scholarly journals Molecular Characterisation and Plasmid Profiling of Hydrocarbon Utilizing Bacteria Isolates from Wetlands in Rivers State, Southern Nigeria

2021 ◽  
pp. 50-59
Author(s):  
D. N. Ogbonna ◽  
P. M. Chibuike ◽  
J. O. Williams
Keyword(s):  
Open Water ◽  
Soil Samples ◽  
Bacillus Species ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Bacillus Flexus ◽  
Southern Nigeria ◽  
Plasmid Profiling ◽  
Rivers State ◽  
Hydrocarbon Utilizing Bacteria

Wetlands can intercept runoff from surfaces prior to reaching open water and remove pollutants through physical, chemical, and biological processes thereby protecting and preserving the environment.  Because of unsustainable oil exploration activities, most wetlands in Rivers State, Southern Nigeria have suffered severe petroleum-damaged ecosystems. This research was carried out to characterize and identify the hydrocarbon utilizing bacteria associated with crude oil polluted wetlands and to screen for the presence of plasmids that could confer resistance to antibiotics using both cultural and molecular methods. Soil samples were collected from three different wetlands across the state with hand auger at two depths of 0-15cm and 15-30cm twice monthly for three months. The presence of microbial activity was determined by the enumeration and isolation of total heterotrophic and hydrocarbon utilizing bacteria. Eight (8) most occuring hydrocarbon utilizing bacterial isolates were isolated and identified culturally and phenotypically from the 54 wetland soil samples. These bacteria isolates were confirmed to be Bacillus flexus, Bacillus subtilis, Lysinibacillus macroides, Staphylococcus aureus, Chryseobacterium aquifrigidense, Pseudomonas aeruginosa and Salmonella enterica molecularly via sequencing of the 16S rRNA gene. The most common bacteria isolated were Bacillus species, followed by Pseudomonas at a dilution of 106.   Seven (7) out of the eight (8) isolates (except Salmoella enterica) showed the presence of the 25kb plasmids at various intensities.

scholarly journals New Insights into Molecular Basis Identification of Three Novel Strains of the Bacillus Subtilis Group Produce Cry Proteins Isolated from Soil Samples in Adana, Turkey

2021 ◽  
Author(s):  
Semih Yilmaz ◽  
Abeer Babiker Idris ◽  
Abdurrahman Ayvaz ◽  
Aysun Cetin ◽  
Funda Ulgen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Evolutionary Relationship ◽  
Cross Sectional Study ◽  
Soil Samples ◽  
Bacillus Species ◽  
Rrna Gene ◽  
Specific Information ◽  
Cross Sectional ◽  
Cry Proteins ◽  
Subtilis Group

Aims: This study aimed to analyze the evolutionary relationship between Bacillus species isolated from agricultural soil using in-silico tools. Methods and Results: A cross-sectional study was conducted in Adana province, in Turkey. A total of 120 Bacillus species were isolated from 80 soil samples. However, the phylogenetic tree diverged into two lineages; one belongs to B. subtilis group while the other belongs to B. cereus group. Interestingly, three native strains (SY27.1A, SY35.3A, and SY58.5A), which produce Cry proteins, shared high similarity with B. subtilis group (over 99%) and less than 95% similarity with known B. thuringiensis and other species of B. cereus group. Furthermore, 11 canonical SNPs (canSNPs) were identified in strains that belong to B. pumilus group when compared with B. subtilis reference sequences. Conclusions: Phylogenetic analysis of 16S rRNA sequences was found valuable for differentiation between Bacillus species isolated from soil samples. In addition, SNPs analysis provided more intra-specific information in the cases of B. subtilis group. Significance and Impact of Study: A detailed analysis was provided for the SNPs present in a conserved region of 16S rRNA gene of Bacillus species. Also, we proposed three novel Bacillus strains that produce Cry proteins and belong to B. subtilis group.

scholarly journals Characterization of Indigenous Bacterial Communities in Crude-Oil Impacted Sites at Obagi Town, Onelga, Rivers State, Nigeria

Fine Focus ◽  
2016 ◽  
Vol 2 (1) ◽  
pp. 7-14
Author(s):  
Chioma Blaise Chikere ◽  
Chinyere Augusta Ajuzieogu ◽  
Michael Chukwugoziem Miller
Keyword(s):  
Crude Oil ◽  
Heterotrophic Bacteria ◽  
Bacterial Species ◽  
Polluted Soil ◽  
Soil Samples ◽  
Isolation And Characterization ◽  
Significant Difference ◽  
Rivers State ◽  
Hydrocarbon Utilizing Bacteria

