scholarly journals Remediation of Hydrocarbon Polluted Soil Offsets Methanogenic Microbial Communities and Improves Soil Recovery of Crude Oil-Polluted Site

2021 ◽  
Author(s):  
Chinedu Christopher Obieze ◽  
Chioma Blaise Chikere ◽  
Rasheed Adeleke ◽  
Ramganesh Selvarajan ◽  
Khayalethu Ntushelo ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Niger Delta ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
High Energy ◽  
Polluted Soil ◽  
Polluted Site ◽  
Bacterial Phyla ◽  
Poultry Droppings

Abstract Hydrocarbon pollution amplified by artisanal refining has led to the devastating destruction of farmlands and fishing settlements of subsistence farmers in the Niger Delta. The relatively slow natural attenuation of these polluted sites is the motivation for this study. The natural response and the influence of intermittent tillage and nutrient addition on bacterial community ecological functions were investigated using 16S rRNA metabarcoding. Representative soil samples were drawn from the surface (0 – 15cm) and subsurface (1m and 1.5m depths) of the polluted site pre-remediation and during remediation on Days 0, 14, 49, 70 and 91. Nutrient in the form of poultry droppings was added to the polluted soil while aeration was improved by tillage at 3-weeks interval throughout the duration of remediation. Total petroleum hydrocarbon was reduced from 93,720 mg kg–1 on timepoint zero to 9,029.76 mg kg–1 on day 91. Alpha diversity analysis revealed that the proportionality (evenness) of bacterial species significantly reduced during remediation. The bacterial community structure during remediation was significantly different compared to the structure pre-remediation. Spearman’s rank correlation revealed that soil pH, total phosphorus and total potassium were the chemical factors that influenced diversity. During remediation, the most responsive bacterial phyla were Proteobacteria and Cyanobacteria while Hydrogenedentes and Spirochaetes were among biomarkers pre-remediation. PICRUSt2-based functional prediction revealed that pre-remediation, pathways for methanogenesis and terpenoids biosynthesis were differentially abundant while high energy-yielding TCA cycle and pathways for both fatty acid biosynthesis and the degradation of aromatic hydrocarbons were differentially abundant during remediation. Overall, the addition of poultry droppings and intermittent tillage improved nutrient availability and this subsequently led to a significant change in the bacterial community structure and the rate of hydrocarbon sequestration. The authors concluded that incorporation of poultry droppings by tillage may serve as a suitable remediation method to reduce hydrocarbon in oil-polluted Niger Delta soils.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

scholarly journals Characterization of the Vaginal DNA Virome in Health and Dysbiosis

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1143 ◽  
Author(s):  
Rasmus Riemer Jakobsen ◽  
Thor Haahr ◽  
Peter Humaidan ◽  
Jørgen Skov Jensen ◽  
Witold Piotr Kot ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
Metagenomic Sequencing ◽  
Nugent Score ◽  
Double Stranded Dna ◽  
Viral Community ◽  
Atopobium Vaginae

Bacterial vaginosis (BV) is characterized by a reduction in Lactobacillus (L.) spp. abundance and increased abundance of facultative anaerobes, such as Gardnerella spp. BV aetiology is not fully understood; however, bacteriophages could play a pivotal role in the perturbation of the vaginal bacterial community. We investigated the vaginal viral community, including bacteriophages and the association to the bacterial community and BV-status. Vaginal samples from 48 patients undergoing IVF treatment for non-female factor infertility were subjected to metagenomic sequencing of purified virus-like particles. The vaginal viral community was characterized and correlated with the BV-status by Nugent score, bacterial community, structure, and the presence of key vaginal bacterial species. The majority of identified vaginal viruses belonged to the class of double-stranded DNA bacteriophages, with eukaryotic viruses constituting 4% of the total reads. Clear links between the viral community composition and BV (q = 0.006, R = 0.26) as well as the presence of L. crispatus (q = 0.001, R = 0.43), L. iners, Gardnerella spp., and Atopobium vaginae were found (q < 0.002, R > 0.15). The eukaryotic viral community also correlated with BV-status (q = 0.018, R = 0.20). In conclusion, the vaginal virome was clearly linked with bacterial community structure and BV-status.

scholarly journals Long-Term Combined Effects of Crude Oil and Dispersant on Sediment Bacterial Community

2020 ◽  
Vol 9 (1) ◽  
pp. 259-263
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Crude Oil ◽  
Bacterial Community Structure ◽  
Oil Spills ◽  
Bacterial Species ◽  
Combined Effects ◽  
Set Up ◽  
Sediment Bacterial Community

