Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa) rhizosphere gradient

Abstract

Aims: The response of microbial metagenome to polycyclic aromatic hydrocarbons (PAHs) degradation in the rice rhizosphere remains poorly understood. We investigated the spatial and temporal variations of microbial communities and reconstructed metagenomes along the rice rhizosphere gradient during PAHs degradation. Methods and Results: The experiment was performed in rhizoboxes, in which the rhizosphere region was divided into five 1-mm thick layers. Based on denaturant gradient gel electrophoresis profiling and sequencing of bacterial and archaeal 16S rRNA genes, predicted metagenomes were reconstructed. The microbial communities in the rice rhizosphere were influenced by the PAHs concentration and distance from the root surface during PAHs degradation. Correlation network analysis showed that archaea played an important role in PAHs degradation. Predicted metagenomes can be clustered into two groups with high and low PAHs degrading potential, respectively. The relative abundance of genes for defense mechanisms, replication, recombination and reparation was significantly higher in samples with high PAHs degrading potentials. The relative abundance of the dioxygenase gene was greater near the root surface of the rice. However, the abundance of aldolase and dehydrogenase was constant in rhizosphere soils at different distances from the root surface. Conclusions: Distance from root surface and PAH concentrations affected the microbial communities and metagenomes in rice rhizosphere. The abundance of dioxygenase genes relating to PAH degradation in metagenomes mirrored the PAH degradation potential in rice rhizosphere. Significance and Impact of the Study: Our findings suggested that the predicted metagenomes reconstructed from 16S rRNA marker gene sequences provide further insights into the spatial variation and dynamics of microbial functioning that occur during bioremediation.

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil

“…Recently, Langille et al [22] developed the software Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), which analyzes microbial function by combining phylogenetic analyses and genome database data to predict functional profiles. To date, PICRUSt has contributed to our understanding of microbial functional profiles in the animal gut [23], human mouth [24], ocean [25], and soil [26]. …”

Implementation of Omics Research to Enhance Phytoremediation Efficiency - a Review

“…As an example, hybrid poplars had been used to take up and degrade trichloroethylene (TCE), which is a common pollutant of groundwater that is both hepatoxic and carcinogenic for humans [21]. Other example of victorious application of phytodegradation includes the use of multiple plant species to degrade carbon tetrachloride (CT) and perchloroethylene [22]. Phytodegradation also had been shown to be successful for polycyclic aromatic hydrocarbons (PAHs) and explosives including trinitrotoluene (TNT) [21,23].…”

“…Moreover, microorganisms can also impact the potential uptake of pollutants including the uptake and translocation of heavy metals from roots to shoots of plants [23]. Overall, microbial communities that are able to create associations with plants can influence plants growth and development both positively and negatively which as a consequence will alter plants ability to remediate the soil [22]. Contaminants such as heavy metals can be also either transformed by specific microorganisms in rhizosphere or be taken up and translocated by plants.…”

“…Such approach can be used to sequence many cultured microorganisms. Overall, the shotgun sequencing reveals all genes present in environmental samples [22]. In the study by Hao et al shotgun high throughput metagenomic sequencing was used in order to capture the PAHs degrading features of Taxus rhizosphere microbiome.…”

Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites

“…Microbial taxa are defined by genetic variation of any genomic locus grouped as operational taxonomic units (OTUs) (Koeppel & Wu, 2013). In recent decades, the development of cultivation-independent techniques associated with next-generation sequencing (NGS) have stimulated the investigation of the microbial diversity involved in the PAHs degradation (Flocco, Gomes, Mac Cormack, & Smalla, 2009;Gomes et al, 2007;Jurelevicius et al, 2012;Ma et al, 2015;Wu et al, 2014). In addition, biogeography studies has helped to elucidate the evolutionary relationship (governed by selection, drift, dispersal, and mutation processes) of living creatures through genetic proximity between samples from different environments, and thus understand their distribution patterns in space and over time (Hanson, Fuhrman, Horner-Devine, & Martiny, 2012).…”