| 1. |
- Beckers, Bram, et al.
(författare)
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Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome.
- 2016
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 113:8, s. 2312-2317
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Tidskriftsartikel (refereegranskat)abstract
- Cinnamoyl-CoA reductase (CCR), an enzyme central to the lignin biosynthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. However, silencing of the CCR gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. Here, we evaluated host genotype-dependent effects of field-grown, CCR-down-regulated poplar trees (Populus tremula × Populus alba) on the bacterial rhizosphere microbiome and the endosphere microbiome, namely the microbiota present in roots, stems, and leaves. Plant-associated bacteria were isolated from all plant compartments by selective isolation and enrichment techniques with specific phenolic carbon sources (such as ferulic acid) that are up-regulated in CCR-deficient poplar trees. The bacterial microbiomes present in the endosphere were highly responsive to the CCR-deficient poplar genotype with remarkably different metabolic capacities and associated community structures compared with the WT trees. In contrast, the rhizosphere microbiome of CCR-deficient and WT poplar trees featured highly overlapping bacterial community structures and metabolic capacities. We demonstrate the host genotype modulation of the plant microbiome by minute genetic variations in the plant genome. Hence, these interactions need to be taken into consideration to understand the full consequences of plant metabolic pathway engineering and its relation with the environment and the intended genetic improvement.
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| 2. |
- Cherian, Sam, et al.
(författare)
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Phytoremediation of Trace element Contaminated Environments and the Potential of Endophytic Bacteria for Improving this Process
- 2012
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Ingår i: Critical reviews in environmental science and technology. - : Informa UK Limited. - 1064-3389 .- 1547-6537. ; 42:21, s. 2215-2260
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Forskningsöversikt (refereegranskat)abstract
- Trace elements (heavy metals and metalloids) are among the most widespread contaminants that pose serious threat to all living organisms. Plant and microbial-assisted remediation holds great promise for in situ remediation of trace element contaminated environments. An extended knowledge of plant processes generally involved in the uptake, translocation, storage and detoxification of contaminants, and plant-microbe interactions were essential in developing improved technologies for environmental clean up. Currently, with the initiation of transgenic technologies, great strides have been made in trace element phytoremediation research. In this review, we provide an overview of the current knowledge of how plants cope with trace elements and discuss the development of transgenic plants with improved trace element remediation capabilities. In addition, this review also addresses the recent progress made towards understanding the plant-microbe interactions, especially of endophytic bacteria (natural and genetically engineered), and their contribution in improving the efficiency and versatility of trace element phytoremediation.
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| 3. |
- Cox, Bianca, et al.
(författare)
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Ambient temperature as a trigger of preterm delivery in a temperate climate
- 2016
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Ingår i: Journal of Epidemiology and Community Health. - : BMJ. - 0143-005X .- 1470-2738. ; 70:12, s. 1191-1199
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Recent evidence suggests that elevated ambient temperatures may trigger preterm delivery. Since results from studies in temperate climates are inconclusive, we investigated the association between temperature and the risk of preterm birth in Flanders (Belgium).METHODS: We used data on 807 835 singleton deliveries (January 1998-July 2011). We combined a quasi-Poisson model with distributed lag non-linear models to allow for delayed and non-linear temperature effects, accounting for the daily pregnancies at risk and their gestational age distribution.RESULTS: For moderate heat (95th vs 50th centile) up to 1 day before delivery (lag 0-1), the risk of preterm birth increased by 8.5% (95% CI 2.4% to 15.0%) when minimum temperature increased from 8.3°C to 16.3°C and by 9.6% (95% CI 1.1% to 18.7%) when maximum temperature increased from 14.7°C to 26.5°C. Corresponding estimates for extreme heat (99th vs 50th centile) were 15.6% (95% CI 4.8% to 27.6%) for minimum temperature (19.0°C vs 8.3°C) and 14.5% (95% CI 0.5% to 30.6%) for maximum temperature (30.7°C vs 14.7°C). Despite the increased risk of preterm birth associated with cold at lag 2 (and lag 1 for minimum temperature), cumulative cold effects were small. The per cent change in preterm birth associated with moderate cold (5th vs 50th centile) up to 3 days before delivery (lag 0-3) was 2.1% (95% CI -4.1% to 8.7%) for minimum temperature (-2.0°C vs 8.3°C) and 0.6% (95% CI -7.3% to 9.2%) for maximum temperature (2.5°C vs 14.7°C).CONCLUSIONS: Even in a temperate climate, ambient temperature may trigger preterm delivery, suggesting that pregnant women should avoid temperature extremes.