To better understand long-term combined effects of crude oil and dispersant on bacterial community, sediments microcosms were set up in triplicates and treated with dispersant (Corexit 9500A), crude oil, and Corexit 9500A plus crude oil. After 60 days exposure, there was a significant change in the bacterial community structure in all treatments. The shift in the bacterial community structure in Corexit 9500A plus crude oil treatment was considerably different from those by either Corexit 9500A or crude oil. DNA sequence analysis showed that Hydrocarboniphaga effuse, Parvibaculum lavamentivorans,and Alicyclobacillus ferrooxydans were the major bacterial species in crude oil treatment. Pandoraea thiooxydans, Janthinobacterium sp. and Hyphomicrobium nitrativorans were the most dominant species in Corexit 9500A treatment. The species Janthinobacterium sp., Parvibaculum lavamentivorans, and Dyella sp. were enriched in Corexit 9500A plus crude oil treatment. The majority of the detected species were hydrocarbons degraders. The study showed that Corexit 9500A addition enhanced the biodegradation rate by increasing the diversity and richness of hydrocarbons degrading species. Corexit A9500 application should be considered during crude oil spills to evaluate environmental impacts.

scholarly journals Characterization of the vaginal DNA virome in health and dysbiosis: an opening study in patients with non-female factor infertility

2019 ◽  
Author(s):  
Rasmus R. Jakobsen ◽  
Thor Haahr ◽  
Peter Humaidan ◽  
Jørgen Skov Jensen ◽  
Witold Kot ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
Gardnerella Vaginalis ◽  
Metagenomic Sequencing ◽  
Double Stranded Dna ◽  
Viral Community ◽  
Atopobium Vaginae

AbstractBackgroundBacterial vaginosis (BV) is characterised by a reduction in Lactobacillus spp. abundance and increased abundance of facultative anaerobes, like Gardnerella vaginalis. BV aetiology is not fully understood, but bacteriophages could play a pivotal role causing perturbation of the vaginal bacterial community. Here we investigate the vaginal viral community, including bacteriophages, and its association to the bacterial community and BV-status.MethodsVaginal samples from 48 patients undergoing IVF treatment for non-female factor infertility were subjected to metagenomic sequencing of purified virus-like particles. The vaginal viral community was characterized and correlated with BV-status, bacterial community structure and presence of key vaginal bacterial species.ResultsThe majority of identified vaginal viruses belonged to the class of double-stranded DNA bacteriophages, with eukaryotic viruses constituting 4% of total reads. Clear links between viral community composition and BV (q = 0.006, R = 0.26) as well as presence of L. crispatus (q = 0.001, R = 0.43), L. iners, Gardnerella vaginalis and Atopobium vaginae were found (q < 0.002, R > 0.15). Interestingly, also the eukaryotic viral community was correlated with BV-status (q = 0.018, R = 0.20).ConclusionsThe vaginal virome is clearly linked with bacterial community structure and BV-status.Clinical Trials RegistrationNCT02042352.

scholarly journals Bacterial community structure analysis of soil treated with Parthenium hysterophorus L. derived green medium

2020 ◽  
Vol 7 (2) ◽  
pp. 281
Author(s):  
Amit Kumar ◽  
Abhaya Shikhar Panwar ◽  
Babita Rana ◽  
Gopal Krishna Joshi
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Species Level ◽  
The Other ◽  
Parthenium Hysterophorus ◽  
Bacterial Phyla ◽  
Maximum Proportion ◽  
Microbiome Profiling ◽  
Number Of Bacteria

The present study encompasses the analysis of bacterial community structure of soil in the presence of Parthenium hysterophorus derived green medium. The 16S microbiome profiling of the soil revealed that it consists of members from 15 bacterial phyla with the most prominent being Proteobacteria. The other predominant phyla were Plantomycetes, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi and Firmicutes. The maximum proportion of the bacterial community remained unclassified at genus and species level. Among the classified population the maximum number of bacteria belonged to Flavisolibacter followed by Kaistobacter, Bacillus, Optitutus, Balneimonas, Steroidobacter, Rhodoplanes and Gemmata.

scholarly journals Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India

3 Biotech ◽  
2015 ◽  
Vol 5 (5) ◽  
pp. 727-734 ◽  
Author(s):  
Gagandeep Kaur ◽  
Rohit Sharma ◽  
Kashmir Singh ◽  
Pushpender K. Sharma
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Polluted Soil ◽  
Soil Samples

Temporally invariable bacterial community structure in the Arabian Sea oxygen minimum zone

2014 ◽  
Vol 73 (1) ◽  
pp. 51-67 ◽  
Author(s):  
A Jain ◽  
M Bandekar ◽  
J Gomes ◽  
D Shenoy ◽  
RM Meena ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Arabian Sea ◽  
Oxygen Minimum Zone ◽  
Minimum Zone ◽  
Oxygen Minimum
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