Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil

Zhao, Jun; Li, Xiaoming; Ai, Guomin; Deng, Ye; Liu, Shuang‐Jiang; Jiang, Cheng‐Ying

doi:10.1016/j.jhazmat.2016.06.055

Cited by 47 publications

(21 citation statements)

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“…LEfSe was used to explore potential biomarkers for distinguishing taxonomy 53 . A linear discriminant analysis (LDA) threshold score (0.05) for the factorial Kruskal-Wallis test and the all-against-all multi-class analysis strategy were used to detect significantly different microbes 54 . Contribution rates of functional genes were predicted from PICRUSt 55 through inputting the 16S rRNA OTU table.…”

Section: Methodsmentioning

confidence: 99%

Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation

Zhang

Liu

et al. 2017

Sci Rep

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To solve the competition problem of acidophilic bacteria and sulfate-reducing bacteria in the practical application of mine tailing bioremediation, research into the mechanisms of using different nutrients to adjust the microbial community was conducted. Competition experiments involving acidophilic bacteria and sulfate-reducing bacteria were performed by supplementing the media with yeast extract, tryptone, lactate, and glucose. The physiochemical properties were determined, and the microbial community structure and biomass were investigated using MiSeq sequencing and qRT-PCR, respectively. Four nutrients had different remediation mechanisms and yielded different remediation effects. Yeast extract and tryptone (more than 1.6 g/L) promoted sulfate-reducing bacteria and inhibited acidophilic bacteria. Lactate inhibited both sulfate-reducing and acidophilic bacteria. Glucose promoted acidophilic bacteria more than sulfate-reducing bacteria. Yeast extract was the best choice for adjusting the microbial community and bioremediation, followed by tryptone. Lactate kept the physiochemical properties stable or made slight improvements; however, glucose was not suitable for mine tailing remediation. Different nutrients had significant effects on the abundance of the second enzyme of the sulfate-reducing pathway (p < 0.05), which is the rate-limiting step of sulfate-reducing pathways. Nutrients changed the remediation effects effectively by adjusting the microbial community and the abundance of the sulfate-reducing rate-limiting enzyme.

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Section: Methodsmentioning

confidence: 99%

Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation

Zhang

Liu

et al. 2017

Sci Rep

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“…The 16S rRNA genes were processed and analysed using the open-source software QIIME 73, 74 , and in-house Perl scripts were used to analyse alpha (within samples) and beta (among samples) diversity. First, sequence reads were filtered (fastq maxee = 0.5 and fastq trunclen = 289), replication was removed, and singletons were discarded 75 . The Chimera Slayer (CS) tool was used for chimaera detection 18 .…”

Section: Methodsmentioning

confidence: 99%

Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident

Zhang

Huang

Wang

et al. 2017

Sci Rep

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A shocking Longjiang River cadmium pollution accident occurred in 2012, the effects of which on microbial communities remain unclear. Alkaline precipitation technology was applied for remediation, but concerns rose about the stability of this technology. To understand the geographic distribution of cadmium and its correlation with microbes, in this study, 39 water samples and 39 sludge samples from this river and 2 soil samples from the nearby farmland were collected for chemical and microbial analyses. The Cd concentrations of all water samples were lower than 0.005 mg/L and reached the quality standards for Chinese surface water. A ranking of sludge samples based on Cd contents showed sewage outfall > dosing sites > farmland, all of which were higher than the quality standard for soil. Alkaline precipitation technology was effective for Cd precipitation. Cd was unstable; it was constantly dissolving and being released from the sludge. The Cd content of each phase was mainly influenced by the total Cd content. Over 40,000 effective sequences were detected in each sample, and a total of 59,833 OTUs and 1,273 genera were found using Illumina MiSeq sequencing. Two phyla and 39 genera were notably positively correlated with the Cd distribution, while the cases of 10 phyla and 6 genera were the opposite.

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“…; Zhao et al . ; Rabbi et al . ), and to a lesser extent agro‐industrial samples, such as polluted soils (Zhao et al .…”

Section: Applications In Aquaculturementioning

confidence: 99%

“…), and to a lesser extent agro‐industrial samples, such as polluted soils (Zhao et al . ; Hou et al . ), faecal microbiota of pig (Mu et al .…”

Section: Applications In Aquaculturementioning

confidence: 99%

“…However, most of these reports used PICRUSt (probably because it was the first published programme) to study the metabolic capacities of microbial communities that are essential in medical samples, e.g. faecal microbiota of human, saliva, skin (Acharya et al 2017;Fuentes et al 2017;Maffei et al 2017), or model organisms such as mice (Garcia-Mazcorro et al 2016;Zhao et al 2016;Rabbi et al 2017), and to a lesser extent agro-industrial samples, such as polluted soils (Zhao et al 2016;Hou et al 2017), faecal microbiota of pig (Mu et al 2017), chicken (Yan et al 2017), honey bee (Kakumanu et al 2016) and others. However, the analysis of metagenomic 16S rRNA data from marine or aquatic samples using these predictive programmes has been scarcely executed (Table 1); for example, only 11 reports related to aquaculture or marine environments were found in PubMed [(PICRust OR Tax4Fun OR Vikodak) AND (aquaculture OR marine)].…”

Section: Applications In Aquaculturementioning

confidence: 99%

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Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems

Ortiz-Estrada

Gollas‐Galván

Martínez‐Córdova³

et al. 2018

Reviews in Aquaculture

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Micro‐organisms are an essential component of natural marine ecosystems, but also play important roles in anthropogenically modified ecosystems, including aquaculture. Although metagenomics is currently used to explore microbial communities, its application has not been as extensive in aquaculture. Although some taxonomic profiles and phylogenetic studies have been deciphered using biomarker genes, the functional potential of microbial communities associated with aquaculture systems is still unknown in most cases. Predicting functional profiles through 16S rRNA gene‐based metagenomics analysis is perhaps the most promising tool to elucidate the metabolic capabilities of microbial communities because there is no need to perform shotgun sequencing to have an idea of these capabilities. Moreover, robust bioinformatics background is not required to assess this information, and so the same data (16S rRNA sequences) are used to estimate both taxonomic and functional profiles, therefore providing deeper insights into these kinds of communities. In this review, we suggest the need to major use of novel bioinformatics tools that construct functional profiles from metagenomic 16S rRNA data, as strategy to obtain a preliminary approach about metabolic capacities of microbes that coexist in aquaculture systems.

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Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil

Cited by 47 publications

References 50 publications

Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation

Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation

Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident

Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems

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