Microbial diversity and metaproteomic analysis of activated sludge responses to naphthalene and anthracene exposure

Li, Shanshan; Hu, Shaoda; Shi, Sanyuan; Ren, Lu; Yan, Wei; Zhao, Huabing

doi:10.1039/c9ra04674g

Cited by 24 publications

(6 citation statements)

References 48 publications

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“…Data also showed that FAD-dependent monooxygenase (Table 1) induced only in the presence of mixture of PAHs, responsible for breakdown of polyaromatic hydrocarbons in the initial steps of degradation. Higher expression of proteins that are involved in a variety of biological process such as purine and pyrimidine metabolism, RNA metabolism, nucleic acid binding activity, fatty acid synthesis, pentose phosphate pathway, glutamate metabolism, protein translation, glycolysis, nitrogen metabolism and xation suggest that the strain PR23 has adapted to mixture of PAHs by modulating its metabolic pathways (Li et al 2019). Eight-fold higher expression of Twin-arginine translocation pathway signal protein in the presence of PAHs is observed.…”

Section: Discussionmentioning

confidence: 99%

Pseudomonas aeruginosa PR23 isolated from oil contaminated soil tolerate and degrades mixture of polyaromatic hydrocarbons and express novel proteins

Jindal,

Aggarwal

2023

Preprint

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Pseudomonas aeruginosa PR23 isolated from the hydrocarbon contaminated soil tolerate and degrades mixture of polyaromatic hydrocarbons (PAHs) having initial concentration of 1300 ppm. The degradation and intermediates formed were assessed through GC-MS analysis. The isolated strain was able to degrade 59.2% mixture of PAHs in 3 days and 71.6% by day 15. Effect of PAHs on protein expression in Pseudomonas aeruginosa PR23 was studied through nano LC-MS/MS. Thirty-six proteins were observed that showed more than 2-fold increased expression in the presence of mixture of PAHs. Out of these proteins, 7 proteins are reported for their role in degradation of naphthalene, phenanthrene, and pyrene. Data also showed the presence of 16 proteins that are uniquely expressed in the presence of mixture of PAHs. A Twin-arginine translocation signal peptide (tat system) known for transportation of folded proteins across the cell membrane showed more than 8-fold increased expression in the presence of mixture of PAHs. Results indicate that isolated strain adopts the conditions in the presence of mixture of PAHs by modulating its metabolic and physiological processes. These findings suggest that Pseudomonas aeruginosa PR23 may be a suitable candidate to be used for the development of strategies for bioremediation of mixture of PAHs.

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Section: Discussionmentioning

confidence: 99%

Pseudomonas aeruginosa PR23 isolated from oil contaminated soil tolerate and degrades mixture of polyaromatic hydrocarbons and express novel proteins

Jindal,

Aggarwal

2023

Preprint

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“…Additionally, designated as environmental proteomics, metaproteomics includes the high-throughput study of all the proteins present in microbial communities and directly harvested from the environment [ 85 , 86 ]. The steps in the omics approach consist of protein extraction from the environmental samples, protein digestion into peptides, and fractionation employing 2D gel electrophoresis and mass spectrometry-mediated identification of proteins.…”

Section: Omics Biology In Deciphering Plant Microbiome and Alleviatio...mentioning

confidence: 99%

Trends in Harnessing Plant Endophytic Microbiome for Heavy Metal Mitigation in Plants: A Perspective

Tiwari

Bae

2023

Plants

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Plant microbiomes represent dynamic entities, influenced by the environmental stimuli and stresses in the surrounding conditions. Studies have suggested the benefits of commensal microbes in improving the overall fitness of plants, besides beneficial effects on plant adaptability and survival in challenging environmental conditions. The concept of ‘Defense biome’ has been proposed to include the plant-associated microbes that increase in response to plant stress and which need to be further explored for their role in plant fitness. Plant-associated endophytes are the emerging candidates, playing a pivotal role in plant growth, adaptability to challenging environmental conditions, and productivity, as well as showing tolerance to biotic and abiotic stresses. In this article, efforts have been made to discuss and understand the implications of stress-induced changes in plant endophytic microbiome, providing key insights into the effects of heavy metals on plant endophytic dynamics and how these beneficial microbes provide a prospective solution in the tolerance and mitigation of heavy metal in contaminated sites.

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“…Metaproteomics, also known as community proteomics or environmental proteomics, involves high-throughput study of all the proteins from microbial communities, extracted directly from the environment (Bastida et al, 2009;Gutleben et al, 2018;Li et al, 2019). A typical metaproteomics approach involves extraction of proteins from the environmental sample (soil, water, sediments, etc.…”

Section: Metaproteomicsmentioning

confidence: 99%

Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome

Phurailatpam

Dalal

Singh

et al. 2022

Front. Sustain. Food Syst.

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Heavy metal (HM) contamination of soil and water resources is a global concern, which not only limits crop yield and quality, but also has serious environmental effects. Due to the non-biodegradable nature and toxicity, high concentration of HMs in food and environment is a serious threat to the entire ecosystem. Moreover, the target of supplying safe and quality food to the rising human population (expected to reach ~9–10 bn by the year 2050), necessitates effective treatment of the HM-contaminated soil. Various microbe-mediated bioremediation strategies such as biosorption, bioprecipiation, biostimulation, etc., have been found to be effective in uptake and conversion of HMs to less toxic forms. Further, in the past few years, the use of soil and plant-associated microbiome for HM stress alleviation is gaining attention among the scientific community. In general, microbes are spectacular in being dynamic and more responsive to environmental conditions in comparison to their host plants. Moreover, with the advancements in high throughput sequencing technologies, the focus is eventually shifting from just structural characterization to functional insights into the microbiome. The microbes inhabiting the HM-contaminated environments or associated with HM-tolerant plants are a source for exploring HM-tolerant microbial communities, which could be used for enhancing bioremediation efficiency and conferring HM tolerance in plants. This review discusses the application of omics techniques including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, for rapid and robust identification of HM-tolerant microbial communities, mining novel HM resistance genes, and fabricating the HM resistome.

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Microbial diversity and metaproteomic analysis of activated sludge responses to naphthalene and anthracene exposure

Cited by 24 publications

References 48 publications

Pseudomonas aeruginosa PR23 isolated from oil contaminated soil tolerate and degrades mixture of polyaromatic hydrocarbons and express novel proteins

Pseudomonas aeruginosa PR23 isolated from oil contaminated soil tolerate and degrades mixture of polyaromatic hydrocarbons and express novel proteins

Trends in Harnessing Plant Endophytic Microbiome for Heavy Metal Mitigation in Plants: A Perspective

Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome

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