Luffa cylindrica (Sponge Gourd) Fibers in Treatment of Greywater: an Aerobic Fixed-Film Reactor Approach

The need for potable water consumption in urban and suburban regions can be decreased by greywater treatment and its reuse. Utilizing natural fibers may provide sustainable solutions in addressing challenges related to water resource management. In this study, a fixed-film reactor was designed with Luffa cylindrica (an annually occurring fruit) as a bio-carrier. The lab-scale reactors were configured with and without Luffa cylindrica and were run for 90 days in fed-batch mode. Scanning electron microscopy (SEM) was performed to validate biofilm production over time. Monitoring COD, nitrogen, and total phosphate removal allowed for analysis of treatment effectiveness. Results demonstrated the treatment efficiency for the experimental reactor was 70.96%, 97.02%, 92.57%, and 81.20% for COD, nitrogen, phosphate, and anionic surfactant (AS), respectively. 16 s rRNA gene sequencing of bio-carrier and control greywater samples was carried out. Many bacteria known to break down anionic surfactants were observed, and microbial succession was witnessed in the control reactor vs. the experimental reactor samples. The three most prevalent genera in the experimental samples were Chlorobium, Chlorobaculum, and Terrimonas. However, it is crucial to underscore that additional research is essential to solidify our understanding in this domain, with this study laying the fundamental groundwork.

Antibiotic resistance in wastewater: Indian scenario

The surge of Antibiotic Resistant Bacteria (ARB) in the environment is poised to be the next health threat. World Health Organisation's (WHO's) Global Antimicrobial Surveillance System (GLASS) report indicates that developing countries may be at a greater risk. Among various factors, the major driver here could be untreated wastewater and poor sanitation. Bacteria are extremely adaptable to their surroundings and develop Antimicrobial Resistance (AMR) when exposed to antibiotics and other pollutants that cause microbial stress. Thus, untreated domestic wastewater drains could easily become hotspots for the occurrence of ARBs. This study reports surveillance of sewage-carrying drains across four urban cities in India and demonstrated the presence of ARBs in the bacterial community against 7 classes of antibiotics, namely, β-Lactams, Chloramphenicol, Glycopeptides, Macrolides, Tetracycline, Third Generation Cephalosporin, and Quinolones. Untreated domestic wastewater flowing in target drains was collected twice a month, for a period of six months and the microbial community was subjected to Antibiotic Susceptibility Testing (AST) by plate assays. The zone of inhibition was recorded and interpreted as per the interpretive chart of The Clinical & Laboratory Standards Institute (CLSI) & The European Committee on Antimicrobial Susceptibility Testing (EUCAST). The total number of samples showing resistance against antibiotics was used to define an Antibiotic Resistance Index (ARI), calculated for all 20 sampling sites (drains). Results demonstrated that the highest ARI was observed in Delhi and Mumbai, ranging from 0.81 to 0.92 in Delhi and 0.49-0.56 in Mumbai. This surveillance study reveals the antibiotic resistance pattern of the representative bacterial community in the drains and goes beyond few targeted bacterial species. The alarming presence of antibiotic resistant bacterial community highlights the concern of ARBs being the next looming health threat. This report aims to demonstrates the importance of considering sewage surveillance on routine basis by state authorities.

Valorization of oily sludge waste using biosurfactant-producing bacteria

Oily sludge generated by the petroleum industry is not only an environmental hazard, but since it contains crude oil too, it is a valuable resource as well. This study demonstrates a methodology for the valorization of the oily sludge that allows the recovery of oil fractions by the action of microbes producing surface-active metabolites. Two bacterial isolates were used in the study that were producing different biosurfactants, identified via FTIR analysis as well as through genomic mapping of the biosurfactant pathways using RAST, ANTISMASH 7.0, STRING databases. Serratia spp. AKBS12, produced a mono-rhamnolipid, while Acinetobacter spp. AKBS16, produced emulsan. Although recovery efficiency of both biosurfactants was similar, the recovery profile with respect to the class of hydrocarbons differed. The rhamnolipid produced by Serratia spp. AKBS12 extracted mono-chained paraffins and linear alkanes, while emulsan, produced by Acinetobacter spp. AKBS16 could extract heavier paraffins. The extraction procedure is simple and involves mixing the biosurfactant with oily sludge at a temperature of 30 °C with an incubation of 9 days. Sulphuric acid precipitation releases the oil trapped in the oily sludge. The study is the first step in developing user-friendly, innovative technologies that can be linked to the concept of a circular economy.

Treatment Options for Municipal Solid Waste by Composting and Its Challenges

Recovery and recycling of municipal solid waste biodegradable fraction (50-55%) are essential for attaining sustainability and a circular economy. Among organic waste treatment methods, composting is used to recycle organic fractions of waste. However, only 10-12% of municipal solid waste is utilized for composting treatment due to a lack of segregation practices and process challenges, including long process periods, odorous and greenhouse gas emissions, nitrogen loss, and low compost quality, which hinders large-scale practice. The current review paper discusses the challenges of composting treatment and its possible solutions. Various strategies were explored to address these challenges, such as utilizing microbial inoculum, additives, and optimization of physicochemical parameters. It also emphasizes the application of metagenomics for exploring key species. The knowledge about the microbial community and biochemical pathways (genome mining) can be exploited for the improvement of treatment efficiency.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01087-4.

Comparative assessment of soil microbial community in crude oil contaminated sites

Petroleum refineries generate oily sludge that contains hazardous polycyclic aromatic hydrocarbons (PAH), and hence, its proper disposal is of foremost concern. Analysis of the physicochemical properties and functions of indigenous microbes of the contaminated sites are essential in deciding the strategy for bioremediation. This study analyses both parameters at two geographically distant sites, with different crude oil sources, and compares the metabolic capability of soil bacteria with reference to different contamination sources and the age of the contaminated site. The results indicate that organic carbon and total nitrogen derived from petroleum hydrocarbon negatively affect microbial diversity. Contamination levels vary widely on site, with levels of PAHs ranging from 5.04 to 1.66 × 10³ μg kg^-1 and 6.20 to 5.64 × 10³ μg kg^-1 in Assam and Gujarat sites respectively, covering a higher proportion of low molecular weight (LMW) PAHs (fluorene, phenanthrene, pyrene, and anthracene). Functional diversity values were observed to be positively correlated (p < 0.05) with acenaphthylene, fluorene, anthracene, and phenanthrene. Microbial diversity was the highest in fresh oily sludge which decreased upon storage, indicating that immediate bioremediation, soon after its generation, would be beneficial. Improvement in the bio-accessibility of hydrocarbon compounds by the treatment of biosurfactant produced by a (soil isolate/isolate) was demonstrated., with respect to substrate utilization.

