Metatranscriptome Analysis Deciphers Multifunctional Genes and Enzymes Linked With the Degradation of Aromatic Compounds and Pesticides in the Wheat Rhizosphere

Abstract

Agricultural soils are becoming contaminated with synthetic chemicals like polyaromatic compounds, petroleum hydrocarbons, polychlorinated biphenyls (PCBs), phenols, herbicides, insecticides and fungicides due to excessive dependency of crop production systems on the chemical inputs. Microbial degradation of organic pollutants in the agricultural soils is a continuous process due to the metabolic multifunctionalities and enzymatic capabilities of the soil associated communities. The plant rhizosphere with its complex microbial inhabitants and their multiple functions, is amongst the most live and dynamic component of agricultural soils. We analyzed the metatranscriptome data of 20 wheat rhizosphere samples to decipher the taxonomic microbial communities and their multifunctionalities linked with the degradation of organic soil contaminants. The analysis revealed a total of 21 different metabolic pathways for the degradation of aromatic compounds and 06 for the xenobiotics degradation. Taxonomic annotation of wheat rhizosphere revealed bacteria, especially the Proteobacteria, actinobacteria, firmicutes, bacteroidetes, and cyanobacteria, which are shown to be linked with the degradation of aromatic compounds as the dominant communities. Abundance of the transcripts related to the degradation of aromatic amin compounds, carbazoles, benzoates, naphthalene, ketoadipate pathway, phenols, biphenyls and xenobiotics indicated abundant degradation capabilities in the soils. The results highlighted a potentially dominant role of crop rhizosphere associated microbial communities in the remediation of contaminant aromatic compounds.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

“…Metatranscriptomic analysis of the wheat rhizosphere identified dominant bacterial communities of diverse taxonomic phyla, including Acidobacteria, Cyanobacteria, Bacteroidetes, Steptophyta, Ascomycota, and Firmicutes, having functional roles in the degradation of various xenobiotic pollutants (Singh D. P. et al, 2018 ). Multiple enzymes such as isomerases, oxygenases, decarboxylases, reductases, kinases, and inner membrane translocators were identified that were associated with 21 different pathways for benzoates, aromatic amines, phenols, bisphenols, and other xenobiotics (Singh et al, 2016 ).…”

“…This study suggested a strain-level discrepancy between the Cryptococcus fungal species and their in-situ mock communities. Thus, transcriptomic analysis provides a large amount of gene information about the potential function of microbial communities in adaptation and survival in extreme environments (Singh D. P. et al, 2018 ; Mao et al, 2019 ; Marcelino et al, 2019 ).…”

“…However, effective implementation of microbial remediation strategies needs advanced technical approaches, which provide an in-depth understanding about the dynamics aspects of microbial activity and survival under stressed environment (Rastogi and Sani, 2011 ; Lima-Morales et al, 2016 ; Mao et al, 2019 ). The development in molecular, biotechnological, bioinformatics and system biology tools pertaining to bio-remedial problems have provided gene level mechanisms of bioremediation (Ahmad and Ahmad, 2014 ; Aora and Bar, 2014 ; Singh D. P. et al, 2018 ; Jaiswal and Shukla, 2020 ; Nkongolo and Kotha, 2020 ; Wolf et al, 2020 ). Moreover, the direct study of microorganisms in a contaminated environment including the whole microbial population granted a new frontier of the scientific community to share the knowledge of the uncultured microbial world (Zepeda et al, 2015 ; Zhao Q. et al, 2017 ; Panigrahi et al, 2019 ; Yan et al, 2020 ).…”

Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm

“…Other reliable approaches to study the functions of the plant-associated microbial communities are meta-transcriptomic and meta-proteomic analyses, which can also reveal the effects of the environment or the host plant genotype on the functions of the microbial communities [ 24 ]. These analyses can serve as useful tools to assess the abundance and functions of transcripts under specific conditions to infer whether these conditions trigger beneficial features, such as disease-suppressive activities, reflected by the high abundance of transcripts promoting plant growth, resistance, xenobiotic production, and pesticide-degrading enzyme secretion, or pathogenic features, reflected by the high abundance of transcripts promoting virulence factors, such as plant cell wall-degrading enzymes or phytopathogen effectors of the avrE family [ 24 , 25 , 26 ]. These analyses can also be useful to clarify the plant response to microbial activity; as such, the transcriptomic analysis may offer insight into plant host genes possibly manipulated by the action of pathogens in a disease setting, such as the downregulation of photosynthesis-related genes, consistent with the development of specific disease symptoms, or the upregulation of genes involved in other physiological processes [ 27 , 28 ].…”

Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities

“…Extensive overlap between core rhizosphere microbiome in different plant species, e.g., citrus [119], Arabidopsis [126,127], millet [120], sugarcane [117], and cooloola [128] has been observed to suggest that various factors driving community assembly may become common among plant species. Similarly, analysis of more than 20 wheat rhizosphere metatranscriptomes have led to identify metabolic pathways related to the degradation of aromatic and xenobiotics compounds [129]. Gene sequences linked with these pathways have also been dominantly observed in the kodo rhizosphere.…”