Asifa Qureshi

In situ bioremediation of organochlorine-pesticide-contaminated microcosm soil and evaluation by gene probe

BACKGROUND Pesticide-formulating industries are contaminating the environment through various activities. Bioremediation is the best method for decontamination, as chemical and physical methods are not only costly but also not very effective in open field systems. In the present study, in situ bioremediation of organochlorine-contaminated soil was demonstrated by combined biostimulation and bioaugmentation strategies, followed by evaluation using a molecular method. RESULTS Three parameters were monitored: microbial biomass (colony-forming units (CFU) g(-1) soil), residual pesticides after treatment and catabolic genes from microcosm soil. Both the biostimulation and the bioaugmentation treatments showed an initial lag phase of 80 days towards colony-forming units. Gas chromatography of soil samples showed that concentrations of residual pesticides in the soil declined by up to 85-90% after 80 days, indicating their utilisation with time. On dot-blot hybridisation of the total DNA from the same soil samples, it was observed that catabolic genes tfdC (catechol 1,2-dioxygenase) and cm genes (chlorophenol monoxygenase) were predominant, whereas other catabolic genes such as catechol 2,3-dioxygenase (xylE) were negligible. CONCLUSION The strategy of in situ bioremediation and its evaluation by gene probe and also by conventional methods was demonstrated for organochlorine-pesticide-contaminated soil in open microcosms. It showed that bioaugmentation along with biostimulation was effective, although initial acclimatization for a period of almost 2-3 months was required in the open field systems.

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.

Antibiofilm activity of biomolecules: gene expression study of bacterial isolates from brackish and fresh water biofouled membranes

Abstract Membrane biofouling is a common and emerging problem, where cells get cemented and create problems in industrial process. Frequent chemical cleaning used for the treatment of biofouled membrane shortens the membrane life time and creates ‘stress’ to existing microflora to trigger more exopolysaccharides production, which becomes the principle cause of biofouling. To understand safe and environmentally feasible antifouling strategies, key biofilm forming representative bacteria isolated from brackish and fresh water biofouled membranes were subjected to natural agents, such as vanillin (0.05–0.4 mg/mL) and salicylic acid (0.1–0.7 mg/mL). Salicylic acid (0.7 mg/mL) was found to be effective against only Pseudomonas group, whereas vanillin was remarkably potent against majority of the isolates because of structural mimicking with signalling autoinducer molecules. The present study showed that vanillin served as a good quorum quencher molecule as it inhibited 90% acyl homoserine lactones production at 0.3 mg/mL concentration in biosensor Chromobacterium violaceum CV026 strain and also inhibited 70% to > 90% biofilm formation in bacterial isolates. Biofilm formation and quorum sensing inhibition activities were validated by real-time quantitative PCR gene expression analysis in key representative membrane isolates. Vanillin served as antifouling natural agent towards broad spectrum community found on membranes.

Draft Genome Sequence of Atrazine-Utilizing Bacteria Isolated from Indian Agricultural Soil

ABSTRACT 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.

Genome Sequence of the Pigment-Producing Bacterium Pseudogulbenkiania ferrooxidans, Isolated from Loktak Lake.

ABSTRACT The whole genome of a pigment-producing isolate from a lake in northern India, Pseudogulbenkiania ferrooxidans strain EGD-HP2, has been sequenced to study the spectrum of biosynthesis of secondary metabolites. The genome annotation data revealed an operon for violacein, which showed homology with the reported operon of a Chromobacterium sp., and also a quinone cofactor.

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.

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

ABSTRACT 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.

Genome Sequence of Alcaligenes sp. Strain HPC1271.

ABSTRACT We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicrobial activity against multidrug-resistant bacteria. Antibiotic production by Alcaligenes has not been frequently reported, and hence, the availability of the genome sequence should enable us to explore new antibiotic-producing gene clusters.

Biofilm Microenvironments: Modeling Approach

Biofilms are resilient and complex microbial communities or populations encased in a self-producing extracellular matrix existing in nature, which account for their robustness against a wide variety of stresses. In nature, multispecies biofilms have been found to occur frequently, whereas monospecies biofilms have been rare and found only when developed. By understanding the sociobiology of biofilm bacteria and harnessing the knowledge based on known biochemical and physical parameters, the underlying complexity of biofilm microenvironment could be better predicted by state-of-the-art advanced modeling approaches. In the present review, in-depth advanced modeling approaches based on the action of substrates on developmental biofilm physiology have been discussed. Equations for forces and adherence, quorum sensing, fluid flow dynamics, the social arrangement of community members in their favorable places, stratification, and pattern formation inside the biofilm have been elaborated. Equations to predict biofilm dispersal stages have been also discussed. Different models which uncover microbial biofilm life cycle stages to predict their complexity and recommended future variables like “omics” for magnification have been reported. This chapter will help to provide additional platform related to the genetic complex networking of biofilm bacteria for conceptual underpinnings of biofilm microenvironment.

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.