Phytoremediation of petroleum hydrocarbons in subarctic regions relies on the successful establishment of plants that stimulate petroleum-degrading microorganisms, which can be challenging due to the extreme climate, limited nutrients, and difficulties in maintaining sites in remote locations. A long-term phytoremediation experiment was initiated in Alaska in 1995 with the introduction of grasses and/or fertilizer to petroleum hydrocarbon (PHC)-contaminated soils that were subsequently left unmanaged. In 2011, the PHC concentrations were below detection limits in all soils tested and the originally planted grasses had been replaced by volunteer plant species that had colonized the site. Here, we sought to understand how the original treatments influenced the structure of prokaryotic communities associated with plant species that colonized the soils and to assess the interactions between the rhizospheric and endophytic communities of the colonizing vegetation 20 years after the experiment was established. Metataxonomic analysis performed using 16S rRNA gene sequencing revealed that the original type of contaminated soil and phytoremediation strategy influenced the structure of both rhizospheric and endophytic communities of colonizing plants, even 20 years after the treatments were applied and following the disappearance of the originally planted grasses. Our findings demonstrate that the choice of initial phytoremediation strategy drove the succession of microorganisms associated with the colonizing vegetation. The outcome of this study provides new insight into the establishment of plant-associated microbial communities during secondary succession of subarctic areas previously contaminated by PHCs and indicates that the strategies for restoring these ecosystems influence the plant-associated microbiota in the long term. IMPORTANCE Subarctic ecosystems provide key services to local communities, yet they are threatened by pollution caused by spills and disposal of petroleum waste. Finding solutions for the remediation and restoration of subarctic soils is valuable for reasons related to human and ecosystem health, as well as environmental justice. This study provides novel insight into the long-term succession of soil and plant-associated microbiota in subarctic soils that had been historically contaminated with different sources of PHCs and subjected to distinct phytoremediation strategies. We provide evidence that even after the successful removal of PHCs and the occurrence of secondary succession, the fingerprint of the original source of contamination and the initial choice of remediation strategy can be detected as a microbial legacy in the rhizosphere, roots, and shoots of volunteer vegetation even 2 decades after the contamination had occurred. Such information needs to be borne in mind when designing and applying restoration approaches for PHC-contaminated soils in subarctic ecosystems.

• Klíčová slova
• bacterial communities, endophyte, petroleum hydrocarbons, phytoremediation, rhizosphere, rhizosphere-inhabiting microbes, secondary succession, subarctic,
• Publikační typ
• časopisecké články MeSH

Polychlorinated biphenyl (PCB)-contaminated soils represent a major treat for ecosystems health. Plant biostimulation of autochthonous microbial PCB degraders is a way to restore polluted sites where traditional remediation techniques are not sustainable, though its success requires the understanding of site-specific plant-microbe interactions. In an historical PCB contaminated soil, we applied DNA stable isotope probing (SIP) using 13C-labeled 4-chlorobiphenyl (4-CB) and 16S rRNA MiSeq amplicon sequencing to determine how the structure of total and PCB-degrading bacterial populations were affected by different treatments: biostimulation with Phalaris arundinacea subjected (PhalRed) or not (Phal) to a redox cycle and the non-planted controls (Bulk and BulkRed). Phal soils hosted the most diverse community and plant biostimulation induced an enrichment of Actinobacteria. Mineralization of 4-CB in SIP microcosms varied between 10% in Bulk and 39% in PhalRed soil. The most abundant taxa deriving carbon from PCB were Betaproteobacteria and Actinobacteria. Comamonadaceae was the family most represented in Phal soils, Rhodocyclaceae and Nocardiaceae in non-planted soils. Planted soils subjected to redox cycle enriched PCB degraders affiliated to Pseudonocardiaceae, Micromonosporaceae and Nocardioidaceae. Overall, we demonstrated different responses of soil bacterial taxa to specific rhizoremediation treatments and we provided new insights into the populations active in PCB biodegradation.

