those encountered in their natural ecosystems. Here, we isolated bacterial consortia, LR-30 (30 °C) and LR-10 (10 °C), from the Antarctic rhizosphere soil of Deschampsia antarctica (Livingston Island), that used diesel oil as the only carbon substrate. We found that LR-30 and LR-10 batch bioreactors metabolized nearly the entire diesel content when the initial concentration was 10 (g/L) in seawater. Increasing the initial diesel concentration to 50 gDiesel/L, LR-30 and LR-10 bioconverted 33.4 and 31.2 gDiesel/L in 7 days, respectively. The 16S rRNA gene sequencing profiles revealed that the dominant bacterial genera of the inoculated LR-30 community were Achromobacter (50.6%), Pseudomonas (25%) and Rhodanobacter (14.9%), whereas for LR-10 were Pseudomonas (58%), Candidimonas (10.3%) and Renibacterium (7.8%). We also established continuous bioreactors for diesel biodegradation where LR-30 bioremediated diesel at an unprecedent rate of (34.4 g/L per day), while LR-10 achieved (24.5 g/L per day) at 10 °C for one month. The abundance of each bacterial genera present significantly fluctuated at some point during the diesel bioremediation process, yet Achromobacter and Pseudomonas were the most abundant member at the end of the batch and continuous bioreactors for LR-30 and LR-10, respectively.

Phytoextraction of anthropogenic heavy metal contamination of the Blesbokspruit wetland: Potential of wetland macrophytes

Blesbokspruit wetland is one of the least conserved ecosystems in the Southern Africa region with active and latent threats of anthropogenic contamination stretching over decades of mining wastewater discharge, agricultural run-off, and a consistent influx of untreated sewage. This study provides an insight into the present-day spatial distribution of heavy metal contamination and the role of localised macrophytes in their phytoremediation. With exception of the first sampling point, the concentration of heavy metals in water samples throughout the wetland was within limits however findings from sediment samples were the inverse. The concentrations of Chromium and Nickel significantly exceeded both effect range low (ERL) and effect range medium (ERM) limits (250-430 mg/Kg and 73-151 mg/Kg respectively) as set out by international sediment quality guidelines. Emergent- Phragmites australis, Typha capensis, and free-flowing-Eichhornia crassipes macrophytes, which are naturally localised to the wetland were found to have varying bioaccumulation potential for different heavy metals; Bioconcentration of heavy metals in emergent macrophytes was relatively low especially for Nickel and Chromium compared to free-flowing macrophytes. E. crassipes accumulated significant amounts of the heavy metals with root concentrations of up to 17.23, 116.6, 330.5, and 342.9 mg/Kg for Arsenic, Lead, Nickel, and Chromium respectively. The emergent macrophytes were however found to bioconcentrate Arsenic up to 1.15 L/Kg (T. capensis) and 9.9 L/Kg (P. Australis) at sites 4 and 5 respectively.   Findings with regards to bioconcentration especially of the E. crassipes, validate recommendations for the utilization of hyperaccumulating macrophytes for the natural recovery of these heavy metals towards alleviating the anthropogenic stress on this valuable ecosystem.

Biodegradation of organophosphorus pesticide profenofos by the bacterium Bacillus sp. PF1 and elucidation of initial degradation pathway

Among the organophosphate pesticides, the wide and indiscriminate use of profenofos (PFF) in agricultural and horticultural crops has resulted in serious environmental and animal health concerns and therefore demands an urgent need to develop a biological solution for its effective removal from the environment. For the bioremediation of PFF, a strain PF1, capable of utilizing profenofos as the sole source of carbon and energy was isolated from the soil samples of apple orchards of Shimla region of Himachal Pradesh, India. Based on the biochemical, FAME, and 16S rRNA gene analysis the bacterium PF1 was identified as Bacillus altitudinis (GenBank: MH986176). The strain was able to degrade 50μg mL^-1 PFF up to 93% within 30 days of incubation at 28°C, pH 7.0. A linear regression analysis performed on the data-set revealed the statistical significance of the relationship between the growth of the bacterial population and the degradation of pesticides. The compound 4-Bromo-2-chlorophenol (BCP) was detected as one of the pathway metabolites which further were completely degraded to lower pathway metabolites. A probable PFF degradation pathway has been proposed which follows the path from PFF to BCP and ultimately enters into the TCA cycle. To the best of our knowledge, this is the first report of PFF biodegradation by any Bacillus species of western Himalayan origin exhibiting close phylogenetic association with Bacillus altitudinis. This indigenous bacterium can be useful to bio-remediate the PFF contaminated soil as this pesticide is extensively used in the different horticulture fields in Himachal Pradesh, India.

