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

Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.

• MeSH
• biodegradace * MeSH
• fylogeneze MeSH
• izotopové značení metody   MeSH
• látky znečišťující životní prostředí metabolismus   MeSH
• metagenomika metody   trendy   MeSH
• uhlík metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• látky znečišťující životní prostředí MeSH
• uhlík MeSH

The aim of this work was to construct transgenic plants with increased capabilities to degrade organic pollutants, such as polychlorinated biphenyls. The environmentally important gene of bacterial dioxygenase, the bphC gene, was chosen to clone into a plant of Nicotiana tabacum. The chosen bphC gene encodes 2,3-dihydroxybiphenyl-1,2-dioxygenase, which cleaves the aromatic ring of dihydroxybiphenyl, and we cloned it in fusion with the gene for β-glucuronidase (GUS), luciferase (LUC) or with a histidine tail. Several genetic constructs were designed and prepared and the possible expression of desired proteins in tobacco plants was studied by transient expression. We used genetic constructs successfully expressing dioxygenase's genes we used for preparation of transgenic tobacco plants by agrobacterial infection. The presence of transgenic DNA , mRNA and protein was determined in parental and the first filial generation of transgenic plants with the bphC gene. Properties of prepared transgenic plants will be further studied.

• Klíčová slova
• 2,3-dihydroxybiphenyl-1,2-dioxygenase, Nicotiana tabacum, bphC, phytoremediation, transgenic plant,
• MeSH
• bakteriální proteiny genetika   metabolismus   MeSH
• biodegradace MeSH
• Burkholderiaceae enzymologie   genetika   MeSH
• dioxygenasy genetika   metabolismus   MeSH
• geneticky modifikované rostliny enzymologie   genetika   metabolismus   MeSH
• glukuronidasa genetika   metabolismus   MeSH
• klonování DNA MeSH
• luciferasy genetika   metabolismus   MeSH
• polychlorované bifenyly metabolismus   MeSH
• rekombinantní fúzní proteiny genetika   metabolismus   MeSH
• tabák enzymologie   genetika   metabolismus   MeSH
• zelené fluorescenční proteiny genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 2,3-dihydroxybiphenyl oxygenase MeSH Prohlížeč
• bakteriální proteiny MeSH
• dioxygenasy MeSH
• glukuronidasa MeSH
• luciferasy MeSH
• polychlorované bifenyly MeSH
• rekombinantní fúzní proteiny MeSH
• zelené fluorescenční proteiny MeSH

PURPOSE: Polychlorinated biphenyls (PCBs) represent a large group of recalcitrant environmental pollutants, differing in the number of chlorine atoms bound to biphenyl ring. Due to their excellent technological properties, PCBs were used as heat-transfer media, for filling transformers and condensers, as paint additives, etc. With increasing knowledge of their toxicity, transfer to food chains and accumulation in living organisms, their production ended in most countries in the 1970s and in 1984 in the former Czechoslovakia. But even a quarter of century after the PCB production ceased, from contaminated areas, the volatile PCBs evaporate and contaminate much larger areas even at very distant parts of the world. For this reason, PCBs still represent a global problem. The main method of PCB removal from contaminated environment is at present the expensive incineration at high temperatures. With the aim of finding effective alternative approaches, we are studying biological methods for PCB removal from the environment. In this paper, we summarise 10 years of studies using long-term PCB-contaminated soil from a dumpsite in South Bohemia, targeted for the use of plants (phytoremediation) and their cooperation with microorganisms in the root zone (rhizoremediation). MATERIALS AND METHODS: Long-term contaminated soil from Lhenice dumpsite, more than hundred kilograms of homogenised material, was used in microcosms (pots and buckets), and field plots were established at the site. Tested plants include among others tobacco, black nightshade, horseradish, alfalfa and willow. Aseptic plant cell and tissue cultures were from the collection of the IOCB. Microorganisms were our own isolates. The paper summarises experiments done between 1998 and 2008 with real contaminated soil, both vegetated and non-vegetated. PCB analysis was performed by GC-ECD, metabolic products identified mostly using 2D-GC/MS-MS and synthetic standards, whereas molecular methods included quantitative PCR and sequencing. RESULTS: The soil was used both for preparation of field plots at the site and for greenhouse and laboratory tests in microcosms. The results include analyses of changes in PCB content in untreated and vegetated soil, PCB uptake and distribution in different parts of various plant species, analysis of products formed, identification and characterisation of cultivable and non-cultivable bacteria both in rhizosphere and in bulk soil. Different treatments and amendments were also tested. Experiments in real contaminated soil were accompanied by in vitro experiments using aseptic cultures of plant biomass, genetically modified (GM) plants and bacteria, to allow identification of players responsible for PCB metabolisation in soil. The time-span of the experiments allows extrapolating some of the results and drawing conclusions concerning the effectivity of exploitation of various plant species and treatments to remove PCBs from soils. DISCUSSION: The approach using plants proved to represent a viable alternative to costly incineration of PCB-contaminated soils. The recent studies using molecular methods show that plants are responsible for the composition of consortia of microorganisms present in their root zone, including those with ability to degrade the chlorinated aromatic compounds. CONCLUSIONS: In addition to uptake, accumulation and partial metabolisation of PCBs by plants, compounds produced by plants allow survival of microorganisms even in poor soils, serve as carbon and energy source, and can even induce the degradation pathways of different xenobiotics. Thus, the choice of proper plant species is crucial for effective cleaning of different polluted sites. Our study shows how the efficiency of PCB removal is dependent on the plant used. RECOMMENDATIONS AND PERSPECTIVES: The use of plants in biological remediation of different organic xenobiotics proved to be a useful approach. Further improvement can be expected by application of specifically tailored GM plants and use of selective conditions ensuring high remediation potential based on optimal composition of the soil microbial consortia designed for the needs of given site.