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| 4. |
- Kumpiene, Jurate, et al.
(författare)
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Assessment of Methods for Determining Bioavailability of Trace Elements in Soils : A Review
- 2017
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Ingår i: Pedosphere. - : Elsevier. - 1002-0160 .- 2210-5107. ; 27:3, s. 389-406
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Tidskriftsartikel (refereegranskat)abstract
- Trace element-contaminated soils (TECSs) are one of the consequences of the past industrial development worldwide. Excessive exposure to trace elements (TEs) represents a permanent threat to ecosystems and humans worldwide owing to the capacity of metal(loid)s to cross the cell membranes of living organisms and of human epithelia, and their interference with cell metabolism. Quantification of TE bioavailability in soils is complicated due to the polyphasic and reactive nature of soil constituents. To unravel critical factors controlling soil TE bioavailability and to quantify the ecological toxicity of TECSs, TEs are pivotal for evaluating excessive exposure or deficiencies and controlling the ecological risks. While current knowledge on TE bioavailability and related cumulative consequences is growing, the lack of an integrated use of this concept still hinders its utilization for a more holistic view of ecosystem vulnerability and risks for human health. Bioavailability is not generally included in models for decision making in the appraisal of TECS remediation options. In this review we describe the methods for determining the TE bioavailability and technological developments, gaps in current knowledge, and research needed to better understand how TE bioavailability can be controlled by sustainable TECS management altering key chemical properties, which would allow policy decisions for environmental protection and risk management
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| 5. |
- Kumpiene, Jurate, et al.
(författare)
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Selecting chemical and ecotoxicological test batteries for risk assessment of trace element-contaminated soils (phyto)managed by gentle remediation options (GRO)
- 2014
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 496, s. 510-522
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Tidskriftsartikel (refereegranskat)abstract
- During the past decades a number of field trials with gentle remediation options (GRO) have been established on trace element (TE) contaminated sites throughout Europe. Each research group selects different methods to assess the remediation success making it difficult to compare efficacy between various sites and treatments. This study aimed at selecting a minimum risk assessment battery combining chemical and ecotoxicological assays for assessing and comparing the effectiveness of GRO implemented in seven European case studies. Two test batteries were pre-selected; a chemical one for quantifying TE exposure in untreated soils and GRO-managed soils and a biological one for characterizing soil functionality and ecotoxicity. Soil samples from field studies representing one of the main GROs (phytoextraction in Belgium, Sweden, Germany and Switzerland, aided phytoextraction in France, and aided phytostabilization or in situ stabilization/phytoexclusion in Poland, France and Austria) were collected and assessed using the selected test batteries. The best correlations were obtained between NH4NO3-extractable, followed by NaNO3-extractable TE and the ecotoxicological responses. Biometrical parameters and biomarkers of dwarf beans were the most responsive indicators for the soil treatments and changes in soil TE exposures. Plant growth was inhibited at the higher extractable TE concentrations, while plant stress enzyme activities increased with the higher TE extractability. Based on these results, a minimum risk assessment battery to compare/biomonitor the sites phytomanaged by GROs might consist of the NH4NO3 extraction and the bean Plantox test including the stress enzyme activities.
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| 6. |
- Moore, Fiona Porteous, et al.
(författare)
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Endophytic bacterial diversity in poplar trees growing on a BTEX-contaminated site: the characterisation of isolates with potential to enhance phytoremediation.
- 2006
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Ingår i: Systematic and applied microbiology. - : Elsevier BV. - 0723-2020. ; 29:7, s. 539-56
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Tidskriftsartikel (refereegranskat)abstract
- The diversity of endophytic bacteria found in association with poplar was investigated as part of a larger study to assess the possibility and practicality of using endophytic bacteria to enhance in situ phytoremediation. Endophytic bacteria were isolated from the root, stem and leaf of two cultivars of poplar tree growing on a site contaminated with BTEX compounds. They were further characterised genotypically by comparative sequence analysis of partial 16S rRNA genes and BOX-PCR genomic DNA fingerprinting, and phenotypically by their tolerance to a range of target pollutants, heavy metals and antibiotics. One hundred and 21 stable, morphologically distinct isolates were obtained, belonging to 21 genera, although six isolates could not be identified with confidence to a genus. The endophytic bacteria exhibited marked spatial compartmentalisation within the plant, suggesting there are likely to be species-specific and non-specific associations between bacteria and plants. A number of isolates demonstrated the ability to degrade BTEX compounds or to grow in the presence of TCE. This study demonstrates that within the diverse bacterial communities found in poplar several endophytic strains are present that have the potential to enhance phytoremediation strategies.
