Phytoextraction of Heavy Metals: A Promising Tool for Clean-Up of Polluted Environment?

Pollution by heavy metals (HM) represents a serious threat for both the environment and human health. Due to their elemental character, HM cannot be chemically degraded, and their detoxification in the environment mostly resides either in stabilization in situ or in their removal from the matrix, e.g., soil. For this purpose, phytoremediation, i.e., the application of plants for the restoration of a polluted environment, has been proposed as a promising green alternative to traditional physical and chemical methods. Among the phytoremediation techniques, phytoextraction refers to the removal of HM from the matrix through their uptake by a plant. It possesses considerable advantages over traditional techniques, especially due to its cost effectiveness, potential treatment of multiple HM simultaneously, no need for the excavation of contaminated soil, good acceptance by the public, the possibility of follow-up processing of the biomass produced, etc. In this review, we focused on three basic HM phytoextraction strategies that differ in the type of plant species being employed: natural hyperaccumulators, fast-growing plant species with high-biomass production and, potentially, plants genetically engineered toward a phenotype that favors efficient HM uptake and boosted HM tolerance. Considerable knowledge on the applicability of plants for HM phytoextraction has been gathered to date from both lab-scale studies performed under controlled model conditions and field trials using real environmental conditions. Based on this knowledge, many specific applications of plants for the remediation of HM-polluted soils have been proposed. Such studies often also include suggestions for the further processing of HM-contaminated biomass, therefore providing an added economical value. Based on the examples presented here, we recommend that intensive research be performed on the selection of appropriate plant taxa for various sets of conditions, environmental risk assessment, the fate of HM-enriched biomass, economical aspects of the process, etc

Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence

The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-togenome blast distance phylogeny (GBDP) algorithm and digital DNA–DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compoundsThis research was funded by GREENER-H2020 (EU), grant number 826312, and MICINN/FEDER EU, grant number RTI2018-0933991- B-I00. D.G.-S. was supported by a MECD FPU fellowship program, grant number FPU14/03965. P.S.-L. was supported by the MICINN FPU fellowship program, grant number FPU18/02169. E.B.-R. was supported by the MECD FPU fellowship program, grant number FPU16/05513. J.S., T.C. and O.U. acknowledge Czech Science Foundation grant number 17–00227S, which enabled PCB co-metabolism experiments to be undertake

Bacterial succession in oil-contaminated soil under phytoremediation with poplars

Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soils, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils had a bacterial community succession through the years, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.Peer reviewe

Bacterial Biotransformation of Pentachlorophenol and Micropollutants Formed during Its Production Process

Pentachlorophenol (PCP) is a toxic and persistent wood and cellulose preservative extensively used in the past decades. The production process of PCP generates polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) as micropollutants. PCDD/Fs are also known to be very persistent and dangerous for human health and ecosystem functioning. Several physico-chemical and biological technologies have been used to remove PCP and PCDD/Fs from the environment. Bacterial degradation appears to be a cost-effective way of removing these contaminants from soil while causing little impact on the environment. Several bacteria that cometabolize or use these pollutants as their sole source of carbon have been isolated and characterized. This review summarizes current knowledge on the metabolic pathways of bacterial degradation of PCP and PCDD/Fs. PCP can be successfully degraded aerobically or anaerobically by bacteria. Highly chlorinated PCDD/Fs are more likely to be reductively dechlorinated, while less chlorinated PCDD/Fs are more prone to aerobic degradation. The biochemical and genetic basis of these pollutants’ degradation is also described. There are several documented studies of effective applications of bioremediation techniques for the removal of PCP and PCDD/Fs from soil and sediments. These findings suggest that biodegradation can occur and be applied to treat these contaminants

Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

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

Image_1_Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates.PDF

<p>Many ecological experiments are based on the extraction and downstream analyses of microorganisms from different environmental samples. Due to its high throughput, cost-effectiveness and rapid performance, Matrix Assisted Laser Desorption/Ionization Mass Spectrometry with Time-of-Flight detector (MALDI-TOF MS), which has been proposed as a promising tool for bacterial identification and classification, could be advantageously used for dereplication of recurrent bacterial isolates. In this study, we compared whole-cell MALDI-TOF MS-based analyses of 49 bacterial cultures to two well-established bacterial identification and classification methods based on nearly complete 16S rRNA gene sequence analyses: a phylotype-based approach, using a closest type strain assignment, and a sequence similarity-based approach involving a 98.65% sequence similarity threshold, which has been found to best delineate bacterial species. Culture classification using reference-based MALDI-TOF MS was comparable to that yielded by phylotype assignment up to the genus level. At the species level, agreement between 16S rRNA gene analysis and MALDI-TOF MS was found to be limited, potentially indicating that spectral reference databases need to be improved. We also evaluated the mass spectral similarity technique for species-level delineation which can be used independently of reference databases. We established optimal mass spectral similarity thresholds which group MALDI-TOF mass spectra of common environmental isolates analogically to phylotype- and sequence similarity-based approaches. When using a mass spectrum similarity approach, we recommend a mass range of 4–10 kDa for analysis, which is populated with stable mass signals and contains the majority of phylotype-determining peaks. We show that a cosine similarity (CS) threshold of 0.79 differentiate mass spectra analogously to 98.65% species-level delineation sequence similarity threshold, with corresponding precision and recall values of 0.70 and 0.73, respectively. When matched to species-level phylotype assignment, an optimal CS threshold of 0.92 was calculated, with associated precision and recall values of 0.83 and 0.64, respectively. Overall, our research indicates that a similarity-based MALDI-TOF MS approach can be routinely used for efficient dereplication of isolates for downstream analyses, with minimal loss of unique organisms. In addition, MALDI-TOF MS analysis has further improvement potential unlike 16S rRNA gene analysis, whose methodological limits have reached a plateau.</p

Stability and Reactivity of Guaiacylglycerol-<i>β</i>-Guaiacyl Ether, a Compound Modeling <i>β</i>-<i>O</i>-4 Linkage in Lignin

Lignin, a complex and abundant biopolymer, is a major constituent of plant cell walls. Due to its chemical and structural complexity, lignin degradation is a challenging task for both natural and engineered systems. Therefore, investigation of lignin degradation using so called “model compounds” has been the focus of many research efforts in recent years. This study addresses the utility of guaiacylglycerol-β-guaiacyl ether (Gβ2) as a model compound for evaluating the β-O-4 bond cleavage under diverse thermal and aqueous medium conditions. Experimental conditions included varied pH (3–10), microbial biodegradation, subcritical water environment (150–250 °C), and mild pyrolysis (150–250 °C). A high-performance liquid chromatography with high-resolution mass spectrometry was employed for accurate detection and quantification of both Gβ2 and its degradation/modification products in an aqueous environment. Pyrolysis experiments were performed using gas chromatography-mass spectrometry analysis with a pyrolyzer. The results showed that Gβ2 remained stable under exposure to moderate pH and several bacterial strains, which were successfully used previously for biodegradation of other recalcitrant pollutants. We report, for the first time, differing Gβ2 breakdown pathways for subcritical water treatment vs. pyrolysis under an inert atmosphere. The scientific novelty lies in the presentation of differences in the degradation pathways of Gβ2 during subcritical water treatment compared to pyrolysis in an inert atmosphere, with water playing a key role. The observed differences are ascribed to the suppression of homolytic reactions by water as a solvent

Microbial Communities in Soils and Endosphere of Solanum tuberosum L. and their Response to Long-Term Fertilization

An understanding of how fertilization influences endophytes is crucial for sustainable agriculture, since the manipulation of the plant microbiome could affect plant fitness and productivity. This study was focused on the response of microbial communities in the soil and tubers to the regular application of manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and chemical fertilizer (NPK; 330-90-300 kg N-P-K/ha). Unfertilized soil was used as a control (CF), and the experiment was set up at two distinct sites. All fertilization treatments significantly altered the prokaryotic and fungal communities in soil, whereas the influence of fertilization on the community of endophytes differed for each site. At the site with cambisol, prokaryotic and fungal endophytes were significantly shifted by MF and SF3 treatments. At the site with chernozem, neither the prokaryotic nor fungal endophytic communities were significantly associated with fertilization treatments. Fertilization significantly increased the relative abundance of the plant-beneficial bacteria Stenotrophomonas, Sphingomonas and the arbuscular mycorrhizal fungi. In tubers, the relative abundance of Fusarium was lower in MF-treated soil compared to CF. Although fertilization treatments clearly influenced the soil and endophytic community structure, we did not find any indication of human pathogens being transmitted into tubers via organic fertilizers

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Abstract Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy