Screening, biochemical characterization and antibiotics resistance/susceptibility of bacteria isolated from native soil and water samples

Abstract The present study was conducted to isolate and characterize bacteria from water and soil sample taken from the Lahore Canal at different sites i.e. Mall Road, Mohlanwal and Khera site. Isolated bacterial strains were identified on the basis of morphological and biochemical tests. Identification was confirmed by culturing bacteria on selective media. Antibiotic resistance test was also performed to observe the resistance of bacteria against different antibiotics. Blood agar test was performed for identification of different pathogenic bacteria. The result revealed that water and soil samples of Lahore Canal Lahore from different sites were contaminated with Escherichia coli, Salmonella sp., Vibrio sp., Bacillus spp., Enterococcus sp. and Staphylococcus spp. Due to presence of these pathogens, this water is not suitable for any domestic and irrigation use. Study also revealed that water of the Lahore Canal is harmful for human health as it is contaminated with bacteria that can cause severe disease e.g., Escherichia coli can cause gastroenteritis, Bacillus spp. can cause nausea and vomiting, Enterococcus may infect urinary tract, Salmonella sp. is responsible for Bacteremia, Staphylococcus spp. can cause mild fever and Vibrio sp. can be the reason of cholera. Thus it is rendered unfit for any kind of human use even other than drinking like swimming, bathing, washing etc., until and unless some remedial measures are employed to eradicate pathogenic microorganisms by WASA and LWMS according to standards of WHO. Similarly, it is quite harmful, when and where ever it is used for irrigation without proper treatment.

Diversity and Abundance of Delineated Earthworm (Annelida: Clitellata) in Pakistan: A Review

Earthworm, a ubiquitous (but neglected) macro-invertebrate, is found in terrestrial vicinity of Pakistan. Moreover, the occurrence of earthworms is often diverse with fluctuating quantity depending upon abiotic factors and land usage patterns. The aim of this study was to summarize all the reported information related to earthworm diversity in different areas of Pakistan. Almost all the data published from year 2001 to 2021 were collected. Following data organization, total 42 earthworm's species including five families (Acanthodrilidae, Lumbricidae, Moniligastridae, Octochaetidae and Megascolecidae) were reported from various researchers. Among five families, family Acanthodrilidae was found to have only one specie (Ramiella bishambari), Lumbricidae consist of 10 species (Apporactodea rosea, Allolobophora trapezoids, Allolobophora chloroticaa, Aporrectodea longa, A. caliginosa, Bimastus parvus, Eisenia fetida, Helodrilus foetidus, Lumbricus terrestris and L. rubillus), Moniligastridae has two species (Drawida nepalensis and D. pellucida) while Octochaetidae possess only one specie (Eutyphoeus incommodus). The most abundant and diverse family Megascolecidae consist of 28 earthworm species in all habitats of different regions of Pakistan. Among geographical areas, Faisalabad was found as the richest territory with most reported earthworm species (i.e. 28). The current study suggests further in depth research to explore the unidentified and/ missing species of earthworms in Pakistan.

Phenotypic and Molecular Characterization of CTX-M Type B-Lactamases in Gram Negative Bacterial Strains Isolated from Hospitals, Lahore, Pakistan

One of the principal mechanisms that contribute resistance to antibiotics is the production of extended spectrum beta lactamase (ESBL) in Gram negative bacteria. In the present study, molecular methods were used to evaluate the prevalence of the extended-spectrum beta-lactamase (ESBL)-encoding CTX-M gene among Gram negative bacterial strains. In total, 148 clinical samples were collected from different tertiary care hospitals of Lahore, Pakistan. Disc synergy diffusion method was used to detect the presence of ESBL production. Moreover, antibiotic resistance patterns and molecular detection of bla _CTX-M ESBLs, were also studied. The pathogens isolated from the 148 samples included Escherichia coli (43%) followed by Klebsiella sp. (28%), Proteus sp. (18%) and Pseudomonas sp. (11%). In all 148 strains, 95 (64%) were ESBL producers while 53 (36%) were non ESBL producers. The strains which were phenotypically ESBL producers, bla _CTX-M were found in 46% E. coli strains, while 50% Klebsiella sp. were harboring the gene. A high resistance rate was observed against cephalosporins (cefopodoxime 67%, cefoperazone 73%, cephalexin 63% sparaxin 61%). Lower resistance was observed against meropenem among all isolated bacterial strains. Genotypic detection of bla _CTX-M genes by PCR revealed 46% of E. coli and 50% of Klebsiella strains harbored bla _CTX-M gene. The present study showed that ESBLs producers were resistant to commonly used antibiotics. Similarly, bla _CTX-M ESBL production is more prevalent in our clinical isolates.

Antimicrobial Efficacy of Biogenic Cobalt and Copper Nanoparticles against Pathogenic Isolates

Biogenic synthesis of cobalt (Co) and copper (Cu) nanoparticles (NPs) was performed using the bacterial strains Escherichia coli and Bacillus subtilis. Prepared NPs were confirmed by a color change to maroon for CoNPs and green for CuNPs. The NPs characterization using FTIR showed the presence of functional groups, i.e., phenols, acids, protein, and aromatics present in the Co and CuNPs. UV-vis spectroscopy of E. coli and B. subtilis CuNPs showed peaks at 550 and 625 nm, respectively. For E. coli and B. subtilis CoNPs, peaks were observed at 300 nm and 350 nm, respectively. Antibacterial and antifungal activity of B. subtilis and E. coli Co and CuNPs was determined at 100 mg/mL concentration against two bacterial strains at 5, 2.5, and 1.5 mg/mL against fungal two strains F. oxysporum and T. viridi, respectively. B. subtilis CuNPs showed significantly higher inhibition zones (ZOI=25.7-29.7 mm) against E. coli and B. subtilis compared to other biogenic NPs. Likewise, B. Subtilis CuNPs showed lower MIC (4.3 ± 6.3) and MBC (5.3 mg/mL) values against both tested isolates. Antifungal activity of B. subtilis and E. coli CuNPs and CoNPs showed a concentration-dependent decrease in ZOI. Among all biogenic NPs, B. subtilis CoNPs showed the highest ZOI (25-30 mm) against F. oxysporum followed by E. coli CuNPs with maximum ZOI (20-27 mm) against T. viridi. Again, B. subtilis CoNPs and E. coli CuNPs showed lowest MIC and MFC values against both fungal isolates. In conclusion, the current study showed that biogenically synthesized B. subtilis Cu or CoNPs can be used as effective antimicrobial agents due to their potential antibacterial and antifungal potential.

Gut dysbiosis, inflammation and type 2 diabetes in mice using synthetic gut microbiota from diabetic humans

The study was aimed to assess impact of high fat diet (HFD) and synthetic human gut microbiota (GM) combined with HFD and chow diet (CD) in inducing type-2 diabetes (T2D) using mice model. To our knowledge, this is the first study using selected human GM transplantation via culture based method coupled dietary modulation in mice for in vivo establishment of inflammation leading to T2D and gut dysbiosis. Twenty bacteria (T2D1-T2D20) from stool samples of confirmed T2D subjects were found to be morphologically different and subjected to purification on different media both aerobically and anerobically, which revealed seven bacteria more common among 20 isolates on the basis of biochemical characterization. On the basis of 16S rRNA gene sequencing, these seven isolates were identified as Bacteroides stercoris (MT152636), Lactobacillus acidophilus (MT152637), Lactobacillus salivarius (MT152638), Ruminococcus bromii (MT152639), Klebsiella aerogenes (MT152640), Bacteroides fragilis (MT152909), Clostridium botulinum (MT152910). The seven isolates were subsequently used as synthetic gut microbiome (GM) for their role in inducing T2D in mice. Inbred strains of albino mice were divided into four groups and were fed with CD, HFD, GM+HFD and GM+CD. Mice receiving HFD and GM+modified diet (CD/HFD) showed highly significant (P<0.05) increase in weight and blood glucose concentration as well as elevated level of inflammatory cytokines (TNF-α, IL-6, and MCP-1) compared to mice receiving CD only. The 16S rRNA gene sequencing of 11 fecal bacteria obtained from three randomly selected animals from each group revealed gut dysbiosis in animals receiving GM. Bacterial strains including Bacteroides gallinarum (MT152630), Ruminococcus bromii (MT152631), Lactobacillus acidophilus (MT152632), Parabacteroides gordonii (MT152633), Prevotella copri (MT152634) and Lactobacillus gasseri (MT152635) were isolated from mice treated with GM+modified diet (HFD/CD) compared to strains Akkermansia muciniphila (MT152625), Bacteriodes sp. (MT152626), Bacteroides faecis (MT152627), Bacteroides vulgatus (MT152628), Lactobacillus plantarum (MT152629) which were isolated from mice receiving CD/HFD. In conclusion, these findings suggest that constitution of GM and diet plays significant role in inflammation leading to onset or/and possibly progression of T2D. .

