ArticleJournal, genetic engineering & biotechnology2019
Comparative metatranscriptome analysis revealed broad response of microbial communities in two soil types, agriculture versus organic soil.
Article in Journal, genetic engineering & biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it, 31 citations in OpenAlex.
- Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities.Frontiers in bioengineering and biotechnology · 2021Pooled it
- Molecular Monitoring in Soil Bioremediation: From Genetic Potential to Verified Pathway Operation.International journal of molecular sciences · 2026Review
- Hormonal and transcriptomic regulation of drought adaptation in barley roots and leaves.Scientific reports · 2025Article
- No-tillage systems promote bacterial photosynthetic gene expression in low carbon, semi-arid surface soils.Applied and environmental microbiology · 2025Article
- Characteristics of Bacterial Community Structure and Function in Artificial Soil Prepared Using Red Mud and Phosphogypsum.Microorganisms · 2024Article
- Unlocking the potential of soil microbial communities for bioremediation of emerging organic contaminants: omics-based approaches.Microbial cell factories · 2024Review
- Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA.Molecular ecology resources · 2023Article
- Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review.International journal of molecular sciences · 2022Review
- Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides.Environmental science and pollution research international · 2021Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundStudying expression of genes by direct sequencing and analysis of metatranscriptomes at a particular time and space can disclose structural and functional insights about microbial communities. The present study reports comparative analysis of metatranscriptome from two distinct soil ecosystems referred as M1 (agriculture soil) and O1 (organic soil).
resultsAnalysis of sequencing reads revealed Proteobacteria as major dominant phyla in both soil types. The order of the top 3 abundant phyla in M1 sample was Proteobacteria > Ascomycota > Firmicutes, whereas in sample O1, the order was Proteobacteria > Cyanobacteria > Actinobacteria. Analysis of differentially expressed genes demonstrated high expression of transcripts related to copper-binding proteins, proteins involved in electron carrier activity, DNA integration, endonuclease activity, MFS transportation, and other uncharacterized proteins in M1 compared to O1. Of the particular interests, several transcripts related to nitrification, ammonification, stress response, and alternate carbon fixation pathways were highly expressed in M1. In-depth analysis of the sequencing data revealed that transcripts of archaeal origin had high expression in M1 compared to O1 indicating the active role of Archaea in metal- and pesticide-contaminated environment. In addition, transcripts encoding 4-hydroxyphenylpyruvate dioxygenase, glyoxalase/bleomycin resistance protein/dioxygenase, metapyrocatechase, and ring hydroxylating dioxygenases of aromatic hydrocarbon degradation pathways had high expression in M1. Altogether, this study provided important insights about the transcripts and pathways upregulating in the presence of pesticides and herbicides.
conclusionAltogether, this study claims a high expression of microbial transcripts in two ecosystems with a wide range of functions. It further provided clue about several molecular markers which could be a strong indicator of metal and pesticide contamination in soils. Interestingly, our study revealed that Archaea are playing a significant role in nitrification process as compared to bacteria in metal- and pesticide-contaminated soil. In particular, high expression of transcripts related to aromatic hydrocarbon degradation in M1 soil indicates their important role in biodegradation of pollutants, and therefore, further investigation is needed.
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Registered trials
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