Oral administration of Bacillus cereus GW-01 alleviates the accumulation and detrimental effects of β-cypermethrin in mice

Pyrethroid insecticides negatively affect feed conversion, reproductive fitness, and food safety in exposed animals. Although probiotics have previously been widely studied for their effect on gut health, comparatively little is known regarding the efficacy of probiotic administration in specifically reducing pesticide toxicity in mice. We demonstrated that oral administration of a β-cypermethrin (β-CY)-degrading bacterial strain (Bacillus cereus GW-01) to β-CY-exposed mice reduced β-CY levels in the liver, kidney, brain, blood, lipid, and feces (18%-53%). Additionally, co-administration of strain GW-01 to β-CY-exposed mice reduced weight loss (22%-31%) and improved liver function (15%-19%) in mice. Additionally, mice receiving GW-01 had near-control levels of numerous β-CY-affected gut microbial taxa, including Muribaculaceae, Alloprevotella, Bacteroides, Dubosiella, and Alistipes. The survival and β-CY biosorption of GW-01 in simulated gastrointestinal fluid conditions were significantly higher than E. coli. These results suggested that GW-01 can reduce β-CY accumulation and alleviate the damage in mice. This study is the first to demonstrate that a probiotic strain can reduce the toxicity of β-CY in mice.

Biofilm-mediated decolorization, degradation and detoxification of synthetic effluent by novel biofilm-producing bacteria isolated from textile dyeing effluent

Biofilm-mediated bioremediation of xenobiotic pollutants is an environmental friendly biological technique. In this study, 36 out of 55 bacterial isolates developed biofilms in glass test tubes containing salt-optimized broth plus 2% glycerol (SOBG). Scanning electron microscopy, Fourier transform infrared (FTIR) spectroscopy, and Congo red- and Calcofluor binding results showed biofilm matrices contain proteins, curli, nanocellulose-rich polysaccharides, nucleic acids, lipids, and peptidoglycans. Several functional groups including -OH, N-H, C-H, CO, COO^-, -NH_2, PO, C-O, and C-C were also predicted. By sequencing, ten novel biofilm-producing bacteria (BPB) were identified, including Exiguobacterium indicum ES31G, Kurthia gibsonii ES43G, Kluyvera cryocrescens ES45G, Cedecea lapagei ES48G, Enterobacter wuhouensis ES49G, Aeromonas caviae ES50G, Lysinibacillus sphaericus ES51G, Acinetobacter haemolyticus ES52G, Enterobacter soli ES53G, and Comamonas aquatica ES54G. The Direct Red (DR) 28 (a carcinogenic and mutagenic dye used in dyeing and biomedical processes) decolorization process was optimized in selected bacterial isolates. Under optimum conditions (SOBG medium, 75 mg L^-1 dye, pH 7, 28 °C, microaerophilic condition and within 72 h of incubation), five of the bacteria tested could decolorize 97.8% ± 0.56-99.7% ± 0.45 of DR 28 dye. Azoreductase and laccase enzymes responsible for biodegradation were produced under the optimum condition. UV-Vis spectral analysis revealed that the azo (-NN-) bond peak at 476 nm had almost disappeared in all of the decolorized samples. FTIR data revealed that the foremost characteristic peaks had either partly or entirely vanished or were malformed or stretched. The chemical oxygen demand decreased by 83.3-91.3% in the decolorized samples, while plant probiotic bacterial growth was indistinguishable in the biodegraded metabolites and the original dye. Furthermore, seed germination (%) was higher in the biodegraded metabolites than the parent dye. Thus, examined BPB could provide potential solutions for the bioremediation of industrial dyes in wastewater.