Hydrocarbon utilizers are expected to be indigenous in crude-oil polluted environments. The isolation and characterization of hydrocarbon utilizers is often a key strategy in bioremediation of hydrocarbon-polluted environments. In this study, crude-oil polluted soil samples from Obagi town, Onelga, Rivers state were enumerated and characterized for putative hydrocarbon utilizing bacterial populations. Biochemical characterization identified five bacterial species representative of five genera: Bacillus, Pseudomonas, Acinetobacter, Micrococcus and Staphylococcus. Amongst the genera of bacteria isolated, Bacillus had the highest frequency of occurrence (40%). The mean count of total heterotrophic bacteria was 1.7 X 107 cfu/g, while hydrocarbon utilizing bacteria (HUB) count mean density was 1.0 X 107 cfu/g for the three soil samples. Statistical analyses revealed no significant difference at p>0.05 between Total Heterotrophic Bacterial (THB) and Hydrocarbon Utilizing Bacterial (HUB) counts, suggesting that most of the bacteria present in the sampled sites were hydrocarbon utilizers. Findings from this study suggest the presence of indigenous putative hydrocarbon utilizing bacteria in the crude-oil polluted soil of Obagi town. Hence, a promising potential exists for future bioremediation studies on the site.

Impacts of Vending Practices on the Microbiological Quality of Bread in the Ojoo Area of Ibadan, Oyo-State, Nigeria

2019 ◽  
Vol 15 (1) ◽  
pp. 31-39
Author(s):  
Oluwadara Oluwaseun Alegbeleye ◽  
Wasiu Akinloye Oyebisi Afolabi ◽  
Beatrice Oluwatoyin Opeolu ◽  
Amin Mousavi Khaneghah
Keyword(s):  
Food Safety ◽  
Microbiological Quality ◽  
Bacillus Species ◽  
Potential Hazard ◽  
Safety Regulations ◽  
Bacillus Flexus ◽  
Microbiological Methods ◽  
Key Factor ◽  
Quality Of Food

Background: Bacterial counts in ready-to-eat foods are a key factor in assessing the microbiological quality and safety of food. Periodic assessment of the microbiological quality of food is necessary to develop a robust database and help to ensure food safety. </P><P> Methods: The bacterial contamination of a total of 336 bread samples collected from two bakeries and 10 vendors in Ojoo Area of Ibadan, Oyo-State, Nigeria (December 2014 -June 2015) was evaluated. The microbiological quality of the bread loaves was investigated using standard microbiological methods (morphological, phenotypic and molecular characterization). </P><P> Results: The results showed that the number of contaminated samples among the vended bread samples was higher than the bakery bread samples and can be summarized as Bacillus megaterium (4.30%), Staphylococcus arlettae (0.005%), Staphylococcus saprophyticus (2.78%), Citrobacter freundii (2.40%), Bacillus flexus (1.64%), Bacillus species (49.59%), Pseudomonas aeruginosa (4.12%), Pseudomonas fluorescens (0.92%), Pseudomonas species (0.045%), Escherichia coli (30.44%) Klebsiella sp. (0.040%) and Aeromonas hydrophila (3.72%). </P><P> Conclusion: The findings demonstrate that the bread samples which become contaminated after transport and handling can be considered a potential hazard to human health in the area. More stringent adherence to food safety regulations should be encouraged and enforced by the appropriate authorities. The findings of this study may be adopted to improve the hygienic conditions of bread distribution chain in the area as well as in other regions of the World.

Bacterial influence on the formation of hematite: implications for Martian dormant life

2021 ◽  
pp. 1-15
Author(s):  
Sudeera Wickramarathna ◽  
Rohana Chandrajith ◽  
Atula Senaratne ◽  
Varun Paul ◽  
Padmanava Dash ◽  
...  
Keyword(s):  
Inductively Coupled Plasma ◽  
Soil Layer ◽  
Soil Samples ◽  
Mineral Weathering ◽  
Compositional Variation ◽  
Rrna Gene ◽  
Potential Candidate ◽  
Metabolic Processes ◽  
Extraterrestrial Life ◽  
X Ray

Abstract Previous exploration missions have revealed Mars as a potential candidate for the existence of extraterrestrial life. If life could have existed beneath the Martian subsurface, biosignatures would have been preserved in iron-rich minerals. Prior investigations of terrestrial biosignatures and metabolic processes of geological analogues would be beneficial for identifying past metabolic processes on Mars, particularly morphological and chemical signatures indicative of past life, where biological components could potentially be denatured following continued exposure to extreme conditions. The objective of the research was to find potential implications for Martian subsurface life by characterizing morphological, mineralogical and microbial signatures of hematite deposits, both hematite rock and related soil samples, collected from Highland Complex of Sri Lanka. Rock samples examined through scanning electron microscopy-energy dispersive X-ray (SEM-EDX) spectroscopy. Analysis showed globular and spherical growth layers nucleated by bacteria. EDX results showed a higher iron to oxygen ratio in nuclei colonies compared to growth layers, which indicated a compositional variation due to microbial interaction. X-ray diffraction analysis of the hematite samples revealed variations in chemical composition along the vertical soil profile, with the top surface soil layer being particularly enriched with Fe2O3, suggesting internal dissolution of hematite through weathering. Furthermore, inductively coupled plasma-mass spectrometry analyses carried out on both rock and soil samples showed a possible indication of microbially induced mineral-weathering, particularly release of trapped trace metals in the parent rock. Microbial diversity analysis using 16S rRNA gene sequencing revealed that the rock sample was dominated by Actinobacteria and Proteobacteria, specifically, members of iron-metabolizing bacterial genera, including Mycobacterium, Arthrobacter, Amycolatopsis, Nocardia and Pedomicrobium. These results suggest that morphological and biogeochemical clues derived from studying the role of bacterial activity in hematite weathering and precipitation processes can be implemented as potential comparative tools to interpret similar processes that could have occurred on early Mars.

Growth enhancement of black pepper (Piper nigrum) by a newly isolated Bacillus tequilensis NII-0943

Biologia ◽  
2011 ◽  
Vol 66 (5) ◽  
Author(s):  
Syed Dastager ◽  
C. Deepa ◽  
Ashok Pandey
Keyword(s):  
Sequence Similarity ◽  
Black Pepper ◽  
Piper Nigrum ◽  
Bacillus Species ◽  
Rrna Gene ◽  
Growth Enhancement ◽  
Nitrogen And Phosphorus ◽  
Bacillus Tequilensis ◽  
Plant Growth Promoting ◽  
The Western Ghats

AbstractA Gram positive, rod-shaped potential strain was selected from the pool of bacterial isolates obtained from the Western Ghats forest (India) on the basis of zone of P-solubilization activity. Identification based on 16S rRNA gene sequence revealed that the strain is of Bacillus species, sharing highest sequence similarity to Bacillus tequilensis NRRL B-41771T (99.5%). Strain NII-0943 was able to produce good amount of indole acetic acid (IAA) and was positive for siderophore production. In addition to IAA and siderophore attributes, strain NII-0943 also possessed the characteristics like Ca3(PO4)2 solubilization and growth in nitrogen-free medium. Seed inoculation with the strain NII-0943 resulted in significantly higher root initiation in black pepper cuttings grown under pots. The contents of nitrogen and phosphorus in both soil and plant were also enhanced significantly in treatments inoculated with these bacterial inocula. Hence, based on this evidence it is proposed that strain NII-0943 could be deployed as a plant growth-promoting inoculant to attain the desired results of bacterization.

scholarly journals Empirical Characterization of Heavy Metals in Crude Oil Spill Sites in Emohua, Rivers State, Nigeria

2021 ◽  
Vol 2 (5) ◽  
pp. 24-28
Author(s):  
Nnamdi Michael Ahiamadu ◽  
Ify L. Nwaogazie ◽  
Yusuf O. L. Momoh
Keyword(s):  
Heavy Metals ◽  
Surface Water ◽  
Oil Spill ◽  
Environmental Protection Agency ◽  
Surface Soil ◽  
Soil Samples ◽  
Petroleum Resource ◽  
Significant Difference ◽  
Rivers State ◽  
Pb Concentration

The study assessed the concentration of heavy metals in three oil spill sites in Emohua local government area in Rivers State, Nigeria. Soil samples were collected at depth 0-30cm for surface soil samples and up to 10m for sub-surface soil samples depending on the depth of borehole. Groundwater samples were collected from drilled boreholes while the surface water samples were collected from fishponds or water bodies (rivers) close to the oil spill sites. The samples taken from the oil spill sites were analysed to determine the level of concentration of 10 Department of Petroleum Resource (DPR) specified heavy metals (Cd, Zn, Cu, Pb, Cr, Ba, Ni, Hg, As, and Co). BUCK Scientific Atomic Absorption Spectrophotometer (AAS) was used in detecting the concentration of the heavy metals. For the surface soil, Pb concentration in site A and B were significantly higher than what was obtained at site C, with a mean concentration of 219.70, 130.01 and 3.41mg/kg respectively for the three sites. The mean lead (Pb) concentration obtained in the surface soil was within DPR and United State Environmental Protection Agency (USEPA) acceptable limits. Barium also has significant concentration in both the surface soil and sub-surface soil. Kruskal Wallis test indicated significant difference in the Pb, Cd, Zn, Cu, Cr and Ba concentration in surface/topsoil among the three sites and also indicated significant difference in the concentrations of Pb, Cd, Cr, Ni, Ba and As in sub-surface soil among the sites. Little heavy metal concentration was found in both the groundwater and surface water. The study showed that even if some heavy metals were detected at the oil spill sites, they do not pose any serious health risk, as all the heavy metals in the four environmental media at the three sampling sites were below the national limit stipulated by the Department of Petroleum Resource (DPR), Nigeria.