• MeSH
• biodegradace * MeSH
• časové faktory MeSH
• kořeny rostlin MeSH
• látky znečišťující půdu metabolismus   MeSH
• polychlorované bifenyly chemie   metabolismus   MeSH
• půda analýza   MeSH
• půdní mikrobiologie MeSH
• rostliny metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• látky znečišťující půdu MeSH
• polychlorované bifenyly MeSH
• půda MeSH

DNA-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (Armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (PCBs) compared to members of the microbial community in initial, uncultivated bulk soil. On the basis of early and recurrent detection of their 16S rRNA genes in clone libraries constructed from [(13)C]DNA, Hydrogenophaga spp. appeared to dominate biphenyl catabolism in the horseradish rhizosphere soil, whereas Paenibacillus spp. were the predominant biphenyl-utilizing bacteria in the initial bulk soil. Other bacteria found to derive carbon from biphenyl in this nutrient-amended microcosm-based study belonged mostly to the class Betaproteobacteria and were identified as Achromobacter spp., Variovorax spp., Methylovorus spp., or Methylophilus spp. Some bacteria that were unclassified at the genus level were also detected, and these bacteria may be members of undescribed genera. The deduced amino acid sequences of the biphenyl dioxygenase alpha subunits (BphA) from bacteria that incorporated [(13)C]into DNA in 3-day incubations of the soils with [(13)C]biphenyl are almost identical to that of Pseudomonas alcaligenes B-357. This suggests that the spectrum of the PCB congeners that can be degraded by these enzymes may be similar to that of strain B-357. These results demonstrate that altering the soil environment can result in the participation of different bacteria in the metabolism of biphenyl.

• MeSH
• Armoracia mikrobiologie   MeSH
• Bacteria klasifikace   genetika   izolace a purifikace   metabolismus   MeSH
• bakteriální geny MeSH
• bakteriální RNA genetika   MeSH
• Betaproteobacteria klasifikace   genetika   izolace a purifikace   metabolismus   MeSH
• bifenylové sloučeniny metabolismus   MeSH
• DNA bakterií genetika   MeSH
• DNA primery genetika   MeSH
• fylogeneze MeSH
• izotopy uhlíku MeSH
• látky znečišťující půdu metabolismus   MeSH
• molekulární sekvence - údaje MeSH
• polychlorované bifenyly metabolismus   MeSH
• půdní mikrobiologie * MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvence nukleotidů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální RNA MeSH
• bifenylové sloučeniny MeSH
• biphenyl MeSH Prohlížeč
• DNA bakterií MeSH
• DNA primery MeSH
• izotopy uhlíku MeSH
• látky znečišťující půdu MeSH
• polychlorované bifenyly MeSH
• RNA ribozomální 16S MeSH