• MeSH
• Actinomycetales * genetika   MeSH
• Bacteria MeSH
• biodegradace MeSH
• DNA bakterií genetika   metabolismus   MeSH
• DNA metabolismus   MeSH
• ekosystém MeSH
• izotopy metabolismus   MeSH
• látky znečišťující půdu * metabolismus   MeSH
• polychlorované bifenyly * metabolismus   MeSH
• půda chemie   MeSH
• půdní mikrobiologie MeSH
• RNA ribozomální 16S genetika   metabolismus   MeSH
• rostliny metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA bakterií MeSH
• DNA MeSH
• izotopy MeSH
• látky znečišťující půdu * MeSH
• polychlorované bifenyly * MeSH
• půda MeSH
• RNA ribozomální 16S MeSH

The involvement of bacterial aromatic ring-hydroxylating dioxygenases (ARHDs) in the degradation of aromatic pollutants, such as polychlorinated biphenyls (PCBs), has been well studied. However, there is considerable speculation as to the origin of this ability. One hypothesis is centered on a connection between the ability to degrade aromatic pollutants and the necessity of soil bacteria to cope with and/or utilize secondary plant metabolites (SPMs). To investigate this connection, we researched the involvement of biphenyl 2,3-dioxygenase (BPDO), an ARHD essential for the degradation of PCBs, in the metabolism of SPMs in the soil bacterium Pseudomonas alcaliphila JAB1, a versatile degrader of PCBs. We demonstrated the ability of the strain JAB1 to transform a variety of SPMs, namely the flavonoids apigenin, flavone, flavanone, naringenin, fisetin, quercetin, morin, and catechin, caffeic acid, trans-cinnamic acid, and the monoterpenes (S)-limonene and (R)-carvone. Of those, the transformation of flavone, flavanone, and (S)-limonene was conditioned by the activity of JAB1-borne BPDO and thus was researched in more detail, and we found evidence for the limonene monooxygenase activity of the BPDO. Furthermore, the bphA gene in the strain JAB1 was demonstrated to be induced by a wide range of SPMs, with monoterpenes being the strongest inducers of the SPMs tested. Thus, our findings contribute to the growing body of evidence that ARHDs not only play a role in the catabolism of aromatic pollutants, but also of natural plant-derived aromatics, and this study supports the hypothesis that ARHDs participate in ecological processes mediated by SPMs.

• Klíčová slova
• aromatic ring-hydroxylating dioxygenases, biphenyl dioxygenase, monoterpenes, phenolics, secondary plant metabolites,
• Publikační typ
• časopisecké články MeSH

Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.

• Klíčová slova
• Pseudomonas veronii strain Pvy, biodegradation, denitrification, dibenzofuran, dioxygenase, heavy-metal tolerance, nanopore technology, organic phosphate mineralization, whole-genome sequencing,
• MeSH
• biodegradace MeSH
• dibenzofurany * MeSH
• genomika * MeSH
• Pseudomonas MeSH
• RNA ribozomální 16S MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• dibenzofurany * MeSH
• RNA ribozomální 16S MeSH

Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.

• Klíčová slova
• bioremediation, carbon flow, community structure, secondary plant metabolites (SPMEs),
• MeSH
• Bacteria klasifikace   izolace a purifikace   metabolismus   MeSH
• biodegradace * MeSH
• látky znečišťující půdu chemie   toxicita   MeSH
• polychlorované bifenyly toxicita   MeSH
• půdní mikrobiologie * MeSH
• rostliny metabolismus   mikrobiologie   MeSH
• sekundární metabolismus MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• látky znečišťující půdu MeSH
• polychlorované bifenyly MeSH

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

• Klíčová slova
• contaminated soil, fertilization, functional potential, microbial community structure, plants,
• Publikační typ
• časopisecké články MeSH