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| 7. |
- Quintela-Sabarís, Celestino, et al.
(författare)
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Assessing phytotoxicity of trace element-contaminated soils phytomanaged with gentle remediation options at ten European field trials
- 2017
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Ingår i: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 599-600, s. 1388-1398
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Tidskriftsartikel (refereegranskat)abstract
- Gentle remediation options (GRO), i.e. in situ stabilisation, (aided) phytoextraction and (aided) phytostabilisation, were implemented at ten European sites contaminated with trace elements (TE) from various anthropogenic sources: mining, atmospheric fallout, landfill leachates, wood preservatives, dredged-sediments, and dumped wastes. To assess the performance of the GRO options, topsoil was collected from each field trial, potted, and cultivated with lettuce (Lactuca sativa L.) for 48 days. Shoot dry weight (DW) yield, photosynthesis efficiency and major element and TE concentrations in the soil pore water and lettuce shoots were measured.GRO implementation had a limited effect on TE concentrations in the soil pore water, although use of multivariate Co-inertia Analysis revealed a clear amelioration effect in phytomanaged soils. Phytomanagement increased shoot DW yield at all industrial and mine sites, whereas in agricultural soils improvements were produced in one out of five sites. Photosynthesis efficiency was less sensitive than changes in shoot biomass and did not discriminate changes in soil conditions.Based on lettuce shoot DW yield, compost amendment followed by phytoextraction yielded better results than phytostabilisation; moreover shoot ionome data proved that, depending on initial soil conditions, recurrent compost application may be required to maintain crop production with common shoot nutrient concentrations.
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| 8. |
- Thijs, Sofie, et al.
(författare)
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Comparative evaluation of four bacteria-specific primer pairs for 16S rRNA gene surveys
- 2017
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 8:MAR
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date. Here we evaluated the performance of four bacterial primers for characterizing complex microbial communities in explosives contaminated and non-contaminated forest soil and by in silico evaluation against the current SILVA123 database. Primer pair 341f/785r produced the highest number of bacterial OTUs, phylogenetic richness, Shannon diversity, low non-specificity and most reproducible results, followed by 967f/1391r and 799f/1193r. Primer pair 68f/518r showed overall low coverage and a bias toward Alphaproteobacteria. In silico, primer pair 341f/785r showed the highest coverage of the domain Bacteria (96.1%) with no obvious bias toward the majority of bacterial species. This suggests the high utility of primer pair 341f/785r for soil and plant-associated bacterial microbiome studies.
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| 9. |
- Touceda-Gonzalez, M., et al.
(författare)
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Microbial community structure and activity in trace elementcontaminatedsoils phytomanaged by Gentle Remediation Options (GRO)
- 2017
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Ingår i: Environmental Pollution. - : Elsevier. - 0269-7491 .- 1873-6424. ; 231:1, s. 237-251
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Tidskriftsartikel (refereegranskat)abstract
- Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR.Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg−1 soil, respiration increased from 7.4 to 40.1 mg C-CO2 kg−1 soil d−1, and enzyme activities were 2–11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term.
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| 10. |
- Xue, K., et al.
(författare)
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Management with willow short rotation coppice increase the functional gene diversity and functional activity of a heavy metal polluted soil
- 2015
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Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 138, s. 469-477
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Tidskriftsartikel (refereegranskat)abstract
- We studied the microbial functional diversity, biochemical activity, heavy metals (HM) availability and soil toxicity of Cd, Pb and Zn contaminated soils, kept under grassland or short rotation coppice (SRC) to attenuate the risks associated with HM contamination and restore the soil ecological functions. Soil microbial functional diversity was analyzed by the GeoChip, a functional gene microarray containing probes for genes involved in nutrient cycling, metal resistance and stress response. Soil under SRC showed a higher abundance of microbial genes involved in C, N, P and S cycles and resistance to various HM, higher microbial biomass, respiration and enzyme activity rates, and lower HM availability than the grassland soil. The linkages between functional genes of soil microbial communities and soil chemical properties, HM availability and biochemical activity were also investigated. Soil toxicity and N, P and Pb availability were important factors in shaping the microbial functional diversity, as determined by CCA. We concluded that in HM contaminated soils the microbial functional diversity was positively influenced by SRC management through the reduction of HM availability and soil toxicity increase of nutrient cycling. The presented results can be important in predicting the long term environmental sustainability of plant-based soil remediation.
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