Construction of CdS-Tetrahymena thermophila hybrid system by efficient cadmium adsorption for dye removal under light irradiation

The water pollution caused by heavy metals and dyes emitted by industries has become a worldwide problem. These pollutants are difficult to be biodegraded. Even at low concentrations, they are toxic and at last threaten human health. Herein, while using Tetrahymena thermophila, a single-celled ciliate protozoa, to enrich and remove the heavy metal Cd²⁺ from water, CdS nanoparticle-Tetrahymena thermophila hybrid system (CdS-T. thermophila) for dye pollution remediation under light irradiation was developed. The conditions of Cd²⁺ enrichment and removal by T. thermophila, construction of efficient CdS-T. thermophila, and decolorization of Congo red using CdS-T. thermophila were investigated. In the presence of cysteine ethyl ester, the removal rate of Cd²⁺ by T. thermophila was 94% at low Cd²⁺ concentration of 1 mg L^-1. The adsorption capacity of T. thermophila to Cd²⁺ reached 43 mg g^-1 at Cd²⁺ concentration of 80 mg L^-1. Using 0.1 g L^-1 constructed CdS-T. thermophila, the decolorization rate of 50 mg L^-1 Congo red solution reached 95% in 60 min under light irradiation. This study provides a new insight to effective removing Cd²⁺ from water by T. thermophila to construct the CdS-T. thermophila and using it to remediate dye pollution in the environment.

Limited Role of Rhamnolipids on Cadmium Resistance for an Endogenous-Secretion Bacterium

Rhamnolipids, a type of biosurfactant, represent a potential strategy for both enhancing organismic resistance and in situ remediation of heavy metals contaminations. In-depth study of the mechanism of rhamnolipids synthesis in response to heavy metals stress, is indispensable for a wide use of biosurfactant-secreting microbes in bioremediation. In this study, we employed the wild-type and the rhlAB deficient strain (ΔrhlAB) of Pseudomonas aeruginosa, a prototypal rhamnolipids-producing soil microorganism, to investigate its responses to cadmium resistance based on its physicochemical, and physiological properties. Compared with the wild-type strain, the ΔrhlAB were more sensitive to Cd-stress at low Cd concentration (<50 mg/L), whereas there was little difference in sensitivity at higher Cd concentrations, as shown by spot titers and cell viability assays. Secreted rhamnolipids reduced intracellular Cd²⁺ accumulation to alleviate Cd²⁺ stress, whereas endogenous rhamnolipids played a limited role in alleviating Cd²⁺ stress. Synthesized rhamnolipids exhibited a higher critical micelle concentration (CMC) (674.1 mg/L) and lower emulsification index (4.7%) under high Cd-stress, while these parameters showed no obvious changes. High Cd-stress resulted in high hydrophilic wild-type bacterial surface and lower bioremediation ability. This study could advance a deeper understanding of the mechanism of cadmium resistance and provide a theoretical foundation for the application of biosurfactant and biosurfactant-secreted bacterium in contaminant bioremediation.

Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach

The ability of microorganisms to detoxify xenobiotic compounds allows them to thrive in a toxic environment using carbon, phosphorus, sulfur, and nitrogen from the available sources. Biotransformation is the most effective and useful metabolic process to degrade xenobiotic compounds. Microorganisms have an exceptional ability due to particular genes, enzymes, and degradative mechanisms. Microorganisms such as bacteria and fungi have unique properties that enable them to partially or completely metabolize the xenobiotic substances in various ecosystems.There are many cutting-edge approaches available to understand the molecular mechanism of degradative processes and pathways to decontaminate or change the core structure of xenobiotics in nature. These methods examine microorganisms, their metabolic machinery, novel proteins, and catabolic genes. This article addresses recent advances and current trends to characterize the catabolic genes, enzymes and the techniques involved in combating the threat of xenobiotic compounds using an eco-friendly approach.

