Metagenomic Approach to Explore Microbial Communities in the Rhizosphere of Date Palm

2016 ◽  
Author(s):  
Ali El Kharbotly ◽  
Noha El Badawy ◽  
Maria Torres ◽  
Imene Mattat ◽  
Ameena Al-Malki ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Date Palm ◽  
Metagenomic Approach

scholarly journals Metagenomic Analysis of Microbial Diversity in Landfill Lysimeter Soil of Ghazipur Landfill Site, New Delhi, India

2017 ◽  
Vol 5 (42) ◽  
Author(s):  
Juhi Gupta ◽  
Rashmi Rathour ◽  
Madan Kumar ◽  
Indu Shekhar Thakur
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Landfill Site ◽  
Metagenomic Analysis ◽  
New Delhi ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Functional Aspects ◽  
Waste Degradation ◽  
Metagenomic Approach

ABSTRACT We report the soil microbial diversity and functional aspects related to degradation of recalcitrant compounds, determined using a metagenomic approach, in a landfill lysimeter prepared with soil from Ghazipur landfill site, New Delhi, India. Metagenomic analysis revealed the presence and functional diversity of complex microbial communities responsible for waste degradation.

scholarly journals Metagenomic Approach: Transforming In-Silico Research for Improved Biogas Production

2019 ◽  
Vol 7 (1) ◽  
pp. 6-11 ◽  
Author(s):  
Roushney Fatima Mukti ◽  
Sanjida Sakhawat Sinthee
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Sequence Data ◽  
Biogas Production ◽  
Biogas Plant ◽  
Rational Approach ◽  
Production Scale ◽  
Specific Element ◽  
Metagenomic Approach ◽  
Metagenome Sequence

The complexity of the microbial communities and metabolic pathways involved in the microbiological process of biogas production is poorly understood and numerous microorganisms in the fermentation sample of the biogas plant are still unclassified or unknown. The structure and function of microbial communities and the effects of the addition of trace elements are needed to be known, to control and channel the energy sources microbes produce and to capture and store the useful by-products or for targeted screening of novel enzymes. In this review, we discussed an emerging idea that Metagenome sequence data from a biogas-producing microbial community residing in a fermenter of a biogas plant provide the basis for a rational approach to improve the biotechnological process of biogas production. The composition and gene content of a biogas-producing consortium can be determined through metagenomic approach which allows the design of the optimal microbial community structure for any biogas plant for the significant progress in the efficacy and economic improvement of biogas production and biofertilizer of either balanced nutrition or rich in specific element for plant growth produced from the sludge of biogas plant. Biogas-producing microbial community from different production-scale biogas plants supplied with different raw materials as substrates can be analyzed by polyphasic approach to find out the best raw material composition for biogas production. The phylogenetic structure of the microbial community residing in a fermentation sample from a biogas plant can be analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing. Int. J. Appl. Sci. Biotechnol. Vol 7(1): 6-11

scholarly journals A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam

Genomics Data ◽  
2017 ◽  
Vol 12 ◽  
pp. 89-96 ◽  
Author(s):  
Saurav Das ◽  
Sudipta Sankar Bora ◽  
R.N.S. Yadav ◽  
Madhumita Barooah
Keyword(s):  
Microbial Communities ◽  
Contaminated Groundwater ◽  
Metagenomic Approach

scholarly journals Study of the Viral and Microbial Communities Associated With Crohnʼs Disease: A Metagenomic Approach

2013 ◽  
Vol 4 (6) ◽  
pp. e36 ◽  
Author(s):  
Vicente Pérez-Brocal ◽  
Rodrigo García-López ◽  
Jorge F Vázquez-Castellanos ◽  
Pilar Nos ◽  
Belén Beltrán ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Metagenomic Approach

Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach

Ecotoxicology ◽  
2018 ◽  
Vol 27 (9) ◽  
pp. 1281-1291 ◽  
Author(s):  
M. H. Hemmat-Jou ◽  
A. A. Safari-Sinegani ◽  
A. Mirzaie-Asl ◽  
A. Tahmourespour
Keyword(s):  
Heavy Metals ◽  
Microbial Communities ◽  
Contaminated Soils ◽  
Metagenomic Approach

scholarly journals Living to the high extreme: unraveling the composition, structure, and functional insights of bacterial communities thriving in the arsenic-rich Salar de Huasco – Altiplanic ecosystem.

2021 ◽  
Author(s):  
Juan Castro-Severyn ◽  
Coral Pardo-Esté ◽  
Katterinne N. Mendez ◽  
Jonathan Fortt ◽  
Sebastián Márquez ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Extreme Environments ◽  
Taxonomic Diversity ◽  
Functional Categories ◽  
Bacterial Composition ◽  
Functional Potential ◽  
Metabolic Versatility ◽  
Composition Structure ◽  
Metagenomic Approach

Microbial communities inhabiting extreme environments like Salar de Huasco (SH) are adapted to thrive while exposed to several abiotic pressures and the presence of toxic elements like arsenic (As). Hence, we aimed to uncover the role of arsenic in shaping bacterial composition, structure, and functional potential in five different sites in this Altiplanic wetland using a shotgun metagenomic approach. The sites exhibit wide gradients of arsenic (9 to 321 mg/kg), and our results showed highly diverse communities and a clear dominance exerted by the Proteobacteria and Bacteroidetes phyla. Functional potential analyses showed broadly convergent patterns, contrasting with their great taxonomic variability. Arsenic-related metabolism is different among the five communities, as well as other functional categories like those related to the CH4 and S cycles. Particularly, we found that the distribution and abundance of As-related genes increase, following along the As concentration gradient. Approximately 75% of the detected genes for As-metabolism belong to expulsion mechanisms, being arsJ and arsP pumps related to sites with higher As concentrations and present almost exclusively in Proteobacteria. Furthermore, taxonomic diversity and functional potential are reflected in the 12 reconstructed high-quality MAGs (Metagenome Assembled Genomes) belonging to the Bacteroidetes (5), Proteobacteria (5), Cyanobacteria (1) and Gemmatimonadota (1) phyla. We conclude that SH microbial communities are diverse and possess a broad genetic repertoire to thrive under extreme conditions, including increasing concentrations of the highly toxic As. Finally, this environment represents a reservoir of unknown and undescribed microorganisms, with a great metabolic versatility, which needs further study.

scholarly journals Effects of Rotations With Legume on Soil Functional Microbial Communities Involved in Phosphorus Transformation

2021 ◽  
Vol 12 ◽  
Author(s):  
Hui Yu ◽  
Fenghua Wang ◽  
Minmin Shao ◽  
Ling Huang ◽  
Yangyang Xie ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
P Cycling ◽  
P Transformation ◽  
Microbial P ◽  
The Impact ◽  
Metagenomic Approach ◽  
Insight Into ◽  
Phosphorus Transformation

Including legumes in the cereal cropping could improve the crop yield and the uptake of nitrogen (N) and phosphorus (P) of subsequent cereals. The effects of legume-cereal crop rotations on the soil microbial community have been studied in recent years, the impact on soil functional genes especially involved in P cycling is raising great concerns. The metagenomic approach was used to investigate the impacts of crop rotation managements of soybean-wheat (SW) and maize-wheat (MW) lasting 2 and 7years on soil microbial communities and genes involved in P transformation in a field experiment. Results indicated that SW rotation increased the relative abundances of Firmicutes and Bacteroidetes, reduced Actinobacteria, Verrucomicrobia, and Chloroflexi compared to MW rotation. gcd, phoR, phoD, and ppx predominated in genes involved in P transformation in both rotations. Genes of gcd, ppa, and ugpABCE showed higher abundances in SW rotation than in MW rotation, whereas gadAC and pstS showed less abundances. Proteobacteria, Acidobacteria, and Gemmatimonadetes played predominant roles in microbial P cycling. Our study provides a novel insight into crop P, which requires strategy and help to understand the mechanism of improving crop nutrient uptake and productivity in different rotations.

scholarly journals On the Road to Strain-Resolved Comparative Metagenomics

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Nicola Segata
Keyword(s):  
Microbial Communities ◽  
Human Health ◽  
Population Genomics ◽  
Meta Analysis ◽  
The Road ◽  
Comparative Metagenomics ◽  
Analysis Strategies ◽  
On The Road ◽  
Study Designs ◽  
Metagenomic Approach

ABSTRACT Metagenomics has transformed microbiology, but its potential has not been fully expressed yet. From computational methods for digging deeper into metagenomes to study designs for addressing specific hypotheses, the Segata Lab is pursuing an integrative metagenomic approach to describe and model human-associated microbial communities as collections of strains. Linking strain variants to host phenotypes and performing cultivation-free population genomics require large cohorts and meta-analysis strategies to synthesize available cohorts but can revolutionize our understanding of the personalized host-microbiome interface which is at the base of human health.

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