Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.

08:00 EDT 13th July 2017 | BioPortfolio

Summary of "Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops."

Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot(-1), respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg(-1) cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems.


Journal Details

This article was published in the following journal.

Name: Ecotoxicology and environmental safety
ISSN: 1090-2414
Pages: 111-118


DeepDyve research library

PubMed Articles [30692 Associated PubMed Articles listed on BioPortfolio]

Responses of bacterial communities to CuO nanoparticles in activated sludge system.

The main objectives of this study were to investigate the influence of copper oxide nanoparticles (CuO NPs) on wastewater nutrient removal, bacterial community and molecular ecological network in acti...

Integrated network analysis reveals potentially novel molecular mechanisms and therapeutic targets of refractory epilepsies.

Epilepsy is a complex neurological disorder and a significant health problem. The pathogenesis of epilepsy remains obscure in a significant number of patients and the current treatment options are not...

MYC and hsa‑miRNA‑423‑5p as biomarkers in nasopharyngeal carcinoma revealed by miRNA‑mRNA‑pathway network integrated analysis.

The present study was performed to identify the dysregulated microRNAs (miRNAs/miRs) and mRNAs, and enriched pathways involved in nasopharyngeal carcinoma (NPC) through the establishment of an miRNA...

Molecular Study of Indigenous Bacterial Community Composition on Exposure to Soil Arsenic Concentration Gradient.

Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme...

Algorithmic Advances and Applications from RECOMB 2017.

This Cell Systems Call features invited summaries of 32 of the 38 papers accepted for presentation in the "regular track" at the 2017 Research in Computational Molecular Biology conference. The editor...

Clinical Trials [5254 Associated Clinical Trials listed on BioPortfolio]

Study by Metagenomics and Culturomicsapproaches of Bacterial and Viral Flora of Diabetic Foot Infection

This work also highlights the presence of an unknown virus double-stranded DNA. In this project we propose 1) incorporating a bank of 150 samples from patients with diabetic foot infection...

Molecular Typing of Community-acquired Pneumonia Based on Multiple-omic Data Analysis

Community-acquired pneumonia (CAP) is a heterogeneous disease causing great morbidity, mortality and health care burden globally. Typing methods for discriminating different clinical condi...

Clinical Metagenomics of Infective Endocarditis

Infective endocarditis (IE) is an infection of cardiac valves. IE mainly involves bacteria, more rarely fungi. IE is an uncommon diseases with an estimated incidence of 1-12 cases per 100,...

Effects of Ecological Rythmic-acoustic Stimulation (E-RAS) on Motor Skills in Individuals With Parkinson's Disease

The use of rhythmic auditory stimulation (RAS) has been proven useful in the management of gait disturbances induced by Parkinson's disease (PD). Typically, the stimuli used to provide RAS...

Assessing Community Cancer Care After Insurance ExpanSionS

This innovative and timely study will measure the impact of Affordable Care Act (ACA) Medicaid expansions on cancer screenings and preventive services. To assess this natural policy experi...

Medical and Biotech [MESH] Definitions

Ongoing collection, analysis, and interpretation of ecological data that is used to assess changes in the components, processes, and overall condition and functioning of an ECOSYSTEM.

The genomic analysis of assemblages of organisms.

Meta-analysis of randomized trials in which estimates of comparative treatment effects are visualized and interpreted from a network of interventions that may or may not have been evaluated directly against each other. Common considerations in network meta-analysis include conceptual and statistical heterogeneity and incoherence.

The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.

MOLECULAR BIOLOGY techniques used in the diagnosis of disease. Included are such techniques as IN SITU HYBRIDIZATION of chromosomes for CYTOGENETIC ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS of gene expression patterns in disease states; identification of pathogenic organisms by analysis of species specific DNA sequences; and detection of mutations with POLYMERASE CHAIN REACTION.

Quick Search

DeepDyve research library

Relevant Topics

GMO Crops
A genetically modified organism (GMO) is an organism whose genetic material has been altered using genetic engineering techniques. Organisms that have been genetically modified include micro-organisms such as bacteria and yeast, insects, plants, fish, an...

DNA sequencing
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Searches Linking to this Article