Catalytic resilience of multicomponent aromatic ring-hydroxylating dioxygenases in Pseudomonas for degradation of polycyclic aromatic hydrocarbons

Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ring-hydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD's ability to accommodate different LMW and HMW PAHs demonstrates its 'plasticity', meeting the catabolic demand of the PAH degraders.

Designing Knowledge-Based Bioremediation Strategies Using Metagenomics

Functional capacities for bioremediation are governed by metabolic mechanisms of inhabiting microbial communities at polluted niches. Process fluctuations lead to stress scenarios where microbes evolve continuously to adapt to sustain the harsh conditions. The biological wastewater treatment (WWT) process harbors the potential of these catabolic microbes for the degradation of organic molecules. In a typical biological WWT or soil bioremediation process, several microbial species coexist which code for enzymes that degrade complex compounds.High throughput DNA sequencing techniques for microbiome analysis in bioremediation processes have led to a powerful paradigm revealing the significance of metabolic functions and microbial diversity. The present chapter describes techniques in taxonomy and functional gene analysis for understanding bioremediation potential and novel strategies built on in silico analysis for the improvisation of existing aerobic wastewater treatment methods. Methods explaining comparative metagenomics by Metagenome Analysis server (MG-RAST) are described with successful case studies by focusing on industrial wastewaters and soil bioremediation studies.

Genome plasticity as a paradigm of antibiotic resistance spread in ESKAPE pathogens

The major reason behind the spread of antibiotic resistance genes (ARGs) is persistent selective pressure in the environment encountered by bacteria. Genome plasticity plays a crucial role in dissemination of antibiotic resistance among bacterial pathogens. Mobile genetic elements harboring ARGs are reported to dodge bacterial immune system and mediate horizontal gene transfer (HGT) under selective pressure. Residual antibiotic pollutants develop selective pressures that force the bacteria to lose their defense mechanisms (CRISPR-cas) and acquire resistance. The present study targets the ESKAPE organisms (namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) causing various nosocomial infections and emerging multidrug-resistant species. The role of CRISPR-cas systems in inhibition of HGT in prokaryotes and its loss due to presence of various stressors in the environment is also focused in the study. IncF and IncH plasmids were identified in all strains of E. faecalis and K. pneumoniae, carrying Beta-lactam and fluoroquinolone resistance genes, whereas sal3, phiCTX, and SEN34 prophages harbored aminoglycoside resistance genes (aadA, aac). Various MGEs present in selected environmental niches that aid the bacterial genome plasticity and transfer of ARGs contributing to its spread are also identified.

Characterization of a potent biosurfactant produced from Franconibacter sp. IITDAS19 and its application in enhanced oil recovery

Biosurfactants are surface-active molecules produced from microorganisms either on the cell surface or secreted extracellularly. Several biosurfactant producing microorganisms have been isolated to date, but they differ in their efficacy towards different types of hydrocarbons. Here, we report the isolation and characterization of a biosurfactant producing bacterium Franconibacter sp. IITDAS19 from crude oil contaminated soil. The biosurfactant was isolated, purified and characterized. It was identified as a glycolipid. It was found to be very stable at wide range of temperatures, pH and salt concentrations. It could reduce the surface tension of the water from 71 mN/m to 31 mN/m. IITDAS19 showed very high efficacy towards both aliphatic and aromatic hydrocarbons. It resulted in about 63% recovery of residual oil in a sand pack column. Our results suggested that the produced biosurfactant can be used for enhanced oil recovery. To our knowledge, this is the first report demonstrating the detailed characterization of a biosurfactant from Franconibacter spp.

Multifunctional applications of bamboo crop beyond environmental management: an Indian prospective

Increasing population, industrialization, and economic growth cause several adverse impacts on the existing environment and living being. Therefore, rising pollutants load and their mitigation strategies, as well as achieving energy requirements while reducing reliance on fossil fuels are the key areas, which needs significant consideration for sustainable environment. Since India has considerable biomass resources, bioenergy is a significant part of the country’s energy policy. However, the selection of feedstock is a crucial step in bioenergy production that could produce raw material without compromising food reserve along with the sustainable environment. Higher growth capacity of bamboo species makes them a suitable lignocellulosic substrate for the production of high-value greener products such as fuels, chemicals, and biomaterials as well as an appropriate candidate for eco-restoration of degraded land. In that context, the current review discusses the multidimensional applications of bamboo species in India. The bioenergy potency of bamboo and probability of aligning its production, cultivation, and operation with economic and social development agendas are also addressed, making it an exceptional crop in India. Additionally, its fast growth, perennial root systems, and capability to restore degraded land make it an essential part of ecological restoration. Furthermore, this review explores additional benefits of bamboo plantation on the environment, economy, and society along with future research prospects.

Biotechnological potential of rumen microbiota for sustainable bioconversion of lignocellulosic waste to biofuels and value-added products

Lignocellulosic biomass is an abundant resource with untapped potential for biofuel, enzymes, and chemical production. Its complex recalcitrant structure obstructs its bioconversion into biofuels and other value-added products. For improving its bioconversion efficiency, it is important to deconstruct its complex structure. In natural systems like rumen, diverse microbial communities carry out hydrolysis, acidogenesis, acetogenesis, and methanogenesis of lignocellulosic biomass through physical penetration, synergistic and enzymatic actions enhancing lignocellulose degradation activity. This review article aims to discuss comprehensively the rumen microbial ecosystem, their interactions, enzyme production, and applications for efficient bioconversion of lignocellulosic waste to biofuels. Furthermore, meta 'omics' approaches to elucidate the structure and functions of rumen microorganisms, fermentation mechanisms, microbe-microbe interactions, and host-microbe interactions have been discussed thoroughly. Additionally, feed additives' role in improving ruminal fermentation efficiency and reducing environmental nitrogen losses has been discussed. Finally, the current status of rumen microbiota applications and future perspectives for the development of rumen mimic bioreactors for efficient bioconversion of lignocellulosic wastes to biofuels and chemicals have been highlighted.

In Silico Docking Studies of Vascular Endothelial Growth Factor-A (VEGFA): Possible Implications in Chronic Myeloid Leukemia (CML) Therapy

Background:

Dysregulated angiogenesis resulting in neovascularization is a critical event in the expansion and progression of Chronic Myeloid Leukemia (CML), hematopoietic cancer. Vascular Endothelial Growth Factor- A (VEGFA), an important angiogenesis mediator, has been a target for treating cancer. Although several anti-VEGFA drugs are available, they are associated with adverse side effects, promoting the need to identify better drugs that may be less toxic.

Objective:

Our aim was to investigate whether Tyrosine Kinase Inhibitors (TKIs) could be repurposed for use as VEGFA inhibitors via in silico docking software. We also investigated the potential of phytochemicals as VEGFA inhibitors.

Methods:

We performed molecular docking using Schrödinger Maestro software suite 2014-3 to determine the most potent phytochemical and TKI VEGFA antagonists.

Results:

Among the TKIs investigated, Bosutinib had the best binding affinity and may be the most potent TKI against VEGFA. The order of binding affinities for the top ten docked ligands was: Ginsenoside Rg3> Bosutinib> Vitamin D> Paclitaxel> Dasatinib> Saponins> Ponatinib> Squalamine> Imatinib> Nilotinib. We found that Ginsenoside Rg3 had the highest binding affinity (MMGBSA score= -99.4 kcal/mol, glide Gscore = -9.16 kcal/mol) to VEGFA.

Conclusion:

Our study has shown for the first time the binding poses of these TKIs and phytochemicals to VEGFA, using computational methods. We propose that the use of the top scoring ligands, in isolation or a combination of phytochemicals plus TKI, could serve as potent angiogenesis inhibitors via their binding to and inhibiting VEGFA expression to prevent CML progression. We have also profiled the ligand binding residues, which may be explored in designing pharmacophores.

Monitoring the growth, survival and phenol utilization of the fluorescent-tagged Pseudomonas oleovorans immobilized and free cells

Bioaugmentation in wastewater treatment plants (WWTPs) is challenging due to low survival and persistence of applied microbes. This study aimed to track the capacity and survival of fluorescent-tagged Pseudomonas oleovoransICTN13 as a model organism applicable in bioaugmentation of phenol-containing wastewater. The isolate was immobilized in alginate biopolymer, and enhanced efficacy and survival for biodegradation of phenol against free cells were studied. Encapsulated cells resulted in enhanced phenol removal efficiency (~94%) compared to free cells (~72%). Encapsulation of cells facilitated an extended storage time of 30 days. Remarkably, phenol and COD removal efficacy of encapsulated cells was sustained up to ~ 92-93% in a reactor after 45 days, while free cells could produce ~ 80-84% removal efficiency. Fluorescence microscopy showed high survival of the encapsulated cells, whereas gradual deterioration of free cells was observed. Thus, the findings highlight the importance of bio augmented strain in WWTPs where encapsulation is a crucial factor.

Multidimensional approaches of biogas production and up-gradation: Opportunities and challenges

The expanding interest towards biogas generation from biowaste via complex anaerobic digestion (AD) opened new avenues in the improvement of biogas production processes and their up-gradation. The adsorption/removal of impurities particularly hydrogen sulfide (H₂S) and carbon dioxide (CO₂) from the biogas stream will significantly improve the efficiency of biogas for its further use as a renewable energy fuel. The production and up-gradation of biogas rely upon the types of feedstocks, AD condition, microbial diversity, purification methods along with the application of various additives. In that context, this review aims to emphasize the current state of the art in the field of biogas production via AD using diverse bio-waste. Further, this review will critically explore the biogas up-gradation technologies adopted so far and their pros and cons. Finally, techno-economic and environmental impact assessment of the biogas production process will be underlined to make the process cost-effective and environmentally sustainable.

Integrated Genomic and Functional Characterization of the Anti-diabetic Potential of Arthrobacter sp. SW1

For decades, bacterial natural products have served as valuable resources for developing novel drugs to treat several human diseases. Recent advancements in the integrative approach of using genomic and functional tools have proved beneficial in obtaining a comprehensive understanding of these biomolecules. This study presents an in-depth characterization of the anti-diabetic activity exhibited by a bacterial isolate SW1, isolated from an effluent treatment plant. As a primary screening, we assessed the isolate for its potential to inhibit alpha-amylase and alpha-glucosidase enzymes. Upon confirmation, we further utilized LC-MS, ESI-MS/MS, and NMR spectroscopy to identify and characterize the biomolecule. These efforts were coupled with the genomic assessment of the biosynthetic gene cluster involved in the anti-diabetic compound production. Our investigation discovered that the isolate SW1 inhibited both α-amylase and α-glucosidase activity. The chemical analysis suggested the production of acarbose, an anti-diabetic biomolecule, which was further confirmed by the presence of biosynthetic gene cluster "acb" in the genome. Our in-depth chemical characterization and genome mining approach revealed the potential of bacteria from an unconventional niche, an effluent treatment plant. To the best of our knowledge, it is one of the first few reports of acarbose production from the genus Arthrobacter.

Association of DNA repair gene XPC Ala499Val (rs2228000 C>T) and Lys939Gln (rs2228001 A>C) polymorphisms with the risk of chronic myeloid leukemia: A case-control study in a South Indian population

BACKGROUND

Xeroderma pigmentosum complementation group C (XPC), a DNA repair protein, plays an important role in the maintenance of genomic integrity and is essential for the nucleotide excision repair pathway. Polymorphisms in the XPC gene may alter DNA repair leading to genetic instability and oncogenesis. The present study aimed to assess the relationship between the XPC Ala499Val (rs2228000 C>T) and Lys939Gln (rs2228001 A>C) non-synonymous polymorphisms and susceptibility to chronic myeloid leukemia (CML) pathogenesis, disease progression and the response to targeted therapeutic regimen, imatinib mesylate.

METHODS

This case-control study included 212 cases and 212 controls, and the genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism assays.

RESULTS

Our results showed significant association of variant CT (odds ratio = 1.92, 95% confidence interval = 1.21-3.06, p = 0.003) and TT (odds ratio = 2.84, 95% confidence interval = 1.22-6.71, p = 0.007) genotypes in patients with the XPC Ala499Val polymorphism and CML risk. In addition, these genotypes were associated with CML progression to advanced phases (p = 0.006), splenomegaly (p = 0.017) and abnormal lactate dehydrogenase levels (p = 0.03). XPC Lys939Gln was found to correlate with a poor response to therapy, showing borderline significant association with minor cytogenetic response (p = 0.08) and a poor molecular response (p = 0.06). Significant association of the Ala499Val and Lys939Gln polymorphisms with prognosis was observed (Hasford high risk, p = 0.031 and p = 0.019, respectively). Haplotype analysis showed a strong correlation of variant TC haplotype with poor therapy responses (minor cytogenetic response, p = 0.019; poor molecular response, p < 0.0001).

CONCLUSIONS

In conclusion, our results suggest that XPC Ala499Val is a high-penetrance CML susceptibility polymorphism. Both polymorphisms studied are considered as genetic markers with respect to assessing disease progression, therapy response and prognosis in CML patients.

Antibiotic resistance: Global health crisis and metagenomics

Antibiotic resistance is a global problem which affects human health. The imprudent use of antibiotics (medicine, agriculture, aquaculture, and food industry) has resulted in the broader dissemination of resistance. Urban wastewater & sewage treatment plants act as the hotspot for the widespread of antimicrobial resistance. Natural environment also plays an important role in the dissemination of resistance. Mapping of antibiotic resistance genes (ARGS) in environment is essential for mitigating antimicrobial resistance (AMR) widespread. Therefore, the review article emphasizes on the application of metagenomics for the surveillance of antimicrobial resistance. Metagenomics is the next generation tool which is being used for cataloging the resistome of diverse environments. We summarize the different metagenomic tools that can be used for mining of ARGs and acquired AMR present in the metagenomic data. Also, we recommend application of targeted sequencing/ capture platform for mapping of resistome with higher specificity and selectivity.

Impact of cyanobacterial bloom on microbiomes of freshwater lakes

Cyanobacterial blooms are harmful because of their cyanotoxins production. It occurs due to the eutrophication of freshwater reserves. Nagpur city has three lakes which serves as public water resource and are affected by algal bloom events. Metagenomic approach was used for the exploration of taxonomic, catabolic, and resistome profile of these lakes. Taxonomic profiling indicated prevalence of cyanobacterial species like Microcystis, Anabaena, Trichodesmium, Microcoleus, and Nodularia. These bacteria are well known for their association with algal bloom and microcystin production. High Performance Liquid Chromatography (HPLC) detected the presence of microcystin toxin and concentration was relatively higher in Ambazari lakewater. In addition, the presence of several antibiotic resistance genes like vancomycin, beta-lactamase, methicillin, and fluoroquinolones were observed. Genes conferring metal resistance such as copper, cadmium, zinc were also mined indicating presence of metal resistant microorganisms. The study suggests that lake water contaminated with Microcystis (algal bloom) harbors complex microbial community having diverse catabolic and resistome profiles, which negatively affect the ecosystems services.

Atrazine Bioremediation and Its Influence on Soil Microbial Diversity by Metagenomics Analysis

Pesticide accumulation in agricultural soils is an environmental concern, often addressed through distinct bioremediation strategies. This study has tried to analyze various soil bioremediation options viz., biostimulation, bioaugmentation, and natural attenuation in terms of efficiency and the response of autochthonous microbial flora by using atrazine as a model contaminant. Soil mesocosms were established with 100 kg of soil simulating the field conditions. The soil previously exposed to the herbicide was used for the bioaugmentation strategy undertaken in this study. We have tried to analyze how the microbial community responds to a foreign compound, both in terms of taxonomic and functional capacities? To answer this, we have analyzed metagenome of the mesocosms at a time point when 90% atrazine was degraded. Bioaugmentation for bioremediation proved to be efficient with a DT90 value of 15.48 ± 0.79 days, in comparison to the natural attenuation where the DT90 value was observed to be 41.20 ± 1.95 days. Metagenomic analysis revealed the abundance of orders Erysipelotrichales, Selemonadales, Clostridiales, and Thermoanaerobacterales exclusively in SBS mesocosm. Besides Pseudomonas, bacterial genera such as Achromobacter, Xanthomonas, Stenotrophomonas, and Cupriavidus have emerged as the dominant members in various bioremediation strategies tested in this study. Inclusive results suggest that inherent microbial flora adjust their community and metabolic machinery upon exposure to the pollutant. The site under pollutant stress showed efficient microbial communities to bio-remediate the newly polluted terrestrial ecologies in relatively less time and by economic means.

Microbial Metabolic Potential of Phenol Degradation in Wastewater Treatment Plant of Crude Oil Refinery: Analysis of Metagenomes and Characterization of Isolates

The drilling, processing and transportation of oil are the main sources of pollution in water and soil. The current work analyzes the microbial diversity and aromatic compounds degradation potential in the metagenomes of communities in the wastewater treatment plant (WWTP) of a crude oil refinery. By focusing on the degradation of phenol, we observed the involvement of diverse indigenous microbial communities at different steps of the WWTP. The anaerobic bacterial and archaeal genera were replaced by aerobic and facultative anaerobic bacteria through the biological treatment processes. The phyla Proteobacteria, Bacteroidetes and Planctomycetes were dominating at different stages of the treatment. Most of the established protein sequences of the phenol degradation key enzymes belonged to bacteria from the class Alphaproteobacteria. From 35 isolated strains, 14 were able to grow on aromatic compounds, whereas several phenolic compound-degrading strains also degraded aliphatic hydrocarbons. Two strains, Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13, were able to degrade various aromatic and aliphatic pollutants and were further characterized by whole genome sequencing and cultivation experiments in the presence of phenol to ascertain their metabolic capacity in phenol degradation. When grown alone, the intermediates of catechol degradation, the meta or ortho pathways, accumulated into the growth environment of these strains. In the mixed cultures of the strains ICP1 and ICTN13, phenol was degraded via cooperation, in which the strain ICP1 was responsible for the adherence of cells and ICTN13 diminished the accumulation of toxic intermediates.

Valuation of air pollution externalities: comparative assessment of economic damage and emission reduction under COVID-19 lockdown

Air pollution (AP) is one of the major causes of health risks as it leads to widespread morbidity and mortality each year. Its environmental impacts include acid rains, reduced visibility, but more importantly and significantly, it affects human health. The price tag of not managing AP is seen in the rise of chronic obstructive pulmonary disease (COPD), cardiovascular disease, and respiratory ailments like asthma and chronic bronchitis. But as the world battles the corona pandemic, COVID-19 lockdown has abruptly halted human activity, leading to a significant reduction in AP levels. The effect of this reduction is captured by reduced cases of morbidity and mortality associated with air pollution. The current study aims to monetarily quantify the decline in health impacts due to reduced AP levels under lockdown scenario, as against business as usual, for four cities-Delhi, London, Paris, and Wuhan. The exposure assessment with respect to pollutants like particulate matter (PM_2.5 and PM₁₀), NO₂, and SO₂ are evaluated. Value of statistical life (VSL), cost of illness (CoI), and per capita income (PCI) for disability-adjusted life years (DALY) are used to monetize the health impacts for the year 2019 and 2020, considering the respective period of COVID-19 lockdown of four cities. The preventive benefits related to reduced AP due to lockdown is evaluated in comparison to economic damage sustained by these four cities. This helps in understanding the magnitude of actual damage and brings out a more holistic picture of the damages related to lockdown.

Exploration of activated sludge resistome using metagenomics

Antibiotic resistance is a global problem. In India poor waste management and inadequate sanitary are key factors which encourage the dissemination of antimicrobial resistance. Microbial biodiversity serves as an invaluable source for diverse types of bioactive compounds that encompass most of the pharmaceuticals to date. Therefore, in this study, we used the metagenomic approach for the surveillance of antibiotic resistance genes, drug resistant microbes and mobile-genetic elements in two activated sludge metagenome samples collected from Ankleshwar, Gujarat, India. Proteobacteria were found to be the most abundant bacteria among the metagenome analyzed. Twenty-four genes conferring resistance to antibiotics and heavy metals were found. Multidrug resistant "ESKAPE pathogens" were also abundant in the sludge metagenome. Mobile genetic elements like IncP-1 plasmid pKJK5, IncP-1beta multi resistance plasmid and pB8 were also noticed in the higher abundance. These plasmids play an important role in the spread of antibiotic resistance by the horizontal gene transfer. Statistical analysis of both metagenome using STAMP software confirmed presence of mobile genetic elements such as gene transfer agents, phages, Prophages etc. which also play important role in the dissemination of antibiotic resistant genes.

Nitrogen-dependent induction of atrazine degradation pathway in Pseudomonas sp. strain AKN5

Soil isolate Pseudomonas sp. strain AKN5 degrades atrazine as the sole source of nitrogen. The strain showed expeditious growth on medium containing citrate as the carbon source and ammonium chloride as the nitrogen source as compared to citrate plus atrazine or cyanuric acid. Biochemical and nitrogen-source-dependent enzyme induction studies revealed that atrazine is metabolized through hydrolytic pathway and has two segments: the upper segment converts atrazine into cyanuric acid while the lower segment metabolizes cyanuric acid to CO2 and ammonia. Bioinformatics and co-transcriptional analyses suggest that atzA, atzB and atzC were transcribed as three independent transcripts while atzDEF were found to be transcribed as a single polycistronic mRNA indicating operonic arrangement. Transcriptional analysis showed inducible expression of atzA/B/C/DEF from atrazine grown cells while cyanuric acid grown cells showed significantly higher expression of atzDEF. Interestingly, growth profiles and enzyme activity measurements suggests that strain utilizes a simple nitrogen source (ammonium chloride) over the complex (atrazine or cyanuric acid) when grown on dual nitrogen source. These results suggest that atrazine degradation genes were up-regulated in the presence of atrazine but repressed in the presence of simple nitrogen source like ammonium chloride.

Decoding microbial community intelligence through metagenomics for efficient wastewater treatment

Activated sludge, a microbial ecosystem at industrial wastewater treatment plants, is an active collection of diverse gene pool that creates the intelligence required for coexistence at the cost of pollutants. This study has analyzed one such ecosystem from a site treating wastewater pooled from over 200 different industries. The metagenomics approach used could predict the degradative pathways of more than 30 dominating molecules commonly found in wastewater. Results were extended to design a bioremediation strategy using 4-methylphenol, 2-chlorobenzoate, and 4-chlorobenzoate as target compounds. Catabolic potential required to degrade four aromatic families, namely benzoate family, PAH family, phenol family, and PCB family, was mapped. Results demonstrated a network of diverse genera, where a few phylotypes were seen to contain diverse catabolic capacities and were seen to be present in multiple networks. The study highlights the importance of looking more closely at the microbial community of activated sludge to harness its latent potential. Conventionally treated as a black box, the activated biomass does not perform at its full potential. Metagenomics allows a clearer insight into the complex pathways operating at the site and the detailed documentation of genes allows the activated biomass to be used as a bioresource.

Plasmonics driven engineered pasteurizers for solar water disinfection (SWADIS)

Rampant environmental pollution is the most ubiquitous concern of current world. A sustainable panacea to overarching contamination of water-borne pathogens demands cheap and eco-friendly oriented research. Solar energy is effortlessly accessible in most of the weather conditions and can be used for water decontamination. In this context, Solar Water Disinfection (SWADIS) appears to be feasible solution. Herein we are reporting newly developed Carbon nanoparticles (CNP) which shows absorption of light in broad region extending from Ultraviolet-Visible (UV) to Infrared Spectroscopy (IR). This CNP with pronounced photothermal effect has been used for SWADIS. Photothermal effect of plasmonic nanomaterials has massive potential and has exploited for disinfection of water. Moving towards practical device design we have developed an efficient CNP based Multipurpose Solar Pasteurizer (MSP) and Nano-Solar Pasteurizer (NSP) which can efficiently perform the SWADIS. Result shows that upon irradiation under natural solar radiation pasteurizers can thermally inactivate the bacteria. The system proves to be able to perform 100% bacterial inactivation in sunny days. We also conducted bacterial inactivation experiments by simulating 106 CFU mL^-1 concentration of E. coli in water to mimic field conditions. Results are evident that pasteurizers achieved 100% bacterial inactivation within period of ˜45 min under sunlight.

Evaluation of biogas production potential of kitchen waste in the presence of spices

Anaerobic digestion (AD) of kitchen waste (KW) for biogas production is a major challenge to all over the world due to significant compositional variations in KW, such as different types and quantities of spices used for preparing food. Spices may affect the AD process owing to their antimicrobial activity. In this paper, the effect of spices (garlic, red chili, cinnamon, coriander, clove, turmeric, cardamom, black pepper) on AD of KW has been investigated. Batch experiments were carried out to determine the maximum biogas production potential, methane production rate and lag phase for biogas production. Analysis of the results revealed different magnitude of inhibition of the AD process of KW in the presence of different spices. Cinnamon, cardamom and clove resulted >85%, black pepper resulted 75%, while coriander, chili, turmeric and garlic resulted 55-70% reduction in cumulative biogas yield. Elemental analysis showed high concentration of heavy metals in the spices, which along with other bioactive components of the spices could be responsible for the inhibitory effect of the spices on biomethanation. Microbial examination of the digestate also showed a decrease in population of fermentative and methanogenic bacteria in the presence of spices.

Microbial population shift caused by sulfamethoxazole in engineered-Soil Aquifer Treatment (e-SAT) system

The engineered-Soil Aquifer Treatment (e-SAT) system was exploited for the biological degradation of Sulfamethoxazole (SMX) which is known to bio-accumulate in the environment. The fate of SMX in soil column was studied through laboratory simulation for a period of 90 days. About 20 ppm SMX concentration could be removed in four consecutive cycles in e-SAT. To understand the microbial community change and biological degradation of SMX in e-SAT system, metagenomic analysis was performed for the soil samples before (A-EBD) and after SMX exposure (B-EBD) in the e-SAT. Four bacterial phyla were found to be present in both the samples, with sample B-EBD showing increased abundance for Actinobacteria, Bacteroidetes, Firmicutes and decreased Proteobacterial abundance compared to A-EBD. The unclassified bacteria were found to be abundant in B-EBD compared to A-EBD. At class level, classes such as Bacilli, Negativicutes, Deltaproteobacteria, and Bacteroidia emerged in sample B-EBD owing to SMX treatment, while Burkholderiales and Nitrosomonadales appeared to be dominant at order level after SMX treatment. Furthermore, in response to SMX treatment, the family Nitrosomonadaceae appeared to be dominant. Pseudomonas was the most dominating bacterial genus in A-EBD whereas Cupriavidus dominated in sample B-EBD. Additionally, the sulfur oxidizing bacteria were enriched in the B-EBD sample, signifying efficient electron transfer and hence organic molecule degradation in the e-SAT system. Results of this study offer new insights into understanding of microbial community shift during the biodegradation of SMX.