Genetic diversity of enterotoxigenic Bacillus cereus strains in coriander in southwestern Mexico

Background

Coriander, like other leafy green vegetables, is available all year round and is commonly consumed raw in Mexico as in other countries in the preparation of street or homemade food. Bacillus cereus (B. cereus) is a microorganism that can reach coriander because it is usually found in the soil and in some regions the vegetables are irrigated with polluted water. Therefore, the aim of this study was to determinate the presence of B. cereus in coriander used for human consumption in southwestern Mexico and determine the toxigenic profile, biofilm production, genes associated with the production of biofilms, sporulation rates, enzymatic profile, psychotropic properties, and genetic diversity of B. cereus.

Methods

Fresh coriander samples were collected from several vegetable retailers in different markets, microbiological analysis was performed. Molecular identification, genes related to the production of biofilm, and toxin gene profiling of B. cereus isolates were determined by PCR. The biofilm formation was measured by performing a crystal violet assay. The genetic diversity of B. cereus strains was determined by PCR of repetitive elements using oligonucleotide (GTG) 5.

Results

We found a frequency of B. cereus in vegetables was 20% (13/65). In this study, no strains with genes for the HBL toxin were found. In the case of genes related to biofilms, the frequency was low for sipW [5.8%, (1/17)] and tasA [11.7%, (2/17)]. B. cereus strains produce a low amount of biofilm with sporulation rates around 80%. As for genetic diversity, we observed that strains isolated from the same market, but different vegetable retailers are grouped into clusters. In the coriander marketed in southwestern Mexico, were found B. cereus strains with genes associated with the production of diarrheal toxins. Together, these results show actual information about the state of art of B. cereus strains circulating in the southwestern of Mexico.

Toxicity analysis of TNT to alfalfa's mineral nutrition and secondary metabolism

Alfalfa has the ability to degrade TNT. TNT exposure caused root disruption of mineral nutrient metabolism. The exposure of TNT imbalanced basal cell energy metabolism. The mechanism of 2,4,6-trinitrotoluene (TNT) toxicity effects was analyzed in alfalfa (Medicago sativa L.) seedlings by examining the mineral nutrition and secondary metabolism of the plant roots. Exposure to 25-100 mg·L^-1 TNT in a hydroponic solution for 72 h resulted in a TNT absorption rate of 26.8-63.0%. The contents of S, K, and B in root mineral nutrition metabolism increased significantly by 1.70-5.46 times, 1.38-4.01 times, and 1.40-4.03 times, respectively, after TNT exposure. Non-targeted metabolomics analysis of the roots identified 189 significantly upregulated metabolites and 420 significantly downregulated metabolites. The altered metabolites were primarily lipids and lipid-like molecules, and the most significant enrichment pathways were alanine, aspartate, and glutamate metabolism and glycerophospholipid metabolism. TNT itself was transformed in the root system into several intermediate products, including 4-hydroxylamino-2,6-dinitrotoluene, 4-amino-2,6-dinitrotoluene, 2-hydroxylamino-4,6-dinitrotoluene, 2,4',6,6'-tetranitro-2',4-azoxytoluene, 4,4',6,6'-tetranitro-2,2'-azoxytoluene, and 2,4-dinitrotoluene. Overall, TNT exposure disturbed the mineral metabolism balance, and significantly interfered with basic plant metabolism.

Genetic Evidences of Biosurfactant Production in Two Bacillus subtilis Strains MB415 and MB418 Isolated From Oil Contaminated Soil

Biosurfactants are a diverse group of amphiphilic compounds obtained from microbes. In the present study, the genomic analysis of biosurfactant-producing Bacillus subtilis MB415 and MB418 obtained from oil-contaminated soil was performed. Initially, the strains were screened for biosurfactant production by hemolytic assay, emulsification index, and oil displacement. Further FTIR analysis of extracted biosurfactants revealed the presence of lipopeptides. The sequenced genomes of MB415 and MB418 were of 4.2 Mbps with 43% GC content. Among more than 4,500 protein-coding genes, many were involved in virulence, metal/multidrug resistances, flagella assembly, chemotactic response, and aromatic ring hydroxylating dioxygenases. An annotation analysis revealed that both genomes possessed non-ribosomal synthetase gene clusters for the lipopeptide synthetases srf and fen responsible for surfactin and fengycin production. Comparative studies of both genomes highlighted variability in gene operons mainly for surfactin biosynthesis.

Microbial Degradation of Aldrin and Dieldrin: Mechanisms and Biochemical Pathways

As members of the organochlorine group of insecticides, aldrin and dieldrin are effective at protecting agriculture from insect pests. However, because of excessive use and a long half-life, they have contributed to the major pollution of the water/soil environments. Aldrin and dieldrin have been reported to be highly toxic to humans and other non-target organisms, and so their use has gradually been banned worldwide. Various methods have been tried to remove them from the environment, including xenon lamps, combustion, ion conversion, and microbial degradation. Microbial degradation is considered the most promising treatment method because of its advantages of economy, environmental protection, and convenience. To date, a few aldrin/dieldrin-degrading microorganisms have been isolated and identified, including Pseudomonas fluorescens, Trichoderma viride, Pleurotus ostreatus, Mucor racemosus, Burkholderia sp., Cupriavidus sp., Pseudonocardia sp., and a community of anaerobic microorganisms. Many aldrin/dieldrin resistance genes have been identified from insects and microorganisms, such as Rdl, bph, HCo-LGC-38, S2-RDL^A302S, CSRDL1A, CSRDL2S, HaRdl-1, and HaRdl-2. Aldrin degradation includes three pathways: the oxidation pathway, the reduction pathway, and the hydroxylation pathway, with dieldrin as a major metabolite. Degradation of dieldrin includes four pathways: oxidation, reduction, hydroxylation, and hydrolysis, with 9-hydroxydieldrin and dihydroxydieldrin as major products. Many studies have investigated the toxicity and degradation of aldrin/dieldrin. However, few reviews have focused on the microbial degradation and biochemical mechanisms of aldrin/dieldrin. In this review paper, the microbial degradation and degradation mechanisms of aldrin/dieldrin are summarized in order to provide a theoretical and practical basis for the bioremediation of aldrin/dieldrin-polluted environment.

Novel pathway of acephate degradation by the microbial consortium ZQ01 and its potential for environmental bioremediation

The microbial degradation of acephate in pure cultures has been thoroughly explored, but synergistic metabolism at the community level has rarely been investigated. Here, we report a novel microbial consortium, ZQ01, capable of effectively degrading acephate and its toxic product methamidophos, which can use acephate as a source of carbon, phosphorus and nitrogen. The degradation conditions with consortium ZQ01 were optimized using response surface methodology at a temperature of 34.1 °C, a pH of 8.9, and an inoculum size of 2.4 × 10⁸ CFU·mL^-1, with 89.5% of 200 mg L^-1 acephate degradation observed within 32 h. According to the main products methamidophos, acetamide and acetic acid, a novel degradation pathway for acephate was proposed to include hydrolysis and oxidation as the main pathways of acephate degradation. Moreover, the bioaugmentation of acephate-contaminated soils with consortium ZQ01 significantly enhanced the removal rate of acephate. The results of the present work demonstrate the potential of microbial consortium ZQ01 to degrade acephate in water and soil environments, with a different and complementary acephate degradation pathway.

Treatment of textile wastewater containing mixed toxic azo dye and chromium (VI) BY haloalkaliphilic bacterial consortium

Scientific empowerment in this century created a positive and negative impact on the ecosystem's biotic and abiotic components. The current scenario of emerging recalcitrant pollutants in the environment is encountered using various remediation approaches are enforced and applied. The need for mineralization of the toxic pollutants to non - toxic forms accomplished the application of microbes (bacteria, fungi and algae) and plants individually or in a combined manner. The current research on the removal of pollutants from synthetic textile wastewater containing 1200 ppm concentration of mixed azo dyes -Reactive red (RR), Reactive Brown (RB) & Reactive Black (RBl) and 300 ppm Cr (VI) metal using haloalkaliphilic bacterial strains LBKVG1, LBKVG2, LBKVG3 & LBKVG4 in a Moving Bed Biofilm Reactor (MBBR), showed decolorization of 82 ± 0.5% of mixed azo dyes and degradation 56 ± 0.5% of Cr (VI) metal at 37 ^°C and pH 8.5 in the fifth day of the study. The isolated bacterial strains in the consortium were molecularly and morphologically characterized by 16SrRNA sequencing and SEM analysis. FT-IR and GC-MS analysis scrutinized the metabolites obtained. The findings suggest the degradation of hazardous pollutants even at higher concentrations and attempt to decolourize the mixed azo dyes simultaneously using the eco-friendly bacterial consortium.

