Phylogenetic Characterization and Community Diversity of Hydrocarbon-Utilizing Bacteria in Soil Microcosms Enriched with Aromatic Hydrocarbons

A, Ola Olapade

doi:10.4172/2155-6199.1000305

Cited by 6 publications

(3 citation statements)

References 23 publications

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“…Determination of DNA quantity was then carried out with a NanoDrop Spectrophotometer (2% accuracy/range of purity, NanoDrop 2000, Thermo Scientific, Delaware, USA). The quality of extracted DNA was further assessed by amplifying with the 16S rRDA universal primer sets, 27F (5' AGA GTT GTA TCM TGG CTC AG 3') and 1492R (5'GGT TAC CTT GTT ACG ACT T3') as previously described in Olapade (2013Olapade ( , 2015. As previously described by Olapade (2020), the Illumina's 16S sequencing library preparation protocol was used in generating amplicon libraries using universal primer pairs that consisted of an Illumina-specific overhang sequence and locusspecific sequence: 92wF_Illum: 5'-TCGTCGGCAGCGTCAGA TGTGTATAAGAGACAGAAACTYAAAKGAATTGRCGG and 1392R_Illum:…”

Section: Dna Extraction and 16s Rrna Gene Pyrosequencingmentioning

confidence: 99%

Cross-site comparison of coastal bacterial occurrences and diversity at selected sites along the North Atlantic Ocean in Monrovia, Liberia

Ola¹

2023

Afr. J. Microbiol. Res.

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Coastal marine sites were examined for the occurrences and diversity of indigenous bacterial populations using high resolution 16S rRNA gene pyrosequencing approach to further understand the ecological importance of environmental variables. Samples containing slurries of seawater and sediments were collected from nine different sites along the north Atlantic Ocean in Monrovia, Liberia and were divided into three spatially distinct groups. The bacterial assemblages were found to be quite diverse in their occurrences among the examined sites. The majority of the sequences that dominated among the assemblages were associated with members of the Actinobacteria (1.3 to 4.8%), Bacteriodetes (2.9 to 5.8%), Acidobacteria (8.0 to 13.7%), Planctomycetes (15.3 to 28.8%), and Proteobacteria (40.7 to 48.8%). Gammaproteobacteria was the most abundant bacterial class, representing between 29 and 39% of the operational taxonomic units (OTUs) in all the coastal sites, while members belonging to the Planctomycetia, ranged between 10 and 18.8%, were relatively more abundant in the southern region of Monrovia which is mostly influenced by a freshwater lagoon. Alphaand beta diversity indices as well as rarefaction analysis were used to determine the species richness, evenness and coverage among the sites. Canonical correspondence analysis (CCA) and clustering using UPGMA (Unweighted pair group method with arithmetic mean) revealed the separation of the OTUs into groups probably based on the influence of various site-specific environmental variables at the coastal sites.

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Section: Dna Extraction and 16s Rrna Gene Pyrosequencingmentioning

confidence: 99%

Cross-site comparison of coastal bacterial occurrences and diversity at selected sites along the North Atlantic Ocean in Monrovia, Liberia

Ola¹

2023

Afr. J. Microbiol. Res.

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“…Community DNA was extracted from the filters using FastDNA rRDA universal primer sets, 27F (5' AGA GTT GTA TCM TGG CTC AG 3') and 1492R (5'GGT TAC CTT GTT ACG ACT T3') as previously described in Olapade (2013Olapade ( , 2015. The Illumina's 16S metagenomic sequencing library preparation protocol was used in generating amplicon libraries using universal primer pairs that consisted of an Illumina-specific overhang sequence and locus-specific sequence: 926wF_Illum: 5'-TCGTCGGCAGCGTCAGA TGTGTATAAGAGACAGAAACTYAAAKGAATTGRCGG and 1392R_Illum:…”

Section: Dna Extraction and 16s Rrna Gene Pyrosequencingmentioning

confidence: 99%

Bacterial community composition and diversity along the southern coastlines of the Atlantic Ocean in Cape Town, South Africa

Olapade¹

2020

Afr. J. Microbiol. Res.

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“…Several researchers have studied the dynamics of soil bacterial community during bioremediation of a single type of petroleum hydrocarbons (Muangchinda et al 2015) or petroleum products. Olapade studied the diversity of indigenous bacterial populations in soil microcosms enriched with mono-aromatic hydrocarbons including benzene, ethyl-benzene and xylene using culture-based and molecular approaches (Olapade 2015). Bordenave et al (2007) Instead of the effects of different hydrocarbons on soil microbial diversity, some other researchers have focused on the microbial community changes due to petroleum contamination in different soils.…”

Section: Introductionmentioning

confidence: 99%

Bacterial community dynamics during bioremediation of alkane- and PAHs-contaminated soil of Siri island, Persian Gulf: a microcosm study

Khomarbaghi

Shavandi²,

Amoozegar

et al. 2019

Int. J. Environ. Sci. Technol.

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Studding the diversity of soil indigenous microorganisms, and monitoring effect of contaminants on microbial population, is very critical for understanding microbial activity during bioremediation and selecting successful remediation strategy.To simulate the natural environment, four microcosms were prepared by artificially contaminating clean soil with defined amounts of petroleum hydrocarbons including alkanes mixture (C 13 -C 20 ), polyaromatic hydrocarbons (PAHs) mixture (anthracene, phenanthrene, fluoranthene, pyrene and benzo (α) pyrene) and both alkanes and PAHs. Contaminants degradation and heterotrophic bacterial count were measured during a 6-month study. Copy number of alkB and C23DO genes was studied using real-time PCR, and bacterial diversity was monitored by 16S rRNA gene PCR and denaturing gradient gel electrophoresis (DGGE). Results indicated that all types of contaminants (except the five ring benzo (α) pyrene) were totally degraded after 6 months and the increase in hydrocarbon degradation rate coincided with the enhancement of total heterotrophic bacterial count in each microcosm. Real-time PCR results showed a significant increase in the copy number of both alkB and C23DO genes in alkane-and PAHs-contaminated microcosm comparing with the control microcosm, indicating selection for special hydrocarbon degraders in hydrocarbon-amended microcosms. The results of DGGE revealed that the type of contaminant in the same soil has a remarkable influence on soil bacterial community structure. Sequencing of DGGE bands suggested that most of the dominant members of the microbial community of contaminated soil are unculturable bacteria from Proteobacteria and the genus Bacillus.

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Phylogenetic Characterization and Community Diversity of Hydrocarbon-Utilizing Bacteria in Soil Microcosms Enriched with Aromatic Hydrocarbons

Cited by 6 publications

References 23 publications

Cross-site comparison of coastal bacterial occurrences and diversity at selected sites along the North Atlantic Ocean in Monrovia, Liberia

Cross-site comparison of coastal bacterial occurrences and diversity at selected sites along the North Atlantic Ocean in Monrovia, Liberia

Bacterial community composition and diversity along the southern coastlines of the Atlantic Ocean in Cape Town, South Africa

Bacterial community dynamics during bioremediation of alkane- and PAHs-contaminated soil of Siri island, Persian Gulf: a microcosm study

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