scholarly journals Culture-Dependent and Metagenomic Profiling of Eukaryal Diversity in Petroleum Hydrocarbon-Polluted Soil from B-Dere, Gokana, Rivers State, Nigeria

2021 ◽  
pp. 64-73
Author(s):  
D. N. Ogbonna ◽  
I. R. Udotong ◽  
N. Basi ◽  
R. R. Nrior
Keyword(s):  
Polluted Soil ◽  
Soil Samples ◽  
Shotgun Sequencing ◽  
Next Generation ◽  
Polluted Soils ◽  
Fungal Isolates ◽  
Total Dna ◽  
Rivers State ◽  
Generation Sequencing ◽  
Culture Dependent

B-Dere is one of the communities in Ogoniland and a major oil producing area in Rivers State where oil exploration and production activities commenced 50 years ago and is now characterized by oil fields and installations that have remained dormant for several decades. Past spills, lack of maintenance, oil trapping and damage to oil infrastructures have been common sight in this region and the environment has been without remediation over the years. B-Dere community has suffered surface water pollution throughout its creeks with massive hydrocarbons for years without remediation. The aim of this study was to determine the Culture- dependent and Metagenomic studies of fungal diversity in petroleum polluted soils in B-Dere community in Gokana LGA of Rivers State, Nigeria. This is to profile fungal communities through next-generation techniques by shotgun sequencing of total DNA isolates directly from the oil polluted environment. Soil samples were collected aseptically with hand auger at a depths of 0-15 and 15-30 cm and made up to a composite sample and transported to the laboratory for analysis using standard microbiological methods for culture- dependent analysis while the Metagenomic studies was carried out at the Microbial Insights, Incorporated; United State of America. In this study next-generation sequencing techniques by shotgun sequencing of total DNA methods were used for identification of fungal isolates from the crude oil polluted soils in B-Dere. Deoxyribonucleic acid (DNA) extraction from crude oil polluted soil samples was performed using ZymoBiomics DNA extraction kits (Zymo Research, Inc; USA). DNA sequencing was performed by the next generation sequencing technique to determine the nucleotide sequence of all eukaryal community structure present in the polluted soil sample using ITS region. Results of the culture-dependent technique showed that only two fungal genera namely Penicillium sp and Aspergillus sp were isolated and identified while the soil was mainly dominated by the genera Penicillium (73.33%), followed by the Rhodotorula (6.54%), Dactylellina(5.09%), Kalmanozyma(2.56%), Fereydounia(1.89%), Xerochrysium(1.36%), Arthrobotrys (1.14%) and Diutina (0.77%) by the metagenomic analysis. However the three major groups were classified as Ascomycota, Basidiomycota and Mucoromycota with Ascomycota having the highest taxonomic reads of 86.76%. However, a total of 60 eukaryal species were identified, in the metagenomic study. In conclusion, these fungal strains can be used in bioremediation process and oil pollution reduction in soil ecosystems because of their high activity in aliphatic hydrocarbon degradation and cell surface hydrophobicity. The next-generation techniques by shotgun sequencing assays appear to be suitable alternatives for rapid identification of the above mentioned fungal isolates.

scholarly journals Bioremediation of lead polluted soil from Obio/Akpor local Government Area, rivers state using African Catfish and tilapia fish bones

2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Daniel UI ◽  
Nwanya A
Keyword(s):  
Lead Concentration ◽  
Polluted Soil ◽  
Soil Samples ◽  
African Catfish ◽  
Polluted Soils ◽  
Lead Battery ◽  
Fish Bones ◽  
Two Samples ◽  
Lead Metal ◽  
Rivers State

A study was undertaken to compare the bones of two fin fish-African Catfish (Clarias gariepinus) and Tilapia (Oreochromis niloticus), in the bioremediation of lead polluted soils. Six soil samples containing different sources of lead were collected from Obio-Akpor LGA, Rivers State. African catfish and Tilapia fishes were sourced from the market; the bones were extracted and dried (using a hot oven). The bones were then crushed with a blender, and weighed using analytical measuring scale. The crushed bones were mixed with lead polluted soil samples and left in the laboratory, in cool transparent plates for 3 weeks and 3 days for group one samples, while group two samples were left in the laboratory for 1 week and 3 days. The results revealed that for group one samples; Acid battery soil mixed with Catfish bones reduced the lead concentration from 3122.30mg/kg to 2574.50mg/kg. Lead battery soil mixed with Tilapia bones reduced the lead concentration from 6718.15mg/kg to 1184.15mg/kg, while Lead metal soil mixed with both Catfish+Tilapia bones increased the lead concentration from 8807.65mg/kg to 11874.50mg/kg. For group two samples; Acid battery soil mixed with both Catfish+Tilapia bones reduced the lead concentration from 3706.75mg/kg to 3144.45mg/kg. Lead metal soil mixed with Catfish bone reduced the lead concentration from 15940.50mg/kg to 3903.90mg/kg, while Lead battery soil mixed with Tilapia bones increased the lead concentration from 6439.20mg/kg to 11671.50mg/kg. The study revealed that Catfish bones, at different weights can be used in the bioremediation of lead polluted soils and the reduction was higher, than using Tilapia or the combination of the fish bones.

scholarly journals Next Generation Sequencing Analysis of Biofilms from Three Dogs with Postoperative Surgical Site Infection

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
L. M. König ◽  
R. Klopfleisch ◽  
D. Höper ◽  
A. D. Gruber
Keyword(s):  
Next Generation Sequencing ◽  
Sequencing Analysis ◽  
Next Generation ◽  
Bacterial Composition ◽  
Tissue Samples ◽  
Next Generation Sequencing Analysis ◽  
Total Dna ◽  
Chronic Wound Infections ◽  
Generation Sequencing ◽  
Formalin Fixed

The composition of biofilms in chronic wound infections of dogs is unclear. In the present study, histologically identified biofilms attached to sutures in chronically infected wounds of three dogs were examined by next generation sequencing of total DNA extracted from formalin-fixed and paraffin-embedded tissue samples. The analysis identified an inhomogeneous bacterial composition in three tissues containing biofilms. Some of the identified bacterial families such as Staphylococci and Streptococci have been found before in biofilms associated with human and canine wounds but in this study were quantitatively in the minority. The majority of the reads classified as bacterial sequences had the highest identity with sequences belonging to the Porphyromonadaceae, Deinococcaceae, Methylococcaceae, Nocardiaceae, Alteromonadaceae, and Propionibacteriaceae and thus taxons of so far minor relevance in veterinary medicine.

scholarly journals Mycoflora of Crude Oil Polluted Soils of Ukwa West of Abia State Nigeria

2021 ◽  
pp. 1-9
Author(s):  
J. M. Madu ◽  
A. I. Ogbonna ◽  
C. I. C. Ogbonna
Keyword(s):  
Crude Oil ◽  
Soil Sample ◽  
Critical Role ◽  
Organic Matter Content ◽  
Chemical Properties ◽  
Polluted Soil ◽  
Soil Samples ◽  
Polluted Soils ◽  
Physico Chemical ◽  
Starch Agar

Aim: Bioremediation of soil play a critical role in removing pollutants from crude oil polluted soil. To investigate the mycoflora of crude oil polluted area of Ukwa West Local Government in the present Abia State. Methodology: Portions of the soil samples collected from three (3) locations were plated out separately on Yeast Starch Agar, Starch Agar, and Cellulose Agar using soil plate methods. The culture plates were examined after 5-7 and 14 days for the presence of fungi. Pure cultures of the isolates were obtained by subculturing and the physico-chemical properties of the soil samples were determined using standard methods. Results: Twenty species (20) of fungi were isolated from the crude oil polluted soil sample and represented by their respective genera. Eight (8) species of Aspergillus representing 40%, two (2) species of Thermomyces representing 10% each, and one (1) species of Penicillium, Cladosporium, Cunninghamella, Curvularia, Trichoderma, Scopulariopsis, Sporotrichum and Basipetospora representing 5% each. Aspergillus species were predominant which include among others A. fumigatus, A. niger, A. parasiticus, A. oryzae, A. terreus. The physico-chemical properties of the soil sample were found to be varied and have affected the distribution and population of fungi. The pH values ranged from 4.81- 5.58 as compared to the control ranging from 5.72- 6.50 for soil samples A, B and C. The moisture content values ranged between 26.46-29.59% as compared to the control ranging from 29.41-32.51%. The soil was found to be high in organic matter content with values of 70.3-82.7% as compared to the control which was 94% for each of the locations. Conclusion: Crude oil polluted soils of Ukwa West of Abia State, Nigeria is rich in fungal biodiversity with the soil’s samples having different physico-chemical properties.

Mycorestoration of crude oil polluted soil using Pleurotus tuberregium

2021 ◽  
Vol 66 (1) ◽  
pp. 73-84
Author(s):  
Beckley Ikhajiagbe ◽  
Kingsley Enerijiofi ◽  
Paul Umendu
Keyword(s):  
Crude Oil ◽  
Pollution Control ◽  
Polluted Soil ◽  
Soil Samples ◽  
Fruiting Bodies ◽  
Soil Environment ◽  
Polluted Soils ◽  
Brachystegia Nigerica ◽  
Asystasia Gangetica ◽  
Pleurotus Tuberregium

Crude oil contamination is known to cause unwholesome damage to man, his environment comprising of soil, air and water bodies as well as other forms of life. This study determined the effect of crude oil polluted soils on the composition of different microorganisms and plants and the growth of Pleurotus tuberregium. Oil polluted soils in bowls were amended with sawdust from Brachystegia nigerica as substrate. Fruiting bodies and the diameter of the mushroom cap were found to increase with increasing weeks of exposure to oil as against the control which had no fruiting bodies throughout the experiment. Pepperomia pellucida was found to be the predominant weed (n = 20), followed by Asystasia gangetica (n = 11). The bacterial and fungal counts were higher at the oil polluted soil attached to sclerotia than the control. The growth of Pleurotus tuberregium in the polluted soil samples showed its ability to degrade and utilize hydrocarbon as the source of carbon and energy, thereby remediating the contaminated soil environment. This work has shown that the fungus has bioremediation and pollution control capacity.

scholarly journals Bacterial Community and Diversity from the Watermelon Cultivated Soils through Next Generation Sequencing Approach

2021 ◽  
Vol 37 (6) ◽  
pp. 521-532
Author(s):  
Mahesh Adhikari ◽  
Sang Woo Kim ◽  
Hyun Seung Kim ◽  
Ki Young Kim ◽  
Hyo Bin Park ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Community ◽  
South Korea ◽  
Genomic Dna ◽  
Soil Samples ◽  
Community Diversity ◽  
Next Generation ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Cultivated Soils

Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.

scholarly journals Molecular characterization of endophytic fungal communities associated with Vitis vinifera L. at Taif region of Saudi Arabia

2021 ◽  
Vol 42 (2) ◽  
pp. 177-185
Author(s):  
S.M. Sayed ◽  
◽  
A.M. El-Shehawi ◽  
S.A. Elarnaouty ◽  
S.A. Al-Otaibi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Endophytic Fungi ◽  
Fungal Communities ◽  
Vitis Vinifera L ◽  
Next Generation ◽  
Operational Taxonomic Units ◽  
Grapevine Leaves ◽  
Total Dna ◽  
Generation Sequencing

Aim: The current study aimed to characterize the composition of endophytic fungal communities related to Taify grapevine leaves. Methodology: Taify grapevine leaves were collected from three different locations at Taif region. Total DNA was extracted and the endophytic fungal communities were investigated using next generation sequencing in a metagenomics approach. Results: The obtained data detected 26 fungal operational taxonomic units (OTUs) in all locations with variation in most taxa among three locations. The phylum Ascomycota dominated relative sequence abundance (90.83%), followed by Basidiomycota at 1.82%. Other unidentified fungi at phylum level dominated 7.35% abundance level. At genus level, Alternaria and Cladosporium genera were present at all locations, while Filobasidium and Didymella were detected in two locations. Most genera, Penicillium, Hanseniaspora, Fusarium, Chrysocorona and Quambalaria were detected in one location only. Interpretation: The present study confirmed the diversity of endophytic fungi in Taify grapevine, including pathogenic and non-pathogenic species. The detected species have potential to be used as biocontrol species against economically important pathogens such as Alternaria and Hanseniaspora. This will contribute to our understanding of grapevine-endophytic fungi interaction and their utilization to enhance grapevine production and quality. Key words: Endophytes, Fungi, Grapevine, Metagenomic, Next generation sequencing

scholarly journals Bioremediation Efficiency of Bacillus amyloliquefaciens and Pseudomonas aeruginosa with the Nutrient Amendment on Crude Oil Polluted the Soil