Enhanced removal of fifteen pesticide mixture by a single bacterial strain using response surface methodology and its application in raw milk

PURPOSE

Environmental contamination with various pesticides accompanied by uncontrolled use contributes to severe ecological and health problems. Although extensive research was conducted on pesticides degradation, very few reports have demonstrated the degradation of mixed pesticides. Consequently, this study aimed to evaluate the removal efficacy of highly potent bacterial isolate for pesticide mixture under optimal culture conditions, followed by their application in milk.

METHODS

Isolation and selection of bacterial isolates were performed from 40 milk samples by enrichment culture technique and were screened to obtain highly potent bacterial strain identified by 16 S rDNA analysis. The statistics-based experimental designs were applied to optimize the culture conditions towards the best degradation of pesticides mixture, followed by subsequent utilization in milk. The degradation ratio of pesticides was analyzed using gas chromatography-mass spectrometry.

RESULTS

In this study, a bacterial strain S6A identified as Bacillus subtilis-mw1 efficiently eliminated environmental contaminants from different groups of pesticide residues. The statistical optimization showcased optimum settings that accomplished the highest pesticide mixture degradation (61.59 %). The application experiment manifested that degradation of pesticide mixtures of sterile milk (STM) was relatively faster than non-sterile milk (NSTM).

CONCLUSIONS

The obtained results assist in eliminating environmental contamination with various groups of pesticide residues. Furthermore, it can be employed in reducing pesticide residues that cause milk contamination to increase safety and quality.Graphical abstract.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s40201-021-00683-0.

Environmental Occurrence, Toxicity Concerns, and Degradation of Diazinon Using a Microbial System

Diazinon is an organophosphorus pesticide widely used to control cabbage insects, cotton aphids and underground pests. The continuous application of diazinon in agricultural activities has caused both ecological risk and biological hazards in the environment. Diazinon can be degraded via physical and chemical methods such as photocatalysis, adsorption and advanced oxidation. The microbial degradation of diazinon is found to be more effective than physicochemical methods for its complete clean-up from contaminated soil and water environments. The microbial strains belonging to Ochrobactrum sp., Stenotrophomonas sp., Lactobacillus brevis, Serratia marcescens, Aspergillus niger, Rhodotorula glutinis, and Rhodotorula rubra were found to be very promising for the ecofriendly removal of diazinon. The degradation pathways of diazinon and the fate of several metabolites were investigated. In addition, a variety of diazinon-degrading enzymes, such as hydrolase, acid phosphatase, laccase, cytochrome P450, and flavin monooxygenase were also discovered to play a crucial role in the biodegradation of diazinon. However, many unanswered questions still exist regarding the environmental fate and degradation mechanisms of this pesticide. The catalytic mechanisms responsible for enzymatic degradation remain unexplained, and ecotechnological techniques need to be applied to gain a comprehensive understanding of these issues. Hence, this review article provides in-depth information about the impact and toxicity of diazinon in living systems and discusses the developed ecotechnological remedial methods used for the effective biodegradation of diazinon in a contaminated environment.

Plasmid-mediated catabolism for the removal of xenobiotics from the environment

The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.

Analysis of the biodegradation and phytotoxicity mechanism of TNT, RDX, HMX in alfalfa (Medicago sativa)

The aim of this study was to reveal the mechanism underlying the toxicity of TNT (trinitrotoluene), RDX (cyclotrimethylene trinitroamine), and HMX (cyclotetramethylene tetranitramine) explosives pollution in plants. Here, the effects of exposure to these three explosives were examined on chlorophyll fluorescence, antioxidant enzyme activity, and the metabolite spectrum in alfalfa (Medicago sativa) plants. The degradation rates for TNT, RDX, and HMX by alfalfa were 26.8%, 20.4%, and 18.4%, respectively, under hydroponic conditions. TNT caused damage to the microstructure of the plant roots and inhibited photosynthesis, whereas RDX and HMX induced only minor changes. Exposure to any of the three explosives caused disturbances in the oxidase system. Non-targeted metabolomics identified a total of 6185 metabolites. TNT exposure induced the appearance of 609 differentially expressed metabolites (189 upregulated, 420 downregulated), RDX exposure induced 197 differentially expressed metabolites (155 upregulated and 42 downregulated), and HMX induced 234 differentially expressed metabolites (132 upregulated and 102 downregulated). Of these differentially expressed metabolites, lipids and lipid-like molecules were the main metabolites induced by explosives poisoning. TNT mainly caused significant changes in the alanine, aspartate, and glutamate metabolism metabolic pathways, RDX mainly caused disorders in the arginine biosynthesis metabolic pathway, and HMX disrupted the oxidative phosphorylation metabolic pathway. Taken together, the results show that exposure to TNT, RDX, and HMX leads to imbalances in plant photosynthetic characteristics and antioxidant enzyme systems, changes the basic metabolism of plants, and has significant ecotoxicity effects.

Biosurfactant is a powerful tool for the bioremediation of heavy metals from contaminated soils

Heavy metal toxicity has become a pressing ecological problem that affects the ecosystems through bioaccumulation, representing a serious public health hazard. Many conventional strategies have been developed and applied to decontaminate and restore metal-contaminated areas. However, these conventional approaches are not very suitable and environmentally safe for heavy metal remediation because of their high operational costs, high energy requirements, post-waste disposal problems, and secondary pollutant generation. Thus, biosurfactant-based bioremediation of heavy metals is a sustainable and promising approach because of its biodegradation capability, economic effectiveness, and ecofriendly nature. Pseudomonas sp., Bacillus sp., Citrobacter freundii, and Candida tropicalis have been isolated as potential sources of biosurfactants and produce compounds such as surfactin, rhamnolipids, and sophorolipids. Owing to the severity of heavy metal pollution in certain parts of the environment, biosurfactants have garnered great interest and attention as an emerging multi-functional technology of the new century for successful removal of heavy metal pollutants. The present study describes the role of biosurfactants in the bioremediation of heavy metals from contaminated environments. Moreover, the interaction mechanism underlying biosurfactant-metal complexation and metal remediation are discussed. Based on the review of the literature, further research is warranted to elucidate the mechanistic roles and explore the structural characterization and gene regulation of biosurfactants to improve their productivity and expand their applicability in bioremediation.

Biodegradation of polystyrene by deep-sea Bacillus paralicheniformis G1 and genome analysis

Polystyrene (PS) films were subjected to in vitro biodegradation by Bacillus paralicheniformis G1 (MN720578) isolated from 3538 m depth sediments of the Arabian Sea. The growth of the isolate was most favourable at pH 7.5, 30 °C and 4% salinity. A series of batch experiments were conducted to investigate the degradation of PS films up to 60 days. The results of this study indicated that the strain degraded 34% of PS film within 60 days of incubation. The complete genome sequence consists of 4,281,959 bp with 45.88% GC content and encodes 4213 protein coding genes. A high number of genes encoding monooxygenase, dioxygenase, peroxidase, esterase and hydrolase involved in the degradation of synthetic polymers were identified. Also genes associated with flagellum dependent motility, chemotaxis, biofilm formation and siderophores biosynthesis were identified in this deep-sea strain G1. This study suggests that B. paralicheniformis G1 could be a potential species for degradation of PS and its genome analysis provides insight into the molecular basis of biodegradation.

Biodegradation and physiological response mechanism of Bacillus aryabhattai to cyclotetramethylenete-tranitramine (HMX) contamination

