Metagenomic analysis of microbial community and function involved in cd-contaminated soil

Feng, Gang; Xie, Tian; Wang, Xin; Bai, Jiuyuan; Tang, Lin; Zhao, Hai; Wei, Wei; Wang, Maolin; Zhao, Yun

doi:10.1186/s12866-018-1152-5

Cited by 183 publications

(84 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…tool id=lefse upload) [39,40]. To correlate lung and intestine microbiota, analysis was performed using PICRUSt, including COG and KEGG function analysis [41,42]. The comparison between the two groups was conducted using t-test.…”

Section: Discussionmentioning

confidence: 99%

Bacterial association and comparison between lung and intestine in rats

et al. 2020

View full text Add to dashboard Cite

The association between lung and intestine has already been reported, but the differences in community structures or functions between lung and intestine bacteria yet need to explore. To explore the differences in community structures or functions, the lung tissues and fecal contents in rats were collected and analyzed through 16S rRNA sequencing. It was found that intestine bacteria was more abundant and diverse than lung bacteria. In intestine bacteria, Firmicutes and Bacteroides were identified as major phyla while Lactobacillus was among the most abundant genus. However, in lung the major identified phylum was Proteobacteria and genus Pseudomonas was most prominent genus. On the other hand, in contrast the lung bacteria was more concentrated in cytoskeleton and function in energy production and conversion. While, intestine bacteria were enriched in RNA processing, modification chromatin structure, dynamics and amino acid metabolism. The study provides the basis for understanding the relationships between lung and intestine bacteria.

show abstract

Section: Discussionmentioning

confidence: 99%

Bacterial association and comparison between lung and intestine in rats

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Another methodological limitation to our approach is that PLFA analysis does not allow for the level of taxonomic resolution needed to assess differences at a fine taxonomic scale, which may be achievable via sequencing approaches (Pérez‐Jaramillo et al, ), or a combination of sequencing and PLFA to evaluate both diversity and abundance. Additionally, PLFA can only infer function of different microbial groupings, whereas a functional metagenomics approach may identify specific microbially expressed genes that are related to plant performance (Feng et al, ). However, an important take‐away from our current results is that it may be possible to determine soil‐mediated performance by a relatively simple microbial biomass estimate, as total microbial biomass measured by PLFA was associated with increased plant performance (Figure b).…”

Section: Discussionmentioning

confidence: 99%

Domesticated tomatoes are more vulnerable to negative plant–soil feedbacks than their wild relatives

Carrillo

Ingwell

et al. 2019

Journal of Ecology

View full text Add to dashboard Cite

Domesticated plants can differ from their wild counterparts in the strength and outcome of species interactions, both above‐ and belowground. Plant–soil feedbacks influence plant success, and plant‐associated soil microbial communities can influence plant interactions with herbivores and their natural enemies, yet, it remains unclear if domestication has changed these relationships. To determine the effects of domestication on plant–soil interactions, we characterized soil microbial communities associated with various cultivars of domesticated tomato and some of its wild relatives. We measured the strength and direction of plant–soil feedbacks for domesticated and wild tomatoes, and the effects of soil on plant resistance to specialist herbivory by Manduca sexta, and the attraction of a parasitoid wasp, Cotesia congregata. Domesticated tomatoes and their wild relatives had negative plant–soil feedbacks, as conspecifics cultivated soil that negatively impacted performance of subsequent plants (longer germination time, lower biomass) than if they grew in non‐tomato soils. Significant variation existed among domesticated and wild tomato varieties in the strength of these feedbacks, ranging from neutral to strongly negative. For above‐ground plant biomass, tomato wild relatives were unaffected by growing in tomato‐conditioned soil, whereas domesticated tomatoes grew smaller in tomato soil, indicating effects of plant domestication. Overall, increased microbial biomass within the rhizosphere resulted in progressively less‐negative plant–soil feedbacks. Plant cultivars had different levels of resistance to herbivory by M. sexta, but this did not depend on plant domestication or soil type. The parasitoid C. congregata was primarily attracted to herbivore damaged plants, independent of plant domestication status, and for these damaged plants, wasps preferred some cultivars over others, and wild plants grown in tomato soil over wild plants grown in non‐tomato soil. Synthesis. These results indicate that crop tomatoes are more likely to show negative plant–soil feedbacks than wild progenitors, which could partially explain their sensitivity to monocultures in agricultural soils. Furthermore, cultivar‐specific variation in the ability to generate soil microbial biomass, independent of domestication status, appears to buffer the negative consequences of sharing the same soil. Last, soil legacies were relatively absent for herbivores, but not for parasitoid wasps, suggesting trophic level specificity in soil feedbacks on plant–insect interactions.

show abstract

“…Cd is a non-essential heavy metal element that is toxic, teratogenic and carcinogenic to humans. When critical Cd levels in soil are reached, biodiversity, agricultural productivity, food safety and human heath can be threatened, as Cd can be accumulated in the food chain [3][4][5][6][7]. Consequently, solutions to remediate heavy metal-contaminated soil, in particular Cdcontaminated soil, are urgently needed.…”

Section: Introductionmentioning

confidence: 99%

An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151–6 and Bacillus marisflavi 151–25

Ding

et al. 2020

BMC Microbiol

View full text Add to dashboard Cite

Background: Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd 2+ resistance. Results: In this study, we isolated two different Cd 2+ resistance Bacillus sp. strains, Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25, which could be grown in the presence of Cd 2+ at concentration up to 0.3 mM and 0.8 mM, respectively. According to the genomic sequencing, transcriptome analysis under cadmium stress, and other related experiments, a gene cluster in plasmid p25 was found to be a major contributor to Cd 2+ resistance in B. marisflavi 151-25. The cluster in p25 contained orf4802 and orf4803 which encodes an ATPase transporter and a transcriptional regulator protein, respectively. Although 151-6 has much lower Cd 2+ resistance than 151-25, they contained similar gene cluster, but in different locations. A gene cluster on the chromosome containing orf4111, orf4112 and orf4113, which encodes an ATPase transporter, a cadmium efflux system accessory protein and a cadmium resistance protein, respectively, was found to play a major role on the Cd 2+ resistance for B. vietamensis 151-6. Conclusions: This work described cadmium resistance mechanisms in newly isolated Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25. Based on homologies to the cad system (CadA-CadC) in Staphylococcus aureus and analysis of transcriptome under Cd 2+ induction, we inferred that the mechanisms of cadmium resistance in B. marisflavi 151-25 was as same as the cad system in S. aureus. Although Bacillus vietamensis 151-6 also had the similar gene cluster to B. marisflavi 151-25 and S. aureus, its transcriptional regulatory mechanism of cadmium resistance was not same. This study explored the cadmium resistance mechanism for B. vietamensis 151-6 and B. marisflavi 151-25 and has expanded our understanding of the biological effects of cadmium.

show abstract

Metagenomic analysis of microbial community and function involved in cd-contaminated soil

Cited by 183 publications

References 70 publications

Bacterial association and comparison between lung and intestine in rats

Bacterial association and comparison between lung and intestine in rats

Domesticated tomatoes are more vulnerable to negative plant–soil feedbacks than their wild relatives

An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151–6 and Bacillus marisflavi 151–25

Contact Info

Product

Resources

About