title: 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.
authors.affiliation: Department of Biosciences, MEM-Group, University of Helsinki, PO Box 56, FI-00014, Helsinki, Finland.
authors.forename: Shinjini
authors.initials: S
authors.lastname: Mukherjee
authors.forename: Timo
authors.initials: T
authors.lastname: Sipilä
authors.forename: Pertti
authors.initials: P
authors.lastname: Pulkkinen
authors.forename: Kim
authors.initials: K
authors.lastname: Yrjälä
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics; D001673:Biodegradation, Environmental; D044822:Biodiversity; D042926:Cytochrome P-450 CYP4A / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D059013:Microbial Consortia; D010105:Oxygenases / Q000235:genetics; D059392:Petroleum Pollution; D010802:Phylogeny; D032107:Populus; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D058441:Rhizosphere; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D012989:Soil Pollutants
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants; D010105:Oxygenases; D042926:Cytochrome P-450 CYP4A; C439587:extradiol dioxygenase
keywords: Populus; alkane monooxygenase; extradiol dioxygenase; field study; petroleum hydrocarbons; pyrosequencing; secondary succession