Maud Viger

More plant growth but less plant defence? First global gene expression data for plants grown in soil amended with biochar.

Biochar is a carbon (C)‐rich solid formed when biomass is used to produce bioenergy. This ‘black carbon’ has been suggested as a solution to climate change, potentially reducing global anthropogenic emissions of greenhouse gases by 12%, as well as promoting increased crop growth. How biochar application to soil leads to better crop yields remains open to speculation. Using the model plant Arabidopsis and the crop plant lettuce (Lactuca sativa L.), we found increased plant growth in both species following biochar application. Statistically significant increases for Arabidopsis in leaf area (130%), rosette diameter (61%) and root length (100%) were observed with similar findings in lettuce, where biochar application also increased leaf cell expansion. For the first time, global gene expression arrays were used on biochar‐treated plants, enabling us to identify the growth‐promoting plant hormones, brassinosteroid and auxin, and their signalling molecules, as key to this growth stimulation, with limited impacts on genes controlling photosynthesis. In addition, genes for cell wall loosening were promoted as were those for increased activity in membrane transporters for sugar, nutrients and aquaporins for better water and nutrient uptake and movement of sugars for metabolism in the plant. Positive growth effects were accompanied by down‐regulation of a large suite of plant defence genes, including the jasmonic acid biosynthetic pathway, defensins and most categories of secondary metabolites. Such genes are critical for plant protection against insect and pathogen attack, as well as defence against stresses including drought. We propose a conceptual model to explain these effects in this biochar type, hypothesizing a role for additional K+ supply in biochar amended soils, leading to Ca2+ and Reactive Oxygen Species (ROS) –mediated signalling underpinning growth and defence signalling responses.

Biochar mineralization and priming effect on SOM decomposition in two European short rotation coppices.

As studies on biochar stability in field conditions are very scarce, the carbon sequestration potential of biochar application to agricultural soils remains uncertain. This study assessed the stability of biochar in field conditions, the effect of plant roots on biochar stability and the effect of biochar on original soil organic matter (SOM) decomposition in two (Italy and United Kingdom) short rotation coppice systems (SRCs), using continuous soil respiration monitoring and periodic isotopic (δ13CO2) measurements. When root growth was excluded, only 7% and 3% of the biochar carbon added was decomposed after 245 and 164 days in Italy and United Kingdom sites respectively. In the presence of roots, this percentage was increased to 9% and 8%, suggesting a small positive priming effect of roots on biochar decomposition. A decreased decomposition rate of original SOM was observed at both sites after biochar incorporation, suggesting a protective effect of biochar on SOM. This study supports the carbon sequestration potential of biochar and highlights the role of root activity on biochar decomposition, questioning the applicability of laboratory incubation studies to assess biochar stability.

Biochar alters the soil microbiome and soil function: results of next‐generation amplicon sequencing across Europe

Wide‐scale application of biochar to soil has been suggested as a mechanism to offset increases in CO2 emissions through the long‐term sequestration of a carbon rich and inert substance to the soil, but the implications of this for soil diversity and function remain to be determined. Biochar is capable of inducing changes in soil bacterial communities, but the exact impacts of its application are poorly understood. Using three European sites [UK SRC, short rotation coppice, French grassland (FR) and Italian SRF, short rotation forestry (IT)] treated with identical biochar applications, we undertook 16S and ITS amplicon DNA sequencing. In addition, we carried out assessments of community change over time and N and P mobilization in the UK. Significant changes in bacterial and community structure occurred due to treatment, although the nature of the changes varied by site. STAMP differential abundance analysis showed enrichment of Gemmatimonadete and Acidobacteria in UK biochar plots 1 year after application, whilst control plots exhibited enriched Gemmataceae, Isosphaeraceae and Koribacteraceae. Increased mobility of ammonium and phosphates was also detected after 1 year, coupled with a shift from acid to alkaline phosphomonoesterase activity, which may suggest an ecological and functional shift towards a more copiotrophic ecology. Italy also exhibited enrichments, in both the Proteobacteria (driven by an increase in the order Rhizobiales) and the Gemmatimonadetes. No significant change in the abundance of individual taxa was noted in FR, although a small significant change in unweighted UNIFRAC occurred, indicating variation in the identities of taxa present due to treatment. Fungal β diversity was affected by treatment in IT and FR, but was unaffected in UK samples. The effects of time and site were greater than that of biochar application in UK samples. Overall, this report gives a tantalizing view of the soil microbiome at several sites across Europe and suggests that although application of biochar has significant effects on microbial communities, these may be small compared with the highly variable soil microbiome that is found in different soils and changes with time.