This study aims to reveal the biodegradation and interaction mechanism of cyclotetramethylenete-tranitramine (HMX) by a newly isolated bacteria. In this study, a bacterial strain (Bacillus aryabhattai) with high efficiency for HMX degradation was used as the test organism to analyze the changes in growth status, cell function, and mineral metabolism following exposure to different stress concentrations (0 and 5 mg L^-1) of HMX. Non-targeted metabonomics was used to reveal the metabolic response of this strain to HMX stress. The results showed that when the HMX concentration was 5 mg L^-1, the removal rate of HMX within 24 h of inoculation with Bacillus aryabhatta was as high as 90.5%, the OD₆₀₀ turbidity was 1.024, and the BOD₅ was 225 mg L^-1. Scanning electron microscope (SEM) images showed that the morphology of bacteria was not obvious Variety, Fourier transform infrared spectroscopy (FTIR) showed that the cell surface -OH functional groups drifted, and ICP-MS showed that the cell mineral element metabolism was disturbed. Non-targeted metabonomics showed that HMX induced the differential expression of 254 metabolites (133 upregulated and 221 downregulated). The main differentially expressed metabolites during HMX stress were lipids and lipid-like molecules, and the most significantly affected metabolic pathway was purine metabolism. At the same time, the primary metabolic network of bacteria was disordered. These results confirmed that Bacillus aryabhattai has a high tolerance to HMX and can efficiently degrade HMX. The degradation mechanism involves the extracellular decomposition of HMX and transformation of the degradation products into intracellular purines, amino sugars, and nucleoside sugars that then participate in cell metabolism.

A New Ciboria sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons

A Ciboria sp. strain (Phylum Ascomycota) was isolated from hydrocarbon-polluted soil of an abandoned oil refinery in Italy. The strain was able to utilize diesel oil as a sole carbon source for growth. Laboratory-scale experiments were designed to evaluate the use of this fungal strain for treatment of the polluted soil. The concentration of total petroleum hydrocarbons (TPH) in the soil was 8,538 mg/kg. Mesocosms containing the contaminated soil were inoculated with the fungal strain at 1 or 7%, on a fresh weight base ratio. After 90 days of incubation, the depletion of TPH contamination was of 78% with the 1% inoculant, and 99% with the 7% inoculant. 16S rDNA and ITS metabarcoding of the bacterial and fungal communities was performed in order to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction indicated Arthrobacter, Dietzia, Brachybacerium, Brevibacterium, Gordonia, Leucobacter, Lysobacter, and Agrobacterium spp. as generalist saprophytes, essential for the onset of hydrocarbonoclastic specialist bacterial species, identified as Streptomyces, Nocardoides, Pseudonocardia, Solirubrobacter, Parvibaculum, Rhodanobacter, Luteiomonas, Planomicrobium, and Bacillus spp., involved in the TPH depletion. The fungal metabolism accelerated the onset of specialist over generalist bacteria. The capacity of the Ciboria sp. to deplete TPH in the soil in treatment was also ascertained.

Degradation of benzo[a]pyrene by halophilic bacterial strain Staphylococcus haemoliticus strain 10SBZ1A

The exploitation of petroleum oil generates a considerable amount of “produced water or petroleum waste effluent (PWE)” that is contaminated with polycyclic aromatic hydrocarbons (PAHs), including Benzo[a]pyrene (BaP). PWE is characterised by its high salinity, which can be as high as 30% NaCl, thus the exploitation of biodegradation to remove PAHs necessitates the use of active halophilic microbes. The strain 10SBZ1A was isolated from oil contaminated soils, by enrichment experiment in medium containing 10% NaCl (w/v). Homology analyses of 16S rRNA sequences identified 10SBZ1A as a Staphylococcus haemoliticus species, based on 99.99% homology (NCBI, accession number GI: MN388897). The strain could grow in the presence of 4–200 μmol l^-1 of BaP as the sole source of carbon, with a doubling time of 17–42 h. This strain optimum conditions for growth were 37 ^oC, 10% NaCl (w/v) and pH 7, and under these conditions, it degraded BaP at a rate of 0.8 μmol l^-1 per day. The strain 10SBZ1A actively degraded PAHs of lower molecular weights than that of BaP, including pyrene, phenanthrene, anthracene. This strain was also capable of removing 80% of BaP in the context of soil spiked with BaP (10 μmol l^-1 in 100 g of soil) within 30 days. Finally, a metabolic pathway of BaP was proposed, based on the identified metabolites using liquid chromatography-high resolution tandem mass spectrometry. To the best of our knowledge, this is the first report of a halophilic BaP degrading bacterial strain at salinity > 5% NaCl.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.