Secondary successional trajectories of structural and catabolic bacterial communities in oil‐polluted soil planted with hybrid poplar

Abstract

Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere-associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere-associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. To investigate the long-term succession of structural and catabolic bacterial communities in oil-polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula × Populus tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at seven different time points during the course of 2 years and sampling time points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing, whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late-phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early-phase communities. The high-dominance/low-diversity functional gene communities underwent a transition to low-dominance/high-diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession.

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons

“…Soils, along with plant roots, were collected within 3 cm of a stem with a spatula to 10 cm deep. Each subsample was taken from the soil surrounding what we thought was the same modular pickleweed plant, so samples were up to 2 or 3 meters apart from one another [16]. Each UV-composite waste sample consisted of 3-subsamples collected from unvegetated soils, at least 2 to 3 meters apart from a plant.…”

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area

“…In this work, alkane hydroxylase (alkB) was selected as reference gene to roughly estimate the diversity of Platanus phyllospheric bacteria possessing the potential ability to degrade alkanes. Diversity of alkane hydroxylases has already been studied in the rhizosphere of different tree and grass species, both in isolates (Fatima et al, 2015;Tesar et al, 2002;Yousaf et al, 2010) and in whole bacterial communities through culture-independent methods (Mukherjee et al, 2015;Tsuboi et al, 2015). However, a characterization of the diversity of alkB phylotypes in phyllospheric communities is still lacking.…”

Bacterial succession in oil-contaminated soil under phytoremediation with poplars

“…The rhizosphere acts as an inoculation and supplementation, providing nutrients for microbes and improving their proliferation (Yrjälä et al, 2017). Next-generation sequencing has enabled a better and more detailed understanding of the bacterial diversity in PHC-polluted soils and rhizospheres, allowing holistic environmental biotechnological studies of phytoremediation (Mukherjee et al, 2015).…”