New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array.

Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water‐use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead‐Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5–7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural‐population based genetic association studies in P. nigra.

Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree

Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001) but negatively correlated with skeletonizer damage (P<0.01) in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast-growing forest tree.

Land‐use change to bioenergy: grassland to short rotation coppice willow has an improved carbon balance

The effect of a transition from grassland to second‐generation (2G) bioenergy on soil carbon and greenhouse gas (GHG) balance is uncertain, with limited empirical data on which to validate landscape‐scale models, sustainability criteria and energy policies. Here, we quantified soil carbon, soil GHG emissions and whole ecosystem carbon balance for short rotation coppice (SRC) bioenergy willow and a paired grassland site, both planted at commercial scale. We quantified the carbon balance for a 2‐year period and captured the effects of a commercial harvest in the SRC willow at the end of the first cycle. Soil fluxes of nitrous oxide (N2O) and methane (CH4) did not contribute significantly to the GHG balance of these land uses. Soil respiration was lower in SRC willow (912 ± 42 g C m−2 yr−1) than in grassland (1522 ± 39 g C m−2 yr−1). Net ecosystem exchange (NEE) reflected this with the grassland a net source of carbon with mean NEE of 119 ± 10 g C m−2 yr−1 and SRC willow a net sink, −620 ± 18 g C m−2 yr−1. When carbon removed from the ecosystem in harvested products was considered (Net Biome Productivity), SRC willow remained a net sink (221 ± 66 g C m−2 yr−1). Despite the SRC willow site being a net sink for carbon, soil carbon stocks (0–30 cm) were higher under the grassland. There was a larger NEE and increase in ecosystem respiration in the SRC willow after harvest; however, the site still remained a carbon sink. Our results indicate that once established, significant carbon savings are likely in SRC willow compared with the minimally managed grassland at this site. Although these observed impacts may be site and management dependent, they provide evidence that land‐use transition to 2G bioenergy has potential to provide a significant improvement on the ecosystem service of climate regulation relative to grassland systems.

Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigra L.)

Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. ‘North eastern’ genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ13C. In contrast, ‘southern’ genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1–3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought.

Evaluation of the ECOSSE model to predict heterotrophic soil respiration by direct measurements

Acknowledgements This work contributes to the ELUM (Ecosystem Land Use Modelling & Soil Carbon GHG Flux Trial) project, which was commissioned and funded by the Energy Technologies Institute (ETI), and to Carbo-BioCrop (http://www.carbobiocrop.ac.uk; a NERC funded project; NE/H010742/1), UKERC Phase II and III (NERC; NE/H013237/1), MAGLUE (http://www.maglue.ac.uk; an EPSRC funded project; EP/M013200/1) and as part of the Seventh Framework For Research Programme of the EU, within the EUROCHAR project (N 265179) and EXPEER within WU FP7-Infrastructures. We acknowledge the use of the E-OBS dataset from the EU-FP6 project ENSEMBLES (http://ensembles-eu.metoffice.com) and the data providers in the ECA&D project (http://www.ecad.eu). We thank two anonymous reviewers and Dr William van Dijk for their valuable suggestions.

Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigra L.): Adaptatie en genomische plasticiteit voor droogte resistentie bij de Europese zwarte populier (Populus nigra L.)

Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. ‘North eastern’ genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ13C. In contrast, ‘southern’ genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1–3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought.

Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigraL.)

Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. ‘North eastern’ genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ13C. In contrast, ‘southern’ genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1–3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought.