Search results for: bacterial abundance

Authors: Xiaoxing Ye

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To investigate complex rumen microbial communities, 16S ribosomal RNA (rRNA) sequencing is widely used. Here, we evaluated the impact of bioinformatics pipelines on the observation of OTUs and taxonomic classification of 750 cattle rumen microbial samples by comparing three commonly used pipelines (LotuS, UPARSE, and QIIME) with Usearch. In LotuS-based analyses, 189 archaeal and 3894 bacterial OTUs were observed. The observed OTUs for the Usearch analysis were significantly larger than the LotuS results. We discovered 1495 OTUs for archaea and 92665 OTUs for bacteria using Usearch analysis. In addition, taxonomic assignments were made for the rumen microbial samples. All pipelines had consistent taxonomic annotations from the phylum to the genus level. A difference in relative abundance was calculated for all microbial levels, including Bacteroidetes (QIIME: 72.2%, Usearch: 74.09%), Firmicutes (QIIME: 18.3%, Usearch: 20.20%) for the bacterial phylum, Methanobacteriales (QIIME: 64.2%, Usearch: 45.7%) for the archaeal class, Methanobacteriaceae (QIIME: 35%, Usearch: 45.7%) and Methanomassiliicoccaceae (QIIME: 35%, Usearch: 31.13%) for archaeal family. However, the most prevalent archaeal class varied between these two annotation pipelines. The Thermoplasmata was the top class according to the QIIME annotation, whereas Methanobacteria was the top class according to Usearch.

Keywords: cattle rumen, rumen microbial, 16S rRNA gene sequencing, bioinformatics pipeline

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Authors: Gimhani Madhushika Hewayalage, Thilini Ariyadasa, Sanja Gunawardena

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In Sri Lanka, the largest contribution for the industrial export earnings is governed by textile and apparel industry. However, this industry generates huge quantities of effluent consists of unfixed dyes which enhance the effluent colour and toxicity thereby leading towards environmental pollution. Therefore, the effluent should properly be treated prior to the release into the environment. The biological technique has now captured much attention as an environmental-friendly and cost-competitive effluent decolourization method due to the drawbacks of physical and chemical treatment techniques. The present study has focused on identifying dye decolourizing potential of several bacterial isolates obtained from the effluent of the local textile industry. Yellow EXF, Red EXF, Blue EXF, Nova Black WNN and Nylosan-Rhodamine-EB dyes have been selected for the study to represent different chromophore groups such as Azo and Xanthene. The rates of decolorization of each dye have been investigated by employing distinct bacterial isolates. Bacterial isolate which exhibited effective dye decolorizing potential was identified as Proteus mirabilis using 16S rRNA gene sequencing analysis. The high decolorizing rates of identified bacterial strain indicate its potential applicability in the treatment of dye-containing wastewaters.

Keywords: azo, bacterial, biological, decolourization, xanthene

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Authors: Rupa Rani, Vipin Kumar

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Endosulfan, an organochlorine pesticide is of environmental concern due to its apparent persistence and toxicity. It has been reported as contaminants in soil, air, and water and is bioaccumulated and magnified in ecosystems. The combined use of microorganisms and plants has great potential for remediating soil contaminated with organic compounds such as pesticides. The objective of this study was to evaluate whether the bacterial inoculation influences plant growth promotion, endosulfan degradation in soil and endosulfan accumulation in different plant parts. Lycopersicon esculentum L. (Tomato) was grown in endosulfan spiked soil and inoculated with endosulfan tolerant bacterial strains. Endosulfan residues from different parts of plants and soil were extracted and estimated by using gas chromatograph equipped with 63Ni electron capture detector (GC-ECD). The inoculation of bacterial strains into the soil with plants showed a beneficial effect on endosulfan degradation and plant biomass production. Maximum endosulfan (90%) degradation was observed after 120 days of bacterial inoculation in the soil. Furthermore, there was significantly less endosulfan accumulation in roots and shoots of bacterial strains inoculated plants as compared to uninoculated plants. The results show the effectiveness of inoculated endosulfan tolerant bacterial strains to increase the remediation of endosulfan contaminated soil.

Keywords: organochlorine pesticides, endosulfan, degradation, plant-bacteria partnerships

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Authors: S. Susanti, V. P. Bintoro, A. Setiadi, S. I. Santoso, D. R. Febriandi

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Meat is a foodstuff of animal origin. It is perishable because a suitable medium for bacterial growth. That is why meat can be a potential hazard to humans. Several ways have been done to inhibit bacterial population in an effort to prolong the meat shelf-life. However, aberration sometimes happens in the practices of meat preservation, for example by using chemical material that possessed strong antibacterial activity like formaldehyde. For health reason, utilization of formaldehyde as a food preservative was forbidden because of DNA damage resulting cancer and birth defects. Therefore, it is important to seek a natural food preservative that is not harmful to the body. This study aims to reveal the potency of cashew apple as natural food preservative by measuring its antibacterial activity and marinating effect on the bacterial growth of beef and chicken meat. Antibacterial activity was measured by The Kirby-Bauer method while bacterial growth was determined by total plate count method. The results showed that inhibition zone of 10-30% cashew apple extract significantly wider compared to 0% extract on the medium of E. coli, S. aureus, S. typii, and Bacillus sp. Furthermore, beef marinated with 20-30% cashew apple extract and chicken meat marinated with 5-15% extract significantly less in the total number of bacteria compared to 0% extract. It can be concluded that marinating with 5-30% cashew apple extract can effectively inhibit the bacterial growth of beef and chicken meat. Moreover, the concentration of extracts to inhibit bacterial populations in chicken meat was reached at the lower level compared to beef. Thus, cashew apple is potential as a natural food preservative.

Keywords: bacterial growth, cashew apple, marinating, meat

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Authors: Azila Adnan, Giridhar R. Nair, Mark C. Lay, Janis E. Swan

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The effect of aeration on bacterial cellulose (BC) production by Gluconacetobacter xylinus DSM46604 was studied in 5-L bioreactor. Four aeration rates were applied (0.3, 0.6, 1.0 and 1.5 vvm) in the fermentation media at constant agitation rate, 150 rpm. One vvm enhanced BC concentration (4.4 g/L) and productivity (0.44 g/L/day) while greater agitation rate (1.5 vvm) decreased BC concentration (4.0 g/L) and productivity (0.40 g/L/day).

Keywords: aeration, bacterial cellulose, fermentation, gluconacetobacter xylinus

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Authors: Khaled Khleifat

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This study detects the bacterial species that responsible for UTI in both diabetic patients and non-diabetic patients, Jordan. 116 urine samples were investigated in order to determine UTI-causing bacteria. These samples distributed unequally between diabetic male (12) and diabetic female (25) and also non-diabetic male (13) and non-diabetic female (66). The results represent that E.coli is responsible for UTI in both diabetic and non-diabetic patients (15.5% and 29.3% respectively) with large proportion (44.8%). This study showed that not all bacterial species that isolated from the non-diabetic sample could be isolated from diabetic samples. E. coli (15.5%), P. aeruginosa (4.3%), K. pneumonia (1.7%), P. mirabilis (2.6%), S. marcescens (0.9%), S. aureus (1.7%), S. pyogenes (1.7%), E. faecalis (0.9%), S. epidermidis (1.7%) and S. saprophyticus (0.9%). But E. aerogenes, E. cloacae, C. freundii, A. baumannii and B. subtilis are five bacterial species that can’t isolate from all diabetic samples. This study shows that for the treatment of UTI in both diabetic and non-diabetic patients, Chloramphenicol (30 μg), Ciprofloxacin (5 μg) and Vancomycin (30 μg) are more favorable than other antibiotics. In the same time, Cephalothin (30μg) is not recommended.

Keywords: urinary tract infections, diabetes mellitus, bacterial species, infections

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Authors: Amel Bouderhem, Aminata Ould El Hadj Khelil, Amina N. Djrarbaoui, Aroussi Aroussi

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The present work aims to find the influence of the nature of the soil on the effectiveness of the biodegradation of hydrocarbons by a mixture of bacterial strains hydrocarbonoclastes. Processes of bioaugmentation and biostimulation trial are applied to samples of soils polluted voluntarily by the crude oil. For the evaluation of the biodegradation of hydrocarbons, the bacterial load, the pH and organic carbon total are followed in the different experimental batches. He bacterial load of the sandy soil varies among the witnesses of 45,2 .108 CFU/ml at the beginning of the experimentation to 214,07.108 CFU/ml at the end of the experiment. Of the soil silty-clay varies between 103,31 .108 CFU/ml and 614,86.108 CFU/ml . It was found a strong increase in the bacterial biomass during the processing of all samples. This increase is more important in the samples of sand bioaugmente or biomass increased from 63.16 .108 CFU/ml to 309.68 .108 CFU/ml than in soil samples silty clay- bioaugmente whose content in bacteria evolved of 73,01 .108 CFU/ml to 631.80 . 108CFU/ml

Keywords: pollution, hydrocarbons, bioremediation, bacteria hydrocarbonoclastes, ground, texture

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Authors: Promil Mehra, Nanthi Bolan, Jack Desbiolles, Risha Gupta

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Agricultural practices affect the soil physical and chemical properties, which in turn influence the soil microorganisms as a function of the soil biological environment. On the return to conventional tillage (CT) from continuing no-till (NT) cropping system, a very little information is available from the impact caused by the intermittent tillage on the soil biochemical properties from a short-term (2-year) study period. Therefore, the contribution made by different microorganisms (fungal, bacteria) was also investigated in order to find out the effective changes in the soil microbial activity under a South Australian dryland faring system. This study was conducted to understand the impact of microbial dynamics on the soil organic carbon (SOC) under NT and CT systems when treated with different levels of mulching (0, 2.5 and 5 t/ha). Our results demonstrated that from the incubation experiment the cumulative CO2 emitted from CT system was 34.5% higher than NT system. Relatively, the respiration from surface layer (0-10 cm) was significantly (P<0.05) higher by 8.5% and 15.8 from CT; 8% and 18.9% from NT system w.r.t 10-20 and 20-30 cm respectively. Further, the dehydrogenase enzyme activity (DHA) and microbial biomass carbon (MBC) were both significantly lower (P<0.05) under CT, i.e., 7.4%, 7.2%, 6.0% (DHA) and 19.7%, 15.7%, 4% (MBC) across the different mulching levels (0, 2.5, 5 t/ha) respectively. In general, it was found that from both the tillage system the enzyme activity and MBC decreased with the increase in depth (0-10, 10-20 and 20-30 cm) and with the increase in mulching rate (0, 2.5 and 5 t/ha). From the perspective of microbial stress, there was 28.6% higher stress under CT system compared to NT system. Whereas, the microbial activity of different microorganisms like fungal and bacterial activities were determined by substrate-induced inhibition respiration using antibiotics like cycloheximide (16 mg/gm of soil) and streptomycin sulphate (14 mg/gm of soil), by trapping the CO2 using an alkali (0.5 M NaOH) solution. The microbial activities were confirmed through platting technique, where it was that found bacterial activities were 46.2% and 38.9% higher than fungal activity under CT and NT system. In conclusion, it was expected that changes in the relative abundance and activity of different microorganisms (bacteria and fungi) under different tillage systems could significantly affect the C cycling and storage due to its unique structures and differential interactions with the soil physical properties.

Keywords: tillage, soil respiration, MBC, fungal-bacterial activity

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Authors: Li Cheng, Zhang Yilei, Cohen Yehuda

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Two motility mechanisms were introduced into iDynoMiCs software, which adopts an individual-based modeling method. Based on the new capabilities, along with the pressure motility developed before, influence of bacterial motility on biofilm formation was studied. Simulation results were evaluated both qualitatively through 3D structure inspections and quantitatively by parameter characterizations. It was showed that twitching motility increased the biofilm surface irregularity probably due to movement of cells towards higher nutrient concentration location whereas free motility, on the other hand, could make biofilms flatter and smoother relatively. Pressure motility showed no significant influence in this study.

Keywords: iDynoMics, biofilm structure, bacterial motility, motility mechanisms

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Authors: Prachi Choudhary, Jai Gopal Sharma

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Microbial cultures determine the type of organism, its abundance in the tested sample, or both. It is one of the primary diagnostic methods of microbiology. It is used to determine the cause of infectious disease by letting the agent multiply in a predetermined medium. Different bacteria produce colonies that may be very distinct from the bacterial species that produced them. To culture any pathogen or microorganism, we should first know about the types of media used in microbiology for culturing. Sometimes sub culturing is also done in various microorganisms if some mixed growth is seen in culture. Nearly 3 types of culture media based on consistency – solid, semi-solid, and liquid (broth) media; are further explained in the report. Then, The Five I's approach is a method for locating, growing, observing, and characterizing microorganisms, including inoculation and incubation. Isolation, inspection, and identification. For identification of bacteria, we have to culture the sample like urine, sputum, blood, etc., on suitable media; there are different methods of culturing the bacteria or microbe like pour plate method, streak plate method, swabbing by needle, pipetting, inoculation by loop, spreading by spreader, etc. After this, we see the bacterial growth after incubation of 24 hours, then according to the growth of bacteria antibiotics susceptibility test is conducted; this is done for sensitive antibiotics or resistance to that bacteria, and also for knowing the name of bacteria. Various methods like the dilution method, disk diffusion method, E test, etc., do antibiotics susceptibility tests. After that, various medicines are provided to the patients according to antibiotic sensitivity and resistance.

Keywords: inoculation, incubation, isolation, antibiotics suspectibility test, characterizing

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Authors: D. Hammad, D. P. Tonge

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Rheumatoid arthritis (RA) is a disabling and common autoimmune disease during which the body's immune system attacks healthy tissues. This results in complicated and long-lasting actions being carried out by the immune system, which typically only occurs when the immune system encounters a foreign object. In the case of RA, the disease affects millions of people and causes joint inflammation, ultimately leading to the destruction of cartilage and bone. Interestingly, the disease mechanism still remains unclear. It is likely that RA occurs as a result of a complex interplay of genetic and environmental factors including an imbalance in the microorganism population inside our body. The human microbiome or microbiota is an extensive community of microorganisms in and on the bodies of animals, which comprises bacteria, fungi, viruses, and protozoa. Recently, the development of molecular techniques to characterize entire bacterial communities has renewed interest in the involvement of the microbiome in the development and progression of RA. We believe that an imbalance in some of the specific bacterial species in the gut, mouth and other sites may lead to atopobiosis; the translocation of these organisms into the blood, and that this may lead to changes in immune system status. The aim of this study was, therefore, to characterize the microbiome of RA serum samples in comparison to healthy control subjects using 16S rRNA gene amplification and sequencing. Serum samples were obtained from healthy control volunteers and from patients with RA both prior to, and following treatment. The bacterial community present in each sample was identified utilizing V4 region 16S rRNA amplification and sequencing. Bacterial identification, to the lowest taxonomic rank, was performed using a range of bioinformatics tools. Significantly, the proportions of the Lachnospiraceae, Ruminococcaceae, and Halmonadaceae families were significantly increased in the serum of RA patients compared with healthy control serum. Furthermore, the abundance of Bacteroides and Lachnospiraceae nk4a136_group, Lachnospiraceae_UGC-001, RuminococcaceaeUCG-014, Rumnococcus-1, and Shewanella was also raised in the serum of RA patients relative to healthy control serum. These data support the notion of a blood microbiome and reveal RA-associated changes that may have significant implications for biomarker development and may present much-needed opportunities for novel therapeutic development.

Keywords: blood microbiome, gut and oral bacteria, Rheumatoid arthritis, 16S rRNA gene sequencing

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Authors: Francesco Pantano, Marta Fogolari, Michele Iuliani, Sonia Simonetti, Silvia Cavaliere, Marco Russano, Fabrizio Citarella, Bruno Vincenzi, Silvia Angeletti, Giuseppe Tonini

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Background: Although immune checkpoint inhibitors (ICIs) have changed the treatment paradigm of non–small cell lung cancer (NSCLC), these drugs fail to elicit durable responses in the majority of NSCLC patients. The gut microbiota, able to regulate immune responsiveness, is emerging as a promising, modifiable target to improve ICIs response rates. Since the oral microbiome has been demonstrated to be the primary source of bacterial microbiota in the lungs, we investigated its composition as a potential predictive biomarker to identify and select patients who could benefit from immunotherapy. Methods: Thirty-five patients with stage IV squamous and non-squamous cell NSCLC eligible for an anti-PD-1/PD-L1 as monotherapy were enrolled. Saliva samples were collected from patients prior to the start of treatment, bacterial DNA was extracted using the QIAamp® DNA Microbiome Kit (QIAGEN) and the 16S rRNA gene was sequenced on a MiSeq sequencing instrument (Illumina). Results: NSCLC patients were dichotomized as “Responders” (partial or complete response) and “Non-Responders” (progressive disease), after 12 weeks of treatment, based on RECIST criteria. A prevalence of the phylum Candidatus Saccharibacteria was found in the 10 responders compared to non-responders (abundance 5% vs 1% respectively; p-value = 1.46 x 10-7; False Discovery Rate (FDR) = 1.02 x 10-6). Moreover, a higher prevalence of Saccharibacteria Genera Incertae Sedis genus (belonging to the Candidatus Saccharibacteria phylum) was observed in "responders" (p-value = 6.01 x 10-7 and FDR = 2.46 x 10-5). Finally, the patients who benefit from immunotherapy showed a significant abundance of TM7 Phylum Sp Oral Clone FR058 strain, member of Saccharibacteria Genera Incertae Sedis genus (p-value = 6.13 x 10-7 and FDR=7.66 x 10-5). Conclusions: These preliminary results showed a significant association between oral microbiota and ICIs response in NSCLC patients. In particular, the higher prevalence of Candidatus Saccharibacteria phylum and TM7 Phylum Sp Oral Clone FR058 strain in responders suggests their potential immunomodulatory role. The study is still ongoing and updated data will be presented at the congress.

Keywords: oral microbiota, immune checkpoint inhibitors, non-small cell lung cancer, predictive biomarker

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Authors: Mohammad Mokhtari, Gires Usup, Zaidi Che Cob

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Bacteria communities as mediators of the biogeochemical process are the main component of the mangrove ecosystems. Crab burrows by increasing oxic-anoxic interfaces and facilitating the flux rate between sediment and tidal water affect biogeochemical properties of sediments. The effect of fiddler crab burrows on the density and diversity of bacteria were investigated to elucidate the effect of burrow on bacterial distribution. Samples collected from the burrow walls of three species of fiddler crabs including Uca paradussumieri, Uca rosea, and Uca forcipata. Sediment properties including grain size, temperature, Redox potential, pH, chlorophyll, water and organic content were measured from the burrow walls to assess the correlation between environmental variables and bacterial communities. Bacteria were enumerated with epifluorescence microscopy after staining with SYBR green. Bacterial DNA extracted from sediment samples and the community profiles of bacteria were determined with Terminal Restriction Fragment Length Polymorphism (T-RFLP). High endemism was observed among bacterial communities. Among the 152 observed OTU’s, 22 were found only in crab burrows. The highest bacterial density and diversity were recorded in burrow wall. The results of ANOSIM indicated a significant difference between the bacterial communities from the three species of fiddler crab burrows. Only 3% of explained bacteria variability in the constrained ordination model of CCA was contributed to depth, while much of the bacteria’s variability was attributed to coarse sand, pH, and chlorophyll content. Our findings suggest that crab burrows by affecting sediment properties such as redox potential, pH, water, and chlorophyll content induce significant effects on the bacterial communities.

Keywords: bioturbation, canonical corresponding analysis, fiddler crab, microbial ecology

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Authors: M.Ayazi, N. Golshan Ebrahimi

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The development of antibacterial surface has devoted extensive researches and important field due to the growing antimicrobial resistance strains. The superhydrophobic surface has raised attention because of reducing bacteria adhesion in the absence of antibiotic agents. Evaluating the current development antibacterial surface has to be investigating to consider the potential of applying superhydrophobic surface to reduce bacterial adhesion or role of patterned surfaces on it. In this study, we present different samples with bio-inspired hierarchical and microstructures to consider their ability in reducing bacterial adhesion. The structures have inspired from rice-like pattern and lotus-leaf that developed on the polydimethylsiloxane (PDMS) and polypropylene (PP). The results of the attachment behaviors have considered on two bacteria strains of gram-negative Escherichia coli (E. coli) bacteria and gram-positive Staphylococcus aureus (S. aureus). The reduction of bacteria adhesion on these roughness surfaces demonstrated the effectiveness of rinsing ability on removing bacterial cells on structured plastic surfaces. Results have also offered the important role of bacterial species, material chemistry and hierarchical structure to prevent bacterial adhesion.

Keywords: hierarchical structure, self-cleaning, lotus-effect, bactericidal

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Authors: Lata Kumari Dhanesh Tiwary, Pradeep Kumar Mishra

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The effluent coming from various industries such as textile, carpet, food, pharmaceutical and many other industries is big challenge due to its recalcitrant and xenobiotiocs in nature. Recently, biodegradation of dye wastewater through biological means was widely used due to eco-friendly and cost effective with the higher percentage of removal of dye from wastewater. The present study deals with the biodegradation and decolourization of Direct Red 23 dye using indigenously isolated bacterial consortium. The bacterial consortium was isolated from soil sample from dye contaminated site near a cluster of Carpet industries of Bhadohi, Uttar Pradesh, India. The bacterial strain formed consortia were identified and characterized by morphological, biochemical and 16S rRNA gene sequence analysis. The bacterial strain mainly Staphylococcus saprophyticus strain BHUSS X3 (KJ439576), Microbacterium sp. BHUMSp X4 (KJ740222) and Staphylococcus saprophyticus strain BHUSS X5 (KJ439576) were used as consortia for further studies of dye decolorization. Experimental investigations were made in a Sequencing Air- lift bioreactor using the synthetic solution of Direct Red 23 dye by optimizing various parameters for efficient degradation of dye. The effect of several operating parameters such as flow rate, pH, temperature, initial dye concentration and inoculums size on removal of dye was investigated. The efficiency of isolated bacterial consortia from dye contaminated area in Sequencing Air- lift Bioreactor with different concentration of dye between 100-1200 mg/l at different hydraulic rate (HRTs) 26h and 10h. The maximum percentage of dye decolourization 98% was achieved when operated at HRT of 26h. The percentage of decolourization of dye was confirmed by using UV-Vis spectrophotometer and HPLC.

Keywords: carpet industry, bacterial consortia, sequencing air-lift bioreactor

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Authors: Waleed S. Alwaneen

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In many countries, cow dung is used as farm manure and for biogas production. Several bacterial strains associated with cow dung such as Campylobacter, Salmonella sp. and Escherichia coli cause serious human diseases. The objective of the present study was to investigate the use of insect larvae including fruit beetle, waxworms and tiger worms to improve the breakdown of agricultural wastes and reduce their pathogen loads. Fresh cow faeces were collected from a cattle farm and distributed into plastic boxes (100 g/box). Each box was provided with 10 larvae of fruit beetle, Waxworms and Tiger worms, respectively. There were 3 replicates in each treatment including the control. Bacteria were isolated weekly from both control and cow faeces to which larvae were added to determine the bacterial populations. Results revealed that the bacterial load was higher in the cow faeces treated with fruit beetles than in the control, while the bacterial load was lower in the cow faeces treated with waxworms and tiger worms than in the control. The activities of the fruit beetle larvae led to the cow faeces being liquefied which provided a more conducive growing media for bacteria. Therefore, higher bacterial load in the cow faeces treated with fruit beetle might be attributed to the liquefaction of cow faeces.

Keywords: fruit beetle, waxworms, tiger worms, waste conditioning, composting

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Authors: Mian Adnan Kakakhel, NIshita Narwal, Majid Rasta, Shi Xiaotao

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The widespread use of nanoparticles means that they are significantly increasing in the aquatic ecosystem, where they are likely to pose threat to aquatic organism. In particular, the influence of nanoparticles exposure combined with varying water velocities on fish behavior remain poorly understood. Emerging evidences suggested a probable correlation between fish swimming behavior and gut bacterial dysbiosis. Therefore, the current study aimed to investigate the effects of nanomaterials in different water velocities on fish gut bacterial composition, which in results change in fish swimming behavior. The obtained findings showed that the contamination of nanoparticles was reduced as the velocity increased. However, the synergetic effects of nanoparticles and water velocity significantly (p < 0.05) decreased the bacterial composition, which plays a critical role in fish development, metabolism, digestion, enzymes production, and energy production such as Bacteroidetes and Firmicutes. This group of bacterial also support fish in swimming behavior by providing them a significant energy during movement. The obtained findings of this study suggested that the presence of nanoparticles in different water velocities have had a significant correlation with fish gut bacterial dysbiosis, as results the gut dysbiosis had been linked to the change in fish behavior. The study provides an important insight into the mechanisms by which the nanoparticles possibly affect the fish behavior.

Keywords: water velocities, fish behavior, gut bacteria, secondary metabolites, regulation

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Authors: Omar Alhamd, Peter A. Thomas, Trevor J. Greenhough, Annette K. Shrive

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The Pseudomonas syringae species complex includes many plant pathogenic strains with highly specific interactions with varied host species and cultivars. The rapid spread of these bacteria over the last ten years has become a cause for concern. Nanoparticles have previously shown promise in microbiological action. We have therefore investigated in vitro and in vivo the effects of different types and sizes of nanoparticles in order to provide quantitative information about their effect on the bacteria. The effects of several different nanoparticles against several bacteria strains were investigated. The effect of NP on bacterial growth was studied by measuring the optical density, biochemical and nutritional tests, and transmission electron microscopy (TEM) to determine the shape and size of NP. Our results indicate that their effects varied, with either a negative or a positive impact on both bacterial and plant growth. Additionally, the methods of exposure to nanoparticles have a crucial role in accumulation, translocation, growth response and bacterial growth. The results of our studies on the behaviour and effects of nanoparticles in model plants showed. Cerium oxide (CeO₂) and silver (Ag) NP showed significant antibacterial activity against several pathogenic bacteria. It was found that titanium nanoparticles (TiO₂) can have either a negative or a positive impact, according to concentration and size. It is also thought that environmental conditions can have a major influence on bacterial growth. Studies were therefore also carried out under some environmental stress conditions to test bacterial survival and to assess bacterial virulence. All results will be presented including information about the effects of different nanoparticles on Pseudomonas syringae bacteria.

Keywords: plant microbiome, nanoparticles, 16S rRNA gene sequencing, bacterial survival

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Authors: Mubashir Hussain, Mu Lv, Xiaohan Dong, Zhiyang Li, Bin Liu, Nongyue He

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Detection and classification of microbes have a vast range of applications in biomedical engineering especially in detection, characterization, and quantification of bacterial contaminants. For identification of pathogens, different techniques are emerging in the field of biomedical engineering. Latest technology uses light scattering, capable of identifying different pathogens without any need for biochemical processing. Bacterial Pathogens Identification System (BPIS) which uses a laser beam, passes through the sample and light scatters off. An assembly of photodetectors surrounded by the sample at different angles to detect the scattering of light. The algorithm of the system consists of two parts: (a) Library files, and (b) Comparator. Library files contain data of known species of bacterial microbes in the form of binned plots, while comparator compares data of unknown sample with library files. Using collected data of unknown bacterial species, highest voltage values stored in the form of peaks and arranged in 3D histograms to find the frequency of occurrence. Resulting data compared with library files of known bacterial species. If sample data matching with any library file of known bacterial species, sample identified as a matched microbe. An experiment performed to identify three different bacteria particles: Enterococcus faecalis, Pseudomonas aeruginosa, and Escherichia coli. By applying algorithm using library files of given samples, results were compromising. This system is potentially applicable to several biomedical areas, especially those related to cell morphology.

Keywords: microbial identification, laser scattering, peak identification, binned plots classification

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Authors: Zakirul Islam, Yugo Kumokawa, Quoc Thinh Tran, Motoki Kubo

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Clubroot is a disease of cruciferous plant caused by soil born pathogen Plasmodiophora brassicae and can significantly limit the production through rapid spreading. The present study was designed to investigate the effect of cultivation practices (chemical and organic soils) on clubroot disease development in Brassica rapa. Disease index and root bacterial composition were investigated for both chemical and organic soils. The bacterial biomass and diversity in organic soil were higher than those in chemical soil. Disease severity was distinct for two different cultivation methods. The number of endophytic bacteria decreased in the infected root for both soils. The increased number of endophytic bacterial number led to reduce the proliferation of pathogen spore inside the root and thus reduced the disease severity in organic plants.

Keywords: clubroot disease, bacterial biomass, root infection, disease index, chemical cultivation, organic cultivation

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Authors: Il Ho Park, Joong Seob Lee, Sung Hun Kang, Jae-Min Shin, Il Seok Park, Seok Min Hong, Seok Jin Hong

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Introduction: The human microbiota is the aggregate of microorganisms, and the bacterial microbiome of the human digestive tract contributes to both health and disease. In health, bacteria are key components in the development of mucosal barrier function and in innate and adaptive immune responses, and they also work to suppress the establishment of pathogens. In human upper airway, the sinonasal microbiota might play an important role in chronic rhinosinusitis (CRS). The purpose of this study is to investigate the human upper airway microbiome in CRS patients and to compare the sinonasal microbiome of adults with children. Materials and methods: A total of 19 samples from 19 patients (Group1; 9 CRS in children, aged 5 to 14 years versus Group 2; 10 CRS in adults aged 21 to 59 years) were examined. Swabs were collected from the middle meatus and/or anterior ethmoid region under general anesthesia during endoscopic sinus surgery or tonsillectomy. After DNA extraction from swab samples, we analysed bacterial microbiome consortia using 16s rRNA gene sequencing approach (the Illumina MiSeq platform). Results: In this study, relatively abundance of the six bacterial phyla and tremendous genus and species found in substantial amounts in the individual sinus swab samples, include Corynebacterium, Hemophilus, Moraxella, and Streptococcus species. Anaerobes like Fusobacterium and Bacteroides were abundantly present in the children group, Bacteroides and Propionibacterium were present in adults group. In genus, Haemophilus was the most common CRS microbiome in children and Corynebacterium was the most common CRS microbiome in adults. Conclusions: Our results show the diversity of human upper airway microbiome, and the findings will suggest that CRS is a polymicrobial infection. The Corynebacterium and Hemophilus may live as commensals on mucosal surfaces of sinus in the upper respiratory tract. The further study will be needed for analysis of microbiome-human interactions in upper airway and CRS.

Keywords: microbiome, upper airway, chronic rhinosinusitis, adult and children

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Authors: Olatunde Sunday Eludoyin, Charles Obiechina Olisa

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The study examined the spatial interactions between earthworm abundance (EA) and tree growth characteristics in ecological belts of Western Niger Delta, Nigeria. Eight 20m x 20m quadrat were delimited in the natural vegetation in each of the rainforest (RF), mangrove (M), fresh water swamp (FWS), and guinea savanna (GS) ecological belts to gather data about the tree species (TS) characteristics which included individual number of tree species (IN), diversity (Di), density (De) and richness (Ri). Three quadrats of 1m x 1m were delineated in each of the 20m x 20m quadrats to collect earthworm species the topsoil (0-15cm), and subsoil (15-30cm) and were taken to laboratory for further analysis. Descriptive statistics and inferential statistics were used for data analysis. Findings showed that a total of 19 earthworm species was found, with 58.5% individual species recorded in the topsoil and 41.5% recorded in the subsoil. The total population ofEudriliuseugeniae was predominantly highest in both topsoil (38.4%) and subsoil (27.1%). The total population of individual species of earthworm was least in GS in the topsoil (11.9%) and subsoil (8.4%). A total of 40 different species of TS was recorded, of which 55.5% were recorded in FWS, while RF was significantly highest in the species diversity(0.5971). Regression analysis revealed that Ri, IN, DBH, Di, and De of trees explained 65.9% of the variability of EA in the topsoil, while 46.9 % of the variability of earthworm abundance was explained by the floristic parameters in the subsoil.Similarly, correlation statistics revealed that in the topsoil, EA is positively and significantly correlated with Ri (r=0.35; p<0.05), IN (r=0.523; p<0.05) and De (r=0.469; p<0.05) while DBH was negatively and significantly correlated with earthworm abundance (r=-0.437; p<0.05). In the subsoil, only Ri and DBH correlated significantly with EA. The study concluded that EA in the study locations was highly influenced by tree growth species especially Ri, IN, DBH, Di, and De. The study recommended that the TSabundance should be improved in the study locations to ensure the survival of earthworms for ecosystem functions.

Keywords: interactions, earthworm abundance, tree growth, ecological zones, western niger delta

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Authors: Sanam Pudasaini, A. T. K. Perera, Ahmed Syed Shaheer Uddin, Sum Huan Ng, Chun Yang

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Development of high-efficiency and environment friendly bacterial inactivation methods is of great importance for preventing waterborne diseases which are one of the leading causes of death in the world. Traditional bacterial inactivation methods (e.g., ultraviolet radiation and chlorination) have several limitations such as longer treatment time, formation of toxic byproducts, bacterial regrowth, etc. Recently, an electroporation-based inactivation method was introduced as a substitute. Here, an electroporation-based continuous flow microfluidic device equipped with an array of micropillars is developed, and the device achieved high bacterial inactivation performance ( > 99.9%) within a short exposure time ( < 1 s). More than 99.9% reduction of Escherichia coli bacteria was obtained for the flow rate of 1 mL/hr, and no regrowth of bacteria was observed. Images from scanning electron microscope confirmed the formation of electroporation-induced nano-pore within the cell membrane. Through numerical simulation, it has been shown that sufficiently large electric field strength (3 kV/cm), required for bacterial electroporation, were generated using PDMS micropillars for an applied voltage of 300 V. Further, in this method of inactivation, there is no involvement of chemicals and the formation of harmful by-products is also minimum.

Keywords: electroporation, high-efficiency, inactivation, microfluidics, micropillar

Procedia PDF Downloads 153

Authors: Hafiza Javaria Ashraf, Xinghong Wang, Zhanghong Shi, Youming Hou

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Insect’s innate immunity depends on a variety of defense responses for the recognition of invading pathogens. Pathogen recognition involves particular proteins known as pattern recognition receptors (PRRs). These PRRs interact with pathogen-associated molecular patterns (PAMPs) present on the surface of pathogens to distinguish between self and non-self. C-type lectins (CTLs) belong to a superfamily of PPRs which involved in insect immunity and defense mechanism. Rhynchophorus ferrugineus Olivier is a devastating pest of Palm cultivations in China. Although studies on R. ferrugineus immune mechanism and host defense have conducted, however, the role of CTL in immune responses of R. ferrugineus remains elusive. Here, we report RfCTL, which is a secreted protein containing a single-CRD domain. The open reading frame (ORF) of CTL is 226 bp, which encodes a putative protein of 168 amino acids. Transcript expression analysis revealed that RfCTL highly expressed in immune-related tissues, i.e., hemolymph and fat body. The abundance of RfCTL in the gut and fat body dramatically increased upon Staphylococcus aureus and Escherichia coli bacterial challenges, suggesting a role in defense against gram-positive and gram-negative bacterial infection. Taken together, we inferred that RfCTL might be involved in the immune defense of R. ferrugineus and established a solid foundation for future studies on R. ferrugineus CTL domain proteins for better understanding of insect immunity.

Keywords: biological invasion, c-type lectin, insect immunity, Rhynchophorus ferrugineus Oliver

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Authors: Ramachandran Manivannan, B. Sakthi Swaroop, Selvam Noyel Victoria

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Microbial corrosion of brass gauze by the aerobic film forming bacteria Arthrobacter sulfurous in neutral media was investigated using gravimetric studies. Maximum weight loss of 166.98 mg was observed for a period of 28 days of exposure to the bacterial medium as against the weight loss of 13.69 mg for control. The optical density studies for the bacterial culture was found to show attainment of stationary phase in 48 h. Scanning electron microscopy analysis of the samples shows the presence of pitting corrosion. The energy dispersive X-ray analysis of the samples showed increased oxygen and phosphorus content in the sample due to bacterial activity.

Keywords: Arthrobacter sulfureus, biocorrosion, brass, neutral medium

Procedia PDF Downloads 142

Authors: Desouky Abd El Haleem, Sahar Zaki

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This work was conducted to develop a one-step multiplex PCR system for rapid, sensitive, and specific detection of three different bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, and Salmonella spp, directly in wastewater without prior isolation on selective media. As a molecular confirmatory test after isolation of the pathogens by classical microbiological methods, PCR-RFLP of their amplified 16S rDNA genes was performed. It was observed that the developed protocols have significance impact in the ability to detect sensitively, rapidly and specifically the three pathogens directly in water within short-time, represents a considerable advancement over more time-consuming and less-sensitive methods for identification and characterization of these kinds of pathogens.

Keywords: multiplex PCR, bacterial pathogens, Escherichia coli, Pseudomonas aeruginosa, Salmonella spp.

Procedia PDF Downloads 416

Authors: O. E. Obayemi, M. A. Ayoade, O. O. Komolafe

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Fish survey was carried out for an annual cycle covering both rainy and dry seasons using cast nets, gill nets and traps at two different reservoirs. The objective was to examined the fish assemblages of the reservoirs and provide more additional information on the reservoir. The fish species in the reservoirs comprised of twelve species of six families. The results of the study also showed that five species of fish were caught in reservoir five while ten fish species were captured in reservoir six. Species such as Malapterurus electricus, Ctenopoma kingsleyae, Mormyrus rume, Parachanna obscura, Sarotherodon galilaeus, Tilapia mariae, C. guntheri, Clarias macromystax, Coptodon zilii and Clarias gariepinus were caught during the sampling period. There was a significant difference (p=0.014, t = 1.711) in the abundance of fish species in the two reservoirs. Seasonally, reservoirs five (p=0.221, t = 1.859) and six (p=0.453, t = 1.734) showed there was no significant difference in their fish populations. Also, despite being impacted with gold mining the diversity indices were high when compared to less disturbed waterbodies. The study concluded that the environments recorded low abundant fish species which suggests the influence of mining on the abundance and diversity of fish species.

Keywords: Igun, fish, Shannon-Wiener Index, Simpson index, Pielou index

Procedia PDF Downloads 51

Authors: Futo Asano, Yusuke Yatsushiro, Hirokuni Miyamoto, Hiroaki Kodama

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A thermophile-fermented compost is produced using small fishes, crabs, and shrimps under a high temperature (approximately 75℃) by fermentation-associated self-heating. This compost has been used as a feed additive for pigs and hens in Japan, and the fecundity of this livestock is enhanced. Firmicutes is a dominant phylum in the microbial composition of the compost. We first reported that improvement of female larval fitness of Hercules beetle can be achieved by amendment of this compost to the humus. When the 90-d-old larvae were reared for subsequent 72 days in the humus with this compost, the growth of female larvae was significantly enhanced when compared with the growth of female larvae in the humus without the compost. In contrast, the growth of male larvae in the compost-free humus was the same as the larvae grow in the compost-amended humus. The bacterial composition of the feces of larvae was determined at 0 days and 46 days after transfer to the humus with or without the compost. The most dominant bacterium in the feces was Xylanimonas. Interestingly, the growth improvement of female larvae was associated with an increased abundance of Mollicutes in the fecal samples. These results indicate that the compost act as a probiotic material for enhancing the female larvae growth by supporting Mollicutes. Here, we tried to isolate Mollicutes from the contents of the midgut and hindgut of the 3rd instar female larvae of the Hercules beetle. These gut contents were spread onto a selective agar medium for Mollicutes (PPLO agar broth, BD Difco, NJ, USA). Although we isolated none of the Mollicutes until now, several bacteria that are closely related to Xylanimonas and Luteimicrobium were isolated. These isolates have xylanase and glucanase (CMCase) activities. We show the gut bacterial profiles of larvae and discuss how the fitness of female larvae of the Hercules beetle is improved by the compost.

Keywords: compost, beetle, mollicutes, woody biomass

Procedia PDF Downloads 51

Authors: Theoktisti Makridou, Konstantinos Tsaprailis, George Arvanitakis, Charalampos Kontoes

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In the literature, the data-driven approaches for mosquito abundance prediction relaying on supervised machine learning models that get trained with historical in-situ measurements. The counterpart of this approach is once the model gets trained on pointlevel (specific x,y coordinates) measurements, the predictions of the model refer again to point-level. These point-level predictions reduce the applicability of those solutions once a lot of early warning and mitigation actions applications need predictions for an area level, such as a municipality, village, etc... In this study, we apply a data-driven predictive model, which relies on public-open satellite Earth Observation and geospatial data and gets trained with historical point-level in-Situ measurements of mosquito abundance. Then we propose a methodology to extract information from a point-level predictive model to a broader area-level prediction. Our methodology relies on the randomly spatial sampling of the area of interest (similar to the Poisson hardcore process), obtaining the EO and geomorphological information for each sample, doing the point-wise prediction for each sample, and aggregating the predictions to represent the average mosquito abundance of the area. We quantify the performance of the transformation from the pointlevel to the area-level predictions, and we analyze it in order to understand which parameters have a positive or negative impact on it. The goal of this study is to propose a methodology that predicts the mosquito abundance of a given area by relying on point-level prediction and to provide qualitative insights regarding the expected performance of the area-level prediction. We applied our methodology to historical data (of Culex pipiens) of two areas of interest (Veneto region of Italy and Central Macedonia of Greece). In both cases, the results were consistent. The mean mosquito abundance of a given area can be estimated with similar accuracy to the point-level predictor, sometimes even better. The density of the samples that we use to represent one area has a positive effect on the performance in contrast to the actual number of sampling points which is not informative at all regarding the performance without the size of the area. Additionally, we saw that the distance between the sampling points and the real in-situ measurements that were used for training did not strongly affect the performance.

Keywords: mosquito abundance, supervised machine learning, culex pipiens, spatial sampling, west nile virus, earth observation data

Procedia PDF Downloads 105

Authors: Muna Al-Tarshi

Abstract:

The distribution and accumulation dynamics of anthropogenic marine debris (AMD) and microplastic particles in mangrove habitats in the region are poorly understood. The abundance, sorting, and diversity aspects of AMD and microplastics were investigated in three types of mangroves creeks ( Natural mangrove, afforested mangrove, and non-planted). Abundance, concentration, and particles form of microplastics have been illustrated in three substrate in mangrove habitats e.g. sediment, water, and aquatic organisms. Density separation method by using highly saturated solution was implemented to extract the plastic particles from the sediment samples. The average size of particles in each transect was done using image software, and the polymer type was determined via FTIR. There was variability in abundance of microplastics and marine debris between the habitats and within the substrates in the habitats.Biomonitoring program was developed to detect the pollution of microplastics in mangrove habitats in Sultanate of Oman. Sediment dwelling species were the best choice. Testing whether the zooplankton (Artemia) eating the microplastics via FlowCam technique have been studied. The zooplanktons (Artemia) were eating the microplastics as mistaken food.

Keywords: microplastics, marine debris, flowcam, FTIR, polymer, artemia

Procedia PDF Downloads 86