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High doses of ozone (O3) and nitrogen dioxide (NO2) cause damage and cell death in plants. These two gases are among the most harmful air pollutants for ecosystems and therefore it is important to understand how plant resistance or sensitivity to these gases work at the molecular level and its genetic control. We compared transcriptome data from O3 and NO2 fumigations to other cell death related treatments, as well as individual marker gene transcript level in different Arabidopsis thaliana accessions. Our analysis revealed that O3 and NO2 trigger very similar gene expression responses that include genes involved in pathogen resistance, cell death and ethylene signaling. However, we also identified exceptions, for example RBOHF encoding a reactive oxygen species producing RESPIRATORY BURST OXIDASE PROTEIN F. This gene had increased transcript levels by O3 but decreased transcript levels by NO2, showing that plants can identify each of the gases separately and activate distinct signaling pathways. To understand the genetics, we conducted a genome wide association study (GWAS) on O3 and NO2 tolerance of natural Arabidopsis accessions. Sensitivity to both gases seem to be controlled by several independent small effect loci and we did not find an overlap in the significantly associated regions. Further characterization of the GWAS candidate loci identified new regulators of O3 and NO2 induced cell death including ABH1, a protein that functions in abscisic acid signaling, mRNA splicing and miRNA processing. The GWAS results will facilitate further characterization of the control of programmed cell death and differences between oxidative and nitrosative stress in plants.

Organic soil amendments such as manure, biochar and compost are among the most efficient and widely used methods to increase soil carbon sequestration in agricultural soils. Even though their benefits are well known, many wood-derived materials are not yet utilized in Nordic agriculture due to a lack of incentives and knowledge of their effects in the local climate. We studied greenhouse gas exchange, plant growth and soil properties of a clay soil cultivated with oat in southern Finland in an extremely dry year. Two years earlier, the field was treated with three ligneous soil amendments—lime-stabilized fiber from the pulp industry, willow biochar and spruce biochar—which we compared against fertilized and non-fertilized controls. We found that the soil amendments increased porosity and the mean soil water holding capacity, which was most noticeable in plots amended with spruce biochar. There was a trend indicating that the mean yield and overall biomass production were larger in plots with soil amendments; however, the difference to unamended control was seldom significant due to the high variance among replicates. Manual chamber measurements revealed that carbon dioxide and methane exchange rates were reduced most probably by the exceptionally hot and dry weather conditions, but no differences could be found between the amended and unamended treatments. The nitrous oxide emissions were significantly smaller from the vegetated soil amended with willow biochar compared with the unamended control. Emissions from non-vegetated soil, representing heterotrophic respiration, were similar but without significant differences between treatments. Overall, the studied soil amendments indicated positive climatic impact two years after their application, but further research is needed to conclusively characterize the specific effects of organic soil amendments on processes affecting greenhouse gas exchange and plant growth.

Drought is significant abiotic stress that affects the development and yield of many crops. The present study is to investigate the effect of arbuscular mycorrhizal fungi (AMF) and biochar on root morphological traits, growth, and physiological traits in soybean under water stress. Impact of AMF and biochar on development and root morphological traits in soybean and AMF spores number and the soil enzymes’ activities were studied under drought conditions. After 40 days, plant growth parameters were measured. Drought stress negatively affected soybean growth, root parameters, physiological traits, microbial biomass, and soil enzyme activities. Biochar and AMF individually increase significantly plant growth (plant height, root dry weight, and nodule number), root parameters such as root diameter, root surface area, total root length, root volume, and projected area, total chlorophyll content, and nitrogen content in soybean over to control in water stress. In drought conditions, dual applications of AMF and biochar significantly enhanced shoot and root growth parameters, total chlorophyll, and nitrogen contents in soybean than control. Combined with biochar and AMF positively affects AMF spores number, microbial biomass, and soil enzyme activities in water stress conditions. In drought stress, dual applications of biochar and AMF increase microbial biomass by 28.3%, AMF spores number by 52.0%, alkaline phosphomonoesterase by 45.9%, dehydrogenase by 46.5%, and fluorescein diacetate by 52.2%, activities. The combined application of biochar and AMF enhance growth, root parameters in soybean and soil enzyme activities, and water stress tolerance. Dual applications with biochar and AMF benefit soybean cultivation under water stress conditions.

Plants live in a world of changing environments, where they are continuously challenged by alternating biotic and abiotic stresses. To transfer information from the environment to appropriate protective responses, plants use many different signaling molecules and pathways. Reactive oxygen species (ROS) are critical signaling molecules in the regulation of plant stress responses, both inside and between cells. In natural environments, plants can experience multiple stresses simultaneously. Laboratory studies on stress interaction and crosstalk at regulation of gene expression, imply that plant responses to multiple stresses are distinctly different from single treatments. We analyzed the expression of selected marker genes and reassessed publicly available datasets to find signaling pathways regulated by ozone, which produces apoplastic ROS, and high light treatment, which produces chloroplastic ROS. Genes related to cell death regulation were differentially regulated by ozone versus high light. In a combined ozone + high light