Genomic and phenotypic characterisation of Enterococcus mundtii AM_AQ_BC8 for its anti-biofilm, antimicrobial and probiotic potential.

Enterococcus mundtii AM_AQ_BC8 isolated from biofouled filtration membrane was characterised as a potential probiotic bacterium showing strong L-lactic acid-producing capability. Experimental studies revealed that E. mundtii AM_AQ_BC8 possess antibiofilm and antimicrobial ability too, as tested against strong biofilm-forming bacteria like Pseudomonas spp. The present study has evaluated the genetic potential of E. mundtii AM_AQ_BC8 through genome sequencing. Whole genome analysis revealed the presence of key genes like ldh_1 and ldh_2 responsible for lactic acid production along with genes encoding probiotic features such as acid and bile salt resistance (dnaK, dnaJ, argS), fatty acid synthesis (fabD, fabE) and lactose utilisation (lacG, lacD). The phylogenomic analysis based on OrthoANI (99.85%) and dDDH (96.8%) values revealed that the strain AM_AQ_BC8 shared the highest homology with E. mundtii. The genome sequence of strain AM_AQ_BC8 has been deposited to NCBI and released with GenBank accession no. SAMN32531201. The study primarily demonstrated the probiotic potential of E. mundtii AM_AQ_BC8 isolate, for L-lactate synthesis in high concentration (8.98 g/L/day), which also showed anti-biofilm and antimicrobial activities.

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, ß-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.

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.

Phytochemical Analysis and Demonstration of Antioxidant, Antibacterial, and Antibiofilm Activities of Ethnomedicinal Plants of North East India.

Ethnomedicinal plants are a rich reservoir of active compounds with potent pharmacological properties. Therefore, plants could serve as a source for the discovery of active antimicrobial and antioxidant agents and are focused because of their low toxicity, economic viability, easy availability, etc. In this regard, phytochemical analyses, viz. ß-carotene, total sugar, reducing sugar, vitamin C, total carotenoids, protein, total phenolic content (TPC), and total flavonoid content (TFC) of 20 ethnomedicinal plants of North East India (NEI) were evaluated in this study. The antibacterial activity against human pathogens and antioxidant potential of plant extracts was also demonstrated. The minimum inhibitory concentration (MIC80), minimum bactericidal concentration (MBC), and total antibacterial activity (TAA) of the active extracts were evaluated against Pseudomonas aeruginosa and Chromobacterium violaceum. The active extracts were also examined for antibiofilm as well as anti-pyocyanin activities against P. aeruginosa and anti-QS activity against C. violaceum at sub-MICs. The study demonstrated variable concentration of phytochemicals of the extracts, viz. ß-carotene (0.29-8.91 mg g-1), total sugar (2.92-30.6 mM), reducing sugar (0.44-14.5 mM), vitamin C (8.41-31.3 mg g-1), total carotenoids (14.9-267.0 mg g-1), protein (5.65-283 mg g-1), TPC (5.32-31.0 mg GAE/g DW), and TFC (1.74-68.2 mg QE/g DW). The plant extracts also exhibited potent antioxidant and antibacterial activities against both Gram-positive and Gram-negative bacteria. Some of the extracts also demonstrated significant biofilm inhibition and eradication, anti-pyocyanin, and anti-QS activities at sub-MICs. The selected ethnomedicinal plants are rich in phytochemicals and demonstrated potent antioxidant, antibacterial, and antibiofilm activities, thus could serve as the important source of novel antioxidant and antimicrobial agents.

Role of plant growth-promoting rhizobacteria in boosting the phytoremediation of stressed soils: Opportunities, challenges, and prospects.

Soil is considered as a vital natural resource equivalent to air and water which supports growth of the plants and provides habitats to microorganisms. Changes in soil properties, productivity, and, inevitably contamination/stress are the result of urbanisation, industrialization, and long-term use of synthetic fertiliser. Therefore, in the recent scenario, reclamation of contaminated/stressed soils has become a potential challenge. Several customized, such as, physical, chemical, and biological technologies have been deployed so far to restore contaminated land. Among them, microbial-assisted phytoremediation is considered as an economical and greener approach. In recent decades, soil microbes have successfully been used to improve plants' ability to tolerate biotic and abiotic stress and strengthen their phytoremediation capacity. Therefore, in this context, the current review work critically explored the microbial assisted phytoremediation mechanisms to restore different types of stressed soil. The role of plant growth-promoting rhizobacteria (PGPR) and their potential mechanisms that foster plants' growth and also enhance phytoremediation capacity are focussed. Finally, this review has emphasized on the application of advanced tools and techniques to effectively characterize potent soil microbial communities and their significance in boosting the phytoremediation process of stressed soils along with prospects for future research.

Ecofriendly phytofabrication of silver nanoparticles using aqueous extract of Cuphea carthagenensis and their antioxidant potential and antibacterial activity against clinically important human pathogens.

The green synthesis of nanoparticles (NPs) is the safest, ecofriendly, cost-effective, and non-hazardous approach of nanotechnology. In the current study, we described the green synthesis of silver nanoparticles (AgNPs) using Cuphea carthagenensis aqueous leaf extract as a reducing, capping, and stabilizing agent. The study aims at the synthesis, characterization, optimization, and determination of the antibacterial activity of Cc-AgNPs against clinically important human pathogens. Coating of cotton fabrics with Cc-AgNPs and their efficacy against skin infection causing organisms was also evaluated. Furthermore, antioxidant activity, growth assay and time kill assay of Cc-AgNPs were also performed in the study. The biosynthesized Cc-AgNPs were characterized by UV-visible spectrometry, energy-dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FTIR). The spectroscopic and microscopic analysis demonstrated biosynthesis of face-centered cubic (fcc) crystalline spherical Cc-AgNPs with an average particle size of 10.65 ± 0.1 nm. Optimized peak synthesis of Cc-AgNPs was reported at pH7, 55 °C, 4 mM silver nitrate, and 5:45 (plant extract: silver nitrate). Cc-AgNPs exhibited potent antioxidant effect and antibacterial activity against both Gram-positive and Gram-negative bacteria. The lowest MIC (15 µg/ml) and MBC (25 µg/ml) values were reported against S. typhimurium. The Cc-AgNPs coated fabrics demonstrated potent antibacterial activity against tested strains. This application could be helpful in wound healing management. Furthermore, the hemolytic analysis demonstrated that Cc-AgNPs exhibit non-toxic nature against Red Blood Cells (RBCs) at the tested concentrations. In conclusion, the investigation demonstrated a fast, stable, and eco-friendly approach to the biosynthesis of Cc-AgNPs along with their antibacterial and antioxidant properties.

Managing gene expression in Pseudomonas simiae EGD-AQ6 for chloroaromatic compound degradation.

Pseudomonas simiae EGD-AQ6 is capable of utilizing chloroaromatic compound i.e., 2-4-D efficiently in its biofilm phenotype. The differential accumulation of intermediate 4-chlorocatechol rates were significant in planktonic and biofilm phenotypes, as well as in the  increased biofilm adapted cell numbers. Interestingly, response surface analysis demonstrated the combined positive effects of 2-4-D degradation and 4-CCA accumulation rates and the gene expression profiles, with significant up-regulation of degradative and biofilm genes, and greater participation of pellicle genes in the biofilm phenotypes than their planktonic counterparts, thereby revealing a phenotype variation. It positively validated the physiological data. Furthermore, the sequence similarity of the 2-4-D catabolic and biofilm-forming proteins (pel ABCDEFG and pga ABCD), which are responsible for building carbohydrate rich extracellular matrix, were significant with the respective organisms. This is the first study, which endorses this strain to be unique in efficient chloro-aromatic degradation through phenotype variation, thereby proving a potential candidate in the improvement of bioremediation technologies.

Nitric oxide-secreting probiotics as sustainable bio-cleaners for reverse osmosis membrane systems.

Membrane biofouling in water purification plants is a serious issue of worldwide concern. Various chemical, physical, and biochemical processes are practised for membrane clean-up. A high-dosage treatment adversely affects the life expectancy of the membrane, and minimum dosage seems unable to deteriorate the biofilms on the membrane. It is reported that quorum quenchers like nitric oxide (NO) disrupt biofilm signals through metabolic rewiring, and also NO is known to be secreted by probiotics (good bacteria). In the present review, it is hypothesized that if probiotic biofilms secreting NO are used, other microbes that aggregate on the filtration membrane could be mitigated. The concept of probiotic administration on filtration membrane seeks to be encouraged because probiotic bacteria will not be hazardous, even if released during filtration. The fundamental motive to present probiotics as a resource for sequestering NO may serve as multifunctional bioweapons for membrane remediation, which will virtually guarantee their long-term sustainability and green approach.

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.

Genomic insight for algicidal activity in Rhizobium strain AQ_MP.

Occurrence of Harmful Algal Blooms (HABs) creates a threat to aquatic ecosystem affecting the existing flora and fauna. Hence, the mitigation of HABs through an eco-friendly approach remains a challenge for environmentalists. The present study provides the genomic insights of Rhizobium strain AQ_MP, an environmental isolate that showed the capability of degrading Microcystis aeruginosa (Cyanobacteria) through lytic mechanisms. Genome sequence analysis of Rhizobium strain AQ_MP unraveled the algal lytic features and toxin degradative pathways in it. Functional genes of CAZymes such as glycosyltransferases (GT), glycoside hydrolases (GH), polysaccharide lyases (PL) which supports algal polysaccharide degradation (lysis) were present in Rhizobium strain AQ_MP. Genome analysis also clarified the presence of the glutathione metabolic pathway, which is the biological detoxification pathway responsible for toxin degradation. The conserved region mlrC, a microcystin toxin-degrading gene was also annotated in the genome. The study illustrated that Rhizobium strain AQ_MP harbored a wide range of mechanisms for the lysis of Microcystis aeruginosa cells and its toxin degradation. In future, this study finds promiscuity for employing Rhizobium strain AQ_MP species for bioremediation, based on its physiological and genomic analysis.

Metagenomic Insight Towards Vanillin-Mediated Membrane Biofouling Prevention: In Silico Docking Validation.

Biofouling leads to water quality deterioration and higher maintenance cost for cleaning of membranes. The present study has demonstrated the application of a biomolecule (vanillin) in scrubbing and destabilizing biofilms of drinking water reverse osmosis (RO) membrane module in lab scale reactor set-up. Reverse osmosis membrane reactor was connected with tap water supply and subjected with optimal concentration of vanillin. The pressure drop was delayed by 17-20 days as compared to control reactor. Real-time PCR analysis of metagenome indicated the reduced copy number of functional biofilm-associated genes (bdlA, lasI, pgaC) in treated membrane. SEM and metagenome analysis revealed that the sticky biofilm communities shifted to loosely bound emboli after vanillin treatment. Metagenome sequence analysis revealed the inhibitory activity against major biofouling biota like members of Proteobacteria, Acidobacteria, Acnitobacteria, Bacteroidetes, Candidatus, Nitrospira, and Firmicutes. Biofouled membrane metagenome sequence was also compared with real-life (brackish water, waste water, domestic drinking water) biofouled membrane communities. In silico docking of vanillin to receptor proteins and chemical configuration simulation along with other phenolic derivatives were performed, which suggested that the autoiducer signal capability of vanillin was effective against representative broad spectrum biofilm population. Vanillin exhibited the quorum-quenching mode of action by virtue of docking towards similar amino acid (Thr 131, Ilu 214) responsible of autoinducer signal anchoring in the transcriptional regulatory proteins.

Biotic control of harmful algal blooms (HABs): A brief review.

The water bodies, mainly coastal and lake, remain tainted worldwide, mostly because of the Cyanobacteria harbored in Harmful Algal Blooms (HABs). The main reason for the flourishing of blooms depends on the eutrophication. Blooms could be toxic as well as non-toxic, depending on the bloom-forming species. The blooms affect the water body, aquatic ecosystem and also dependents like human. A large number of organisms, including bacteria, viruses, fungi, fish and zooplankton have adverse effects on Cyanobacteria either through infection, predation or by the production of the algicidal compounds. It was reported, these microorganisms have species-specific interactions and hence differ in their interaction mechanism. The present review emphasises on the role of selected microbial species and the mechanism they follow for mitigation of HABs. Generally lab-scale entities were reported to involve lytic agents, like cyanobacteriolytic substances, released by bacteria. Cyanobacterial species release Cyanotoxins which may affect the water quality. Growing biotic factors in a large quantity and discharging it into the water-body needs excessive efficacy and economic requisite and hence the feasibility of extrapolation of the laboratory results in the field still finds promiscuity towards mitigation of HABs.

D-Tryptophan governs biofilm formation rates and bacterial interaction in P. mendocina and S. aureus.

Biofilm genesis by Pseudomonasand Staphylococcus sp is associated with biofouling in natural settings. D-Tryptophan (D-Trp) inhibits bacterial biofilms and have been proposed for biofouling control applications. In this study, D-Trp significantly inhibited Pseudomonas mendocina and Staphylococcus aureuscell attachment (biofilm formation) rates on polystyrene96-well microtiter plates in comparison with L-Tryptophan (L-Trp) and mixtures of D-/L-Tryptophan (D-/L-Trp). Theinhibitory effect was greater on P. mendocina,where the rate of cell adherence was declined to 8.79105cells/h from8.09106cells/h (control) inP. mendocina.InS. aureusit was declined to 4.29107cells/h from 9.29107cells/h(control) at 1 mM concentration. It hindered the intracellular communication and adherence in both the strains, as con-firmed by SEM and real time PCR analysis. Addition of D-Trp to preformed biofilms also caused partial disassembly. Intraand interbacterial aggregation were decreased subsequently upon treatment with D-Trp. It repressed the genes involved incell-cell communication, which could be responsible for the diminished biofilm formation of the selected strains. HenceD-Tryptophan has proved to be an effective strategy to control biofilm and may support in the development of surfacecoating technologies.

Intercepting signalling mechanism to control environmental biofouling.

Biofouling in environmental systems employs bacterial quorum sensing signals (autoinducers) and extracellular polymeric substances to onset the event. The present review has highlighted on the fundamental mechanisms behind biofilm formation over broad spectrum environmental niches especially membrane biofouling in water systems and consequent chances of pathogenic contamination leading to global economic loss. It has broadly discussed on bioelectrical signal (via, potassium gradient) and molecular signal (via, AHLs) mediated quorum sensing which help to propagate biofilm formation. The review has illustrated the potential of genomic intervention towards biofouled membrane microbial community and has uncovered possible features of biofilm microenvironment like quorum quenching bacteria, bioelectrical waves capture, siderophores arrest and surface modifications. Based on information, the concept of interception of quorum signals (AHLs) and bioelectrical signals (K+) by employing electro-modified (negative charges) membrane surface have been hypothesized in the present review to favour anti-biofouling.

Detection of Porphyromonas gingivalis and Treponema denticola in chronic and aggressive periodontitis patients: A comparative polymerase chain reaction study.

BACKGROUND: The detection frequency of Porphyromonas gingivalis and Treponema denticola in chronic periodontitis (CP) and aggressive periodontitis (AgP) is not explored well in Indian population. AIM: The study was undertaken to detect P. gingivalis and T. denticola in CP as well as in AgP patients using polymerase chain reaction (PCR), and to determine the relationship between the frequency of these two microorganisms and the severity of clinical periodontal parameters. MATERIALS AND METHODS: Subgingival plaque samples were collected from ninety participants (thirty CP patients, thirty AgP patients, and thirty healthy participants) and the aforementioned two microorganisms were detected using PCR. RESULTS: However, when CP and AgP were compared for the detection frequency of two microorganisms, no statistically significant difference was noted. A statistically significant increase in the number of bacteria-positive sites increased as the score of plaque index (PI), gingival index (GI), and clinical attachment level of CP and AgP patients increased. Coexistence of P. gingivalis and T. denticola was frequently observed in deep periodontal pockets. CONCLUSIONS: Study findings suggest that P. gingivalis and T. denticola are significantly associated with the severity of periodontal tissue destruction. Statistically significant association exists between clinical periodontal parameters such as PI, GI, periodontal pocket depth (PPD), and clinical attachment loss and presence of both the microorganisms.

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.

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.

Genomes of Two Clinical Isolates of Mycobacterium tuberculosis from Odisha, India.

We report whole-genome sequences of two clinical isolates of Mycobacterium tuberculosis isolated from patients in Odisha, India. The sequence analysis revealed that these isolates are of an ancestral type and might represent some of the "pristine" isolates in India that have not admixed with other lineages.

Genome Sequence of Lactobacillus plantarum EGD-AQ4, Isolated from Fermented Product of Northeast India.

We present a draft genome sequence of Lactobacillus plantarum strain EGD-AQ4, isolated from nonalcoholic fermented bamboo shoot products of Northeast India. The size of the draft genome sequence is the largest among all the reported genome sequences of Lactobacillus plantarum, thus enabling the exploration of new gene clusters involved in various functional and probiotic attributes.

Draft genome sequence of atrazine-utilizing bacteria isolated from Indian agricultural soil.

We report the draft genome sequences of two tropical bacterial isolates capable of degrading the herbicide atrazine. Alcaligenes sp. strain EGD-AK7 and Arthrobacter sp. strain AK-YN10 were isolated from Indian agricultural soil in which sugarcane is grown, with a reported history of atrazine use. EGD-AK7 has the atzABCDEF genes and AK-YN10 has the trzN and atzBC genes for atrazine degradation.