2019 ◽  
pp. 1-13
Author(s):  
David N. Ogbonna ◽  
Renner R. Nrior ◽  
Festus E. Ezinwo
Keyword(s):  
Crude Oil ◽  
Bacillus Amyloliquefaciens ◽  
Heterotrophic Bacteria ◽  
Polluted Soil ◽  
Total Petroleum Hydrocarbon ◽  
Polluted Soils ◽  
Fish Waste ◽  
Goat Manure ◽  
Nutrient Amendment ◽  
Rivers State

Aim: To assess the Bioremediation efficiency of Bacillus amyloliquefaciens and Pseudomonas aeruginosa strain CL 9 with nutrient amendment using bio-stimulating agents such as Fish waste and Goat manure on crude oil polluted soils in Rivers State, Nigeria. Study Design: The study employs experimental design, statistical analysis of the data and interpretation. Place and Duration of Study: A portion of Rivers State University demonstration farmland in Nkpolu-Oroworukwo, Mile 3 Diobu area of Port Harcourt, Rivers State was used for this study. The piece of land is situated at Longitude 4°48’18.50’’N and Latitude 6o58’39.12’’E measuring 5.4864 m x 5.1816 m with a total area of 28.4283 m2. Bioremediation monitoring lasted for 56 days, analysis carried out weekly (per 7 days interval). Methodology: Seven (7) experimental plots were employed using a Randomized Block Design each having dimensions of 100 x 50 x 20 cm (Length x Breadth x Height) were formed and mapped out on agricultural soil and left fallow for 6 days before contamination on the seventh day; after which it was allowed for 21 days for proper contamination and exposure to natural environmental factors to mimic crude oil spill site. Thereafter bio stimulating agents usually referred to as nutrient amendment organics in this study (fish waste and goat manure) and bio-augmenting microorganisms were applied. Soil profile before and after contamination was assayed while parameters like Nitrate, Sulphate, Phosphate, Total Organic Carbon (TOC) and Total Petroleum Hydrocarbon (TPH), were monitored throughout the experimental period. Microbial analyses such as Total Heterotrophic Bacteria (THB), Total Heterotrophic Fungi (THF), Hydrocarbon Utilizing Bacteria (HUB) and Hydrocarbon Utilizing Fungi (HUF) were recorded. Bioremediation efficiency was estimated from percentage (%) reduction of Total Petroleum Hydrocarbon (TPH) from day 1 to the residual hydrocarbon at day 56 of bio augmented/ biostimulation plots with the control. Results: Results revealed amount of remediated hydrocarbon and % Bioremediation efficiency at 56 days in the different treatment plots (initial TPH contamination value of  9296.83  mg/kg) in a decreasing order as follows: PS+Bac+Pse+GF+FW (8032.825 mg/kg; 86.40%) >PS+GF+FW (6867.825 mg/kg; 73.87%) >PS+Bac+Pse (6587.825mg/kg; 70.86%) >PS+FW (6441.825mg/kg; 69.29%) >PS+GF (5909.825 mg/kg; 63.57%) >CTRL 2 (Polluted soil without amendment) (3604.825mg/kg; 38.78%). Microbiological results showed increased colonial values with increase time exposure. The results observed on day 56 indicate that Polluted soil + Bacillus + Pseudomonas (10.11 Log10 CFU/g) > Polluted soil but un-amended soil (8.76 Log10 CFU/g) > unpolluted soil (8.68 Log10 CFU/g). Comparatively, Polluted soil +Bacillus + Pseudomonas expressed higher heterotrophic bacteria of 9.77 and 9.67 Log10 CFU/g while fungal counts recorded 6.04 and 6.82 Log10 CFU/g. Conclusion: Study showed that bioremediation of crude oil-polluted soils with bacteria singly is less effective but a combination with other organic nutrients is a better palliative measure. Therefore, amendment with organic nutrients like Goat manure and Fish wastes is recommended for crude oil polluted soils due to its high nutrient content as substrates for biostimulation of indigenous and augmenting biodegrading microbes. This process could be a source of enhanced natural attenuation of oil-contaminated environments in Nigeria.

scholarly journals On Botulinum Neurotoxin Variability

mBio ◽  
2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Cesare Montecucco ◽  
Maria Berica Rasotto
Keyword(s):  
Next Generation Sequencing ◽  
Botulinum Neurotoxin ◽  
Toxin Production ◽  
Soil Samples ◽  
Evolutionary Significance ◽  
Next Generation ◽  
Clostridium Species ◽  
Botulinum Neurotoxins ◽  
Generation Sequencing

ABSTRACT The rapidly growing number of botulinum neurotoxin sequences poses the problem of the possible evolutionary significance of the variability of these superpotent neurotoxins for toxin-producing Clostridium species. To progress in the understanding of this remarkable phenomenon, we suggest that researchers should (i) abandon an anthropocentric view of these neurotoxins as human botulism-causing agents or as human therapeutics, (ii) begin to investigate in depth the role of botulinum neurotoxins in animal botulism in the wilderness, and (iii) devote large efforts to next-generation sequencing of soil samples to identify novel botulinum neurotoxins. In order to compare the fitness of the different toxins, we suggest that assays of all the steps from toxin production to animal death should be performed.

scholarly journals Microbiological and Physicochemical Evaluation of Oil-polluted Soil from Major Auto Mechanic Shops in Port Harcourt Metropolis, Rivers State, Nigeria

2020 ◽  
pp. 1-10
Author(s):  
Janet Olufunmilayo Williams ◽  
Prekebi Peter Akemi
Keyword(s):  
Control Sample ◽  
Pollution Index ◽  
Sole Source ◽  
Polluted Soil ◽  
Soil Samples ◽  
Port Harcourt ◽  
Physicochemical Evaluation ◽  
The Mean ◽  
Ph Level ◽  
Rivers State

The capability of microorganisms to utilize spent oil in polluted soil from some major auto mechanic workshops in Port Harcourt metropolis as the sole source of carbon and energy was studied. Soil samples were collected from three (3) Auto mechanic workshops (Mile 3 Mechanic Village (N 4º48' 34.07'', E 6º59' 10.17''), Ikoku Mechanic Workshop (N 4º47' 54.28'', E 6º59' 36.42'') and Elekahia Zone H Mechanic Workshop (N4º49' 11.62'', E 7º1' 16.58'') in Port Harcourt, Rivers State, Nigeria from depths of 0–30 cm, 30–60 cm and 60–90 cm at the same spot from each station. Soil samples were analysed microbiologically and physicochemically using standard methods. The control sample was obtained behind the Biology Building of Rivers State University, Port Harcourt. The results of the total heterotrophic bacterial and fungal counts showed that the microbial load was high at a depth of 0 to 30 cm for all the samples analysed including the control. With 60-90 cm depth, low microbial counts were obtained. The total heterotrophic bacterial counts from the three mechanic workshops ranged from 6.8 X 108 to 2.3 X 109cfu/g while the total heterotrophic fungal counts ranged from 1.3 X 106 to 8.0X 106 cfu/g. The spent oil-utilizing microbial populations ranged from1.0 X 105 to 3.0 X 106cfu/g and1.0 X 105 to 8.0 X 105 cfu/g for the bacterial and fungal counts respectively. Five spent oil utilizing bacterial isolates of the genera, Pseudomonas, Klebsiella, Bacillus, Micrococcus and Proteus and five fungal isolates of the genera, Penicillium, Candida, Rhizopus, Fusarium and Aspergillus were obtained from spent oil-polluted soil in this study. The pollution index of the different physicochemical parameters obtained from the different sample stations was as follows: Electrical Conductivity (EC): Mile 3 had the highest with the mean of 12.50 ±0.0-13.20±0.0µs/cm, while Ikoku had the lowest with mean of 10.99 ± 0.0-11.50 ± 0.0 µs/cm. Ikoku had the highest pH level with mean of 7.0 ± 0.0- 8.5 ± 0.0 while Mile 3 had the lowest pH level with mean of 6.5 ± 0.0-7.59 ± 0.0. Ikoku had the highest Total Organic Carbon (TOC) with mean of 17.55 ± 0.0-20.60 ± 0.0 mg/kg while Elekahia had the lowest with the mean of 16.99 ± 0.0-18.0 ± 0.0 mg/kg. Ikoku had the highest Total Hydrocarbon Content (THC) with mean of 38,862 ± 0.0-40,500 ± 0.0 mg/kg while Mile 3 had the lowest with the mean of 20,550 ± 0.0-30,000 ± 0.0 mg/kg. From the Pollution Index Analysis, Ikoku Auto Mechanic Workshop is more contaminated with Spent oil than Mile 3 and Elekahia.

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