Atrazine exposure causes mitochondrial toxicity in liver and muscle cell lines

Objective:

Chronic exposure to atrazine and other pesticides is reported to cause metabolic disorders, yet information on effects of atrazine on expression of genes relevant to mitochondrial function is largely missing. In the present study, therefore, we investigated the expression of a battery of nuclear- and mitochondrial-encoded genes involved in oxidative phosphorylation (OXPHOS) in human liver (HepG2) and rat muscle (L6) cell lines due to short-term atrazine exposure.

Materials and Methods:

We have determined the EC₅₀ values of atrazine for cytotoxicity and mitochondrial toxicity (mitotoxicity) in terms of adenosine triphosphate (ATP) content in HepG2 and L6 cells. Further, the mRNA expression of nuclear- and mitochondrial-encoded genes was analyzed using quantitative real-time polymerase chain reaction.

Results:

The EC₅₀ value of atrazine for mitotoxicity in HepG2 and L6 cells was found to be about 0.162 and 0.089 mM, respectively. Mitochondrial toxicity was indicated by reduction in ATP content following atrazine exposure. Atrazine exposure resulted in down-regulation of many OXPHOS subunits expression and affected biogenesis factors’ expression. Most prominently, superoxide dismutase (SOD) and sirtuin 3 (SIRT3) expressions were up-regulated in HepG2 cells, whereas SIRT3 expression was alleviated in L6 cells, without significant changes in SOD levels. Mitochondrial transcription factor A (TFAM) and SIRT1 expression were significantly down-regulated in both cell lines.

Conclusion:

Results suggest that TFAM and SIRT1 could be involved in atrazine-induced mitochondrial dysfunction, and further studies can be taken up to understand the mechanism of mitochondrial toxicity. Further study can also be taken up to explore the possibility of target genes as biomarkers of pesticide toxicity.

Association of Vascular Endothelial Growth Factor A (VEGFA) and its Receptor (VEGFR2) Gene Polymorphisms with Risk of Chronic Myeloid Leukemia and Influence on Clinical Outcome

INTRODUCTION

Vascular endothelial growth factor A (VEGFA) and its kinase insert domain receptor (VEGFR2/KDR) were reported to be upregulated in chronic myeloid leukemia (CML); however, the influence of polymorphisms in VEGFA and VEGFR2 in CML pathogenesis and therapeutic response, have not yet been elucidated.

METHODS

We aimed to analyze these polymorphisms in 212 CML patients and 212 healthy controls by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach.

RESULTS

The VEGFA+936C>T polymorphism did not differ significantly between the CML patients and controls. The frequency of CT genotype was higher in CML patients than in controls (25 vs. 18%), higher in males than in females (29 vs. 18%), was more prevalent in the patients with splenomegaly (p = 0.03), and was negatively associated with lactate dehydrogenase (LDH) levels (p = 0.01). The frequency of VEGFR2 mutant T-allele was higher in CML patients than controls (p < 0.0001). In the dominant model, patients having the combined AT and TT genotypes were associated with 2.6-fold higher risk of CML [odds ratio (OR) = 2.6, 95% confidence interval (CI) = 1.71–3.97, p < 0.0001]. VEGFR2 AT genotype was significantly associated with high blast count (p = 0.006), minor hematological response (p = 0.03) and poor cytogenetic response (p = 0.003), indicating its role in therapeutic resistance. In contrast, poor molecular response was observed in patients with TT genotype (p = 0.02). VEGFA+936C>T polymorphism was found to have synergistic interaction with VEGFR2+1416A>T in inflating the risk for CML further (P(interaction) = 0.0002).

CONCLUSION

Our results indicate that VEGFR2+1416A>T polymorphism may be a useful marker in assessing the disease progression in CML patients. In addition, VEGFA+936C>T was observed to have additive effect in inflating the risk further.

Insights in Waste Management Bioprocesses Using Genomic Tools

Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.

In silico analysis for prediction of degradative capacity of Pseudomonas putida SF1

The study employs draft genome sequence data to explore p-nitrophenol (PNP) degradation activity of Pseudomonas putida strain SF-1 at a genomic scale. Annotation analysis proposes that the strain SF1 not only possesses the gene cluster for PNP utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. Further, the analysis was carried out to understand more details of PNP 4-monooxygenase and its regulator. A comparative analysis of PNP 4-monooxygenase from SF1 was carried out for prediction of its tertiary structure; and also its binding affinity with PNP, FAD, NADH and NADPH using FlexX docking. The tertiary structure of regulator was also predicted along with its conserved DNA binding residues. Regulator binding site (RBS) and promoter region were mapped for the PNP degradation gene cluster. Based on genome sequence analysis, the study unveiled the genomic attributes for a versatile catabolic potential of Pseudomonas putida strain SF-1 for different aromatic compounds.

Association of The Common CYP1A1*2C Variant (Ile462Val Polymorphism) with Chronic Myeloid Leukemia (CML) in Patients Undergoing Imatinib Therapy

OBJECTIVE

Cytochrome P450 is one of the major drug metabolizing enzyme families and its role in metabolism of cancer drugs cannot be less emphasized. The association be- tween single nucleotide polymorphisms (SNPs) in CYP1A1 and pathogenesis of chronic myeloid leukemia (CML) has been investigated in several studies, but the results observed vary based on varied risk factors. The objective of this study was to investigate the risk factors associated with the CYP1A1*2C [rs1048943: A>G] polymorphism in CML patients and its role in therapeutic response to imatinib mesylate (IM) affecting clinico-pathological parameters, in the Indian population.

MATERIALS AND METHODS

In this case-control study, CYP1A1*2C was analysed in CML patients. After obtaining approval from the Ethics Committee of oncology hospital, we collected blood samples from 132 CML patients and 140 matched controls. Genom- ic DNA was extracted and all the samples were analysed for the presence of the CYP1A1*2C polymorphism using allele-specific polymerase chain reaction, and we examined the relationship of genotypes with risk factors such as gender, age, phase of the disease and other clinical parameters.

RESULTS

We observed a significant difference in the frequency distribution of CYP1A1*2C genotypes AA (38 vs. 16%, P=0.0001), AG (57 vs. 78%, P=0.0002) and GG (5 vs. 6%, P=0.6635) between patients and controls. In terms of response to IM therapy, significant variation was observed in the frequencies of AA vs AG in major (33 vs 67%) and poor (62 vs 31%) hematological responders, and AA vs AG in major (34 vs. 65%) and poor (78 vs. 22%) cytogenetic responders. However, the patients with the GG homozygous genotype did not show any significant therapeutic outcome.

CONCLUSION

The higher frequency of AG in controls indicates that AG may play a protec- tive role against developing CML. We also found that patients with the AG genotype showed favorable treatment response towards imatinib therapy, indicating that this polymorphism could serve as a good therapeutic marker in predicting response to such therapy.

Antimicrobial activity of Alcaligenes sp. HPC 1271 against multidrug resistant bacteria

Alcaligenes sp. HPC 1271 demonstrated antibacterial activity against multidrug resistant bacteria, Enterobacter sp., resistant to sulfamethoxazole, ampicillin, azithromycin, and tetracycline, as well as against Serratia sp. GMX1, resistant to the same antibiotics with the addition of netilmicin. The cell-free culture supernatant was analyzed for possible antibacterials by HPLC, and the active fraction was further identified by LC-MS. Results suggest the production of tunicamycin, a nucleoside antibiotic. The draft genome of this bacterial isolate was analyzed, and the 4.2 Mb sequence data revealed six secondary metabolite-producing clusters, identified using antiSMASH platform as ectoine, butyrolactone, phosphonate, terpene, polyketides, and nonribosomal peptide synthase (NRPS). Additionally, the draft genome demonstrated homology to the tunicamycin-producing gene cluster and also defined 30 ORFs linked to protein secretion that could also play a role in the antibacterial activity observed. Gene expression analysis demonstrated that both NRPS and dTDP-glucose 4,6-dehydratase gene clusters are functional and could be involved in antibacterial biosynthesis.

s-triazine degrading bacterial isolate Arthrobacter sp. AK-YN10, a candidate for bioaugmentation of atrazine contaminated soil

The Arthrobacter sp. strain AK-YN10 is an s-triazine pesticide degrading bacterium isolated from a sugarcane field in Central India with history of repeated atrazine use. AK-YN10 was shown to degrade 99 % of atrazine in 30 h from media supplemented with 1000 mg L(-1) of the herbicide. Draft genome sequencing revealed similarity to pAO1, TC1, and TC2 catabolic plasmids of the Arthrobacter taxon. Plasmid profiling analyses revealed the presence of four catabolic plasmids. The trzN, atzB, and atzC atrazine-degrading genes were located on a plasmid of approximately 113 kb.The flagellar operon found in the AK-YN10 draft genome suggests motility, an interesting trait for a bioremediation agent, and was homologous to that of Arthrobacter chlorophenolicus. The multiple s-triazines degradation property of this isolate makes it a good candidate for bioremediation of soils contaminated by s-triazine pesticides.

Comparative metagenomics demonstrating different degradative capacity of activated biomass treating hydrocarbon contaminated wastewater

This study demonstrates the diverse degradative capacity of activated biomass, when exposed to different levels of total dissolved solids (TDS) using a comparative metagenomics approach. The biomass was collected at two time points to examine seasonal variations. Four metagenomes were sequenced on Illumina Miseq platform and analysed using MG-RAST. STAMP tool was used to analyse statistically significant differences amongst different attributes of metagenomes. Metabolic pathways related to degradation of aromatics via the central and peripheral pathways were found to be dominant in low TDS metagenome, while pathways corresponding to central carbohydrate metabolism, nitrogen, organic acids were predominant in high TDS sample. Seasonal variation was seen to affect catabolic gene abundance as well as diversity of the microbial community. Degradation of model compounds using activated sludge demonstrated efficient utilisation of single aromatic ring compounds in both samples but cyclic compounds were not efficiently utilised by biomass exposed to high TDS.

Biophysical, biopharmaceutical and toxicological significance of biomedical nanoparticles

Understanding of interplay between nanoparticles physicochemical and biophysical properties, and their impact on pharmacokinetic biodistribution and toxicological properties help designing of appropriate nanoparticle products for biomedical applications.

Metagenomic analysis of oxygenases from activated sludge

Oxygenases play a key role in degradation of the aromatic compounds in the wastewater. This study explores the oxygenase coding gene sequences from the metagenome of activated biomass. Based on these results, the catabolic capacity of the activated sludge was assessed towards degradation of naphthalene, anthracene, phenol, biphenyl and o-toluidine. Oxygenases found in this study were compared with oxygenases from three other metagenome datasets. Results demonstrate that despite different geographical locations and source, many genes coding for oxygenases were common between treatment plants. 1, 2 Homogentisate dioxygenase and phenylacetate CoA oxygenases were present in all four metagenomes. Metagenomics provides a vast amount of data that needs to be mined with specific targets to harness the potential of the microbial world.

Shifts in microbial community in response to dissolved oxygen levels in activated sludge

This study evaluates the degradative efficiency of activated biomass collected from a Common Effluent Treatment Plant (CETP) under three different dissolved oxygen (DO) levels, 1, 2 and 4mgl(-1). The change in bacterial diversity with reference to DO levels was also analyzed. Results demonstrate that degradative efficiency was the highest, when the reactor was maintained at 4mgl(-1) DO, but amplicon library analysis showed a greater diversity of bacteria in the reactor maintained at 2mgl(-1) DO. Bacteria belonging to the order Desulfuromonadales, Entomoplasmatales, Pasteurellales, Thermales and Chloroflexales have only been detected in this reactor. Ammonia and nitrate levels in all three reactors indicated efficient nitrification process. Results of this study offer new insights into understanding the performance of activated biomass vis-à-vis microbial diversity and degradative efficiency with reference to DO. This information would be useful in improving the efficiency of any wastewater treatment plant.

Soil mesocosm studies on atrazine bioremediation

Accumulation of pesticides in the environment causes serious issues of contamination and toxicity. Bioremediation is an ecologically sound method to manage soil pollution, but the bottleneck here, is the successful scale-up of lab-scale experiments to field applications. This study demonstrates pilot-scale bioremediation in tropical soil using atrazine as model pollutant. Mimicking field conditions, three different bioremediation strategies for atrazine degradation were explored. 100 kg soil mesocosms were set-up, with or without atrazine application history. Natural attenuation and enhanced bioremediation were tested, where augmentation with an atrazine degrading consortium demonstrated best pollutant removal. 90% atrazine degradation was observed in six days in soil previously exposed to atrazine, while soil without history of atrazine use, needed 15 days to remove the same amount of amended atrazine. The bacterial consortium comprised of 3 novel bacterial strains with different genetic atrazine degrading potential. The progress of bioremediation was monitored by measuring the levels of atrazine and its intermediate, cyanuric acid. Genes from the atrazine degradation pathway, namely, atzA, atzB, atzD, trzN and trzD were quantified in all mesocosms for 60 days. The highest abundance of all target genes was observed on the 6th day of treatment. trzD was observed in the bioaugmented mesocosms only. The bacterial community profile in all mesocosms was monitored by LH-PCR over a period of two months. Results indicate that the communities changed rapidly after inoculation, but there was no drastic change in microbial community profile after 1 month. Results indicated that efficient bioremediation of atrazine using a microbial consortium could be successfully up-scaled to pilot scale.