Foliar fertigation of ascorbic acid and zinc improves growth, antioxidant enzyme activity and harvest index in barley (Hordeum vulgare L.) grown under salt stress

Crop productivity is limited by several environmental constraints. Among these, salt stress plays a key role in limiting the growth and yield production of economically important agricultural crops. However, the exogenous fertigation of vitamins and minerals could serve as a "shot-gun" approach for offsetting the deleterious effects of salts present in the rhizosphere. Therefore, an experiment was conducted to quantify the efficacy of foliar fertigation of ascorbic acid (vitamin-C) and zinc (Zn) on the physio-biochemical attributes of barley (Hordeum vulgare L. Genotype B-14011) grown in a saline environment. The salt stress resulted in a reduced biological yield associated with a decrease in chlorophyll pigment, while a significant enhancement in Na⁺ and Zn²⁺ was observed under salinity stress. Similarly, the contents of total soluble proteins, total free amino acids, lipid peroxidation, and H₂O₂ and the activities of antioxidative enzymes (SOD, POD, CAT, APX and proline) were significantly enhanced under salinity stress. Moreover, salinity negatively affected the yield attributes and ion uptake of plants. However, foliar fertigation with AsA +0.03% Zn enhanced vegetative growth, photosynthetic pigments, synchronized ion uptake, the synthesis of enzymatic and non-enzymatic antioxidants, and the harvest index. It is inferred from this study that among all treatments, the effect of foliar fertigation with the AsA+0.03% Zn combination not only improved the salt stress tolerance but also improved the yield attributes, which will aid in the improvement in barley seed yield and is a step to solve the problem of malnutrition through biofortification of vitamin-C and zinc.

RNAseq Analysis Reveals Altered Expression of Key Ion Transporters Causing Differential Uptake of Selective Ions in Canola (Brassica napus L.) Grown under NaCl Stress

Salinity is one of the major abiotic stresses prevailing throughout the world that severely limits crop establishment and production. Every crop has an intra-specific genetic variation that enables it to cope with variable environmental conditions. Hence, this genetic variability is a good tool to exploit germplasms in salt-affected areas. Further, the selected cultivars can be effectively used by plant breeders and molecular biologists for the improvement of salinity tolerance. In the present study, it was planned to identify differential expression of genes associated with selective uptake of different ions under salt stress in selected salt-tolerant canola (Brassica napus L.) cultivar. For the purpose, an experiment was carried out to evaluate the growth response of different salt-sensitive and salt-tolerant canola cultivars. Plants were subjected to 200 mM NaCl stress. Canola cultivars-Faisal Canola, DGL, Dunkled, and CON-II-had higher growth than in cvs Cyclone, Ac-EXcel, Legend, and Oscar. Salt-tolerant cultivars were better able to maintain plant water status probably through osmotic adjustment as compared to salt-sensitive cultivars. Although salt stress increased shoot Na+ and shoot Cl- contents in all canola cultivars, salt-tolerant cultivars had a lower accumulation of these toxic nutrients. Similarly, salt stress reduced shoot K+ and Ca2+ contents in all canola cultivars, while salt-tolerant cultivars had a higher accumulation of K+ and Ca2+ in leaves, thereby having greater shoot K+/Na+ and Ca2+/Na+ ratios. Nutrient utilization efficiency decreased significantly in all canola cultivars due to the imposition of salt stress; however, it was greater in salt-tolerant cultivars-Faisal Canola, DGL, and Dunkled. Among four salt-tolerant canola cultivars, cv Dunkled was maximal in physiological attributes, and thus differentially expressed genes (DEGs) were assessed in it by RNA-seq analysis using next-generation sequencing (NGS) techniques. The differentially expressed genes (DEG) in cv Dunkled under salt stress were found to be involved in the regulation of ionic concentration, photosynthesis, antioxidants, and hormonal metabolism. However, the most prominent upregulated DEGs included Na/K transporter, HKT1, potassium transporter, potassium channel, chloride channel, cation exchanger, Ca channel. The RNA-seq data were validated through qRT-PCR. It was thus concluded that genes related to the regulation of ionic concentrate are significantly upregulated and expressed under salt stress, in the cultivar Dunkled.

Microbial assessment of pathogenic bacterial growth in ice cream and kulfa

Current study was focused to examine the total bacterial count in packed and unpacked ice cream and kulfa collected from 12 different localities of Lahore. The bacterial colonies were isolated and grown on agar-broth media under sterilized conditions. Serial dilution technique was used to compose the replicates to get total viable count of bacteria. Results in case of packed ice cream samples indicated maximum (618 × 10^-6 CFU/g) and minimum (79 × 10^-6 CFU/g) bacterial count while in case of unpacked ice cream samples maximum and minimum bacterial count was 163 × 10^-6 CFU/g and 71 × 10^-6 CFU/g, respectively. Whereas in case of packed kulfa samples, maximum and minimum recorded bacterial count was 163 × 10^-6 CFU/g and 72 × 10^-6 CFU/g, respectively. The LM and SEM of the isolated bacteria were also performed for correct identification. Results indicated that the total bacterial count recorded in the samples exceeded the standard tolerable range which can lead to serious health damage of consumers.