Shifts in diversity and community structure of endophytic bacteria and archaea across root, stem and leaf tissues in the common reed, Phragmites australis, along a salinity gradient in a marine tidal wetland of northern China

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.

Endophyte community composition is associated with dieback occurrence in an invasive tree

“…These results extend current thinking, that multiple organisms within multiple taxonomic domains may be involved in the onset of disease or disease suppression in plants (Coats and Rumpho 2014). Most studies on microbial endophyte communities and dieback investigate one specific microbial taxon, typically fungi (Wilson and Pitkethley 1992;Diplock et al 2006;Kowalski and Holdenrieder 2009;Haque et al 2012;Ismail et al 2012;Sacdalan et al 2012), although there are exceptions (Mendes et al 2011;Knief et al 2012;Ma et al 2013;Oliveira et al 2013;Ruppel et al 2013). Our study found a very diverse microbial community (as assessed using OTUs) whose structure differed with plant health status.…”

“…At least for fungi, high endophytic fungal biodiversity has previously been observed in plants, which can host hundreds of fungal species or genotypes (Hawksworth 2001). High diversity of bacterial and archaeal endophytes is also expected (Ma et al 2013). Archaeal and fungal OTUs were twice as numerous per sample in dieback-affected plants compared to those in healthy plants.…”

Diversity and space–time dynamics of endophytic archaea from sugar beet in the north slope of Tianshan Mountain revealed by 454 pyrosequencing and T-RFLP

“…This study showed that there were negligible differences in archaeal diversity among sampling sites or tissues of Phragmites australis (Ma et al 2013). Endophytic archaeal community was differentiated among sampling zones, but not among tissue types (Ma et al 2013).…”

“…In a previous study, Ma et al investigated the endophytic archaea in roots, stems and leaves of the common reed, Phragmites australis, using T-RF length polymorphism analysis of the 16S rRNA genes (Ma et al 2013). This study showed that there were negligible differences in archaeal diversity among sampling sites or tissues of Phragmites australis (Ma et al 2013).…”

Endophytic Microbiota Associated with the Root Tips and Leaves of Baccharis dracunculifolia

“…Some of these soil bacteria are capable of penetrating the root, which is the main location of entry of bacterial endophytes ([ 12 ]. Ma et al [ 34 ] studied the diversity of endophytic bacteria in roots and leaves of the reed Phragmites australis under stressful saline conditions, and observed that the bacterial diversity in roots was significantly higher than that in the leaves.…”