Mining and assessment of catabolic pathways in the metagenome of a common effluent treatment plant to induce the degradative capacity of biomass

Metagenome analysis was used to understand the microbial community in activated sludge treating industrial wastewaters at a Common Effluent Treatment Plant (CETP) in South India. The taxonomic profile mapped onto National Center for Biotechnology Information (NCBI) taxonomy using MEtaGenome ANalyzer (MEGAN), demonstrated that the most abundant domain belonged to prokaryotes, dominated by bacteria. Bacteria representing nine phyla were identified from the sequence data including representatives from two new phyla, Synergistetes and Elusimicrobia. Functional analysis of the metagenome, with specific reference to the metabolism of aromatic compounds, revealed the dominance of genes of the central meta-cleavage pathway. This information was used to improve the degradative efficiency in the wastewater treatment plant. A pilot scale plant was set up with 200L of activated sludge using salicylate induced sludge and results demonstrated 52% removal in chemical oxygen demand (COD) against non-induced biomass.

Monitoring bioremediation of atrazine in soil microcosms using molecular tools

Molecular tools in microbial community analysis give access to information on catabolic potential and diversity of microbes. Applied in bioremediation, they could provide a new dimension to improve pollution control. This concept has been demonstrated in the study using atrazine as model pollutant. Bioremediation of the herbicide, atrazine, was analyzed in microcosm studies by bioaugmentation, biostimulation and natural attenuation. Genes from the atrazine degrading pathway atzA/B/C/D/E/F, trzN, and trzD were monitored during the course of treatment and results demonstrated variation in atzC, trzD and trzN genes with time. Change in copy number of trzN gene under different treatment processes was demonstrated by real-time PCR. The amplified trzN gene was cloned and sequence data showed homology to genes reported in Arthrobacter and Nocardioides. Results demonstrate that specific target genes can be monitored, quantified and correlated to degradation analysis which would help in predicting the outcome of any bioremediation strategy.

Demonstration of sequential adaptation strategy for developing salt tolerance in bacteria for wastewater treatment: a study using Escherichia coli as model

A wastewater isolate identified as Escherichia coli HPC781 was adapted for high salt concentration through sequential transfers in Luria Broth (LB). The cells were grown in LB with 5% sodium chloride (NaCl) and were analyzed for the acquired salt resistance network through gene expression profiles. Microarray studies revealed TCA, glyoxylate shunt and acetyl Co-A metabolism as key nodes for stress combat to arrive at compromised physiology. It also proposed that the cells were receiving signals from salt environment via OmpR-EnvZ two component systems and stress dependent general regulatory protein rpoH and rpoE. The salt adapted culture, when challenged with wastewater having additional 5% salt showed growth. The work represents a tactic to adjust biochemical network towards stress and reveals its applicability via real-time PCR measurement of genes in wastewater. The study proposes that the recycled biomass with an adaptation strategy could be applied for treatment of wastewater with high salt levels.

Mining the metagenome of activated biomass of an industrial wastewater treatment plant by a novel method

Metagenomic libraries herald the era of magnifying the microbial world, tapping into the vast metabolic potential of uncultivated microbes, and enhancing the rate of discovery of novel genes and pathways. In this paper, we describe a method that facilitates the extraction of metagenomic DNA from activated sludge of an industrial wastewater treatment plant and its use in mining the metagenome via library construction. The efficiency of this method was demonstrated by the large representation of the bacterial genome in the constructed metagenomic libraries and by the functional clones obtained. The BAC library represented 95.6 times the bacterial genome, while, the pUC library represented 41.7 times the bacterial genome. Twelve clones in the BAC library demonstrated lipolytic activity, while four clones demonstrated dioxygenase activity. Four clones in pUC library tested positive for cellulase activity. This method, using FTA cards, not only can be used for library construction, but can also store the metagenome at room temperature.

Characterization of Phragmites cummunis rhizosphere bacterial communities and metabolic products during the two stage sequential treatment of post methanated distillery effluent by bacteria and wetland plants

This study deals with the characterization of rhizosphere bacterial communities and metabolic products produced during the two stage sequential treatment of post methanated distillery effluent by bacteria and constructed wetland plants. Results showed that bacterial treatment followed by wetland plants (Phragmites cummunis) resulted 94.5% and 96.0% reduction in BOD and COD values, respectively. The PCR-RFLP analysis showed the presence of Stenotrophomonas, Enterobacter, Pantoea, Acinetobacter and Klebsiella sp., as dominant rhizosphere bacterial communities which play an important role in degradation and decolorization of PMDE in wetland treatment system. Further, the LC-MS-MS and other spectrophotometric analysis have shown that most of the pollutants detected in untreated PMDE were diminished from bacteria and wetland plant treated PMDE indicating that bacteria and wetland plant rhizosphere microbes utilized them as carbon, nitrogen and energy source. While, methylbenzene, furfuryl alcohol, and 4-vinyl-2-methoxyphenol were detected as metabolites in bacteria and hexadecanol in wetland plant rhizosphere treated PMDE.

Diversity of aromatic ring-hydroxylating dioxygenase gene in Citrobacter

Genetic and functional diversity of Citrobacter spp. for their abilities to degrade aromatic compounds was evaluated to develop mixed cultures or a consortium for bioremediation technology. Thirty Citrobacter strains isolated from various effluent treatment plants were found to degrade a range of aromatic compounds: phenol, benzoate, hydroxy benzoic acid and biotransform mono-chlorophenols and di-chlorophenol within 24 to 48 h of incubation at 30 °C. Sequence similarity and phylogeny of the ARHD gene transcripts (730 nucleotides) depicted their diversity within 9 Citrobacter strains: HPC255, HPC369, HPC560, HPC570, HPC784, HPC1196, HPC1216, HPC1276 and HPC1299. Here, the degree of associations varied up to 84% with (i) ARHD α-sub unit (SU), (ii) LSU of Phenylpropionate dioxygenase (PDO), (iii) Phenol hydroxylase α-SU, (iv) Benzoate 1,2-dioxygenase, α-SU, (v) Naphthalene dioxygenase LSU, etc. This study has provided basic information, which can be used to develop a consortium of bacteria with mutually beneficial characteristics.