scholarly journals Sphingobacterium paludis sp. nov., isolated from wetland soil

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3453-3458 ◽  
Author(s):  
Hao Feng ◽  
Yanhua Zeng ◽  
Yili Huang
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Xixi Wetland

A novel Gram-stain-negative bacteria, designated S37T, was isolated from soil of the Xixi wetland, Zhejiang province, China. Cells of strain S37T were aerobic, non-motile rods. Growth occurred at 10–37 °C (optimum, 25 °C), pH 5.0–9.7 (optimum, pH 7.5) and with 0–6 % (w/v) NaCl (optimum, 0.5 %). Based on 16S rRNA gene sequence analysis, strain S37T was found to be a member of the genus Sphingobacterium and shared highest similarity with Sphingobacterium composti 4M24T (95.78 %). The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH, and the DNA G+C content was 43.8 mol%. The predominant respiratory quinone was MK-7. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S37T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium paludis sp. nov. (type strain S37T = CGMCC 1.12801T = NBRC 110386T) is proposed.

Soil aggregate-based nucleic acid analyses of the impact of maize roots and their root hairs on the structural diversity of microbial communities

2021 ◽  
Author(s):  
Christoph Tebbe ◽  
Damini Damini ◽  
Damien Finn ◽  
Nataliya Bilyera ◽  
Minh Ganther ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Hair ◽  
Soil Aggregates ◽  
Root Hairs ◽  
Soil Samples ◽  
Plant Roots ◽  
Bulk Soil ◽  
Rrna Gene ◽  
The Impact

&lt;p&gt;The deposition of energy rich carbon sources released by plant roots during their growth fuels microbially driven ecosystem processes in soil, but there is a lack of understanding how microorganisms interact and collaborate. The objective of this research was therefore to characterize microbial networks as they assemble under the influence of plant roots. To identify the specific importance of root hairs, we compared the impact of a maize wild-type to a root-air defective mutant (rth3; (1).&lt;/p&gt;&lt;p&gt;The microbial community structure was analyzed by qPCR and 16S rRNA gene amplicon sequencing from soil DNA. In order to increase the probability of detecting truly interacting microbial partners as a basis for network analyses, we first evaluated a new protocol to obtain DNA from as little as 1 mg instead of the usual 250 mg soil samples, thereby approaching the aggregate level (2). While the diversity of bacterial 16S rRNA gene amplicons of 250-mg samples taken from the same soil was not distinct, DNA analyses from individual aggregates clearly differed from each other underlining that soil aggregates represent distinct microbial habitats.&lt;/p&gt;&lt;p&gt;Soil column experiments with maize grown in a loam soil (3) revealed distinct communities between rhizosphere and bulk soil. The community composition of individual aggregates showed more differences in bulk soil compared to rhizosphere. Less elaborated networks were seen in bulk soil and a profound effect of root hairs could be unravelled. Null model testing demonstrated that Actinobacteria were equally important for network connectivity independent of the root hair mutation, but for networks of the wildtype, Acidobacteria were essential for synergistic interactions and overall network structure. In contrast, Proteobacteria and Firmicutes connectivity became more important. The observed differences in community composition and interactions suggests carbon cycling, and perhaps other microbially-driven functions, are markedly affected by the presence of root hairs.&lt;/p&gt;&lt;p&gt;Utilizing maize root soil microcosms for studying soil zymography in the rhizosphere allowed to obtain soil samples from regions with distinct specific enzyme activities. In order to enhance the detection of actively metabolizing bacterial community members, we studied rRNA sequences and compared it to rRNA gene sequences from the same samples. Currently the data are under analysis.&lt;/p&gt;&lt;p&gt;References&lt;/p&gt;&lt;p&gt;(1) Wen, T-J, Schnable PS (1994) Analyses of mutants of three genes that influence root hair development in Zea mays (Gramineae) suggest that root hairs are dispensable. Am. J. Bot. 81, 833&amp;#8211;842.&lt;/p&gt;&lt;p&gt;(2) Szoboszlay M, Tebbe CC (2020) Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates. Microbiol. Open, e1144. DOI: 10.1002/mbo3.1144&lt;/p&gt;&lt;p&gt;(3) Vetterlein D et al. (2020) Experimental platforms for the investigation of spatiotemporal patterns in the rhizosphere &amp;#8211; laboratory and field scale. J. Plant Nutr. Soil Sci., 000, 1&amp;#8211;16 DOI: 10.1002/jpln.202000079&lt;/p&gt;

Sign in / Sign up

Export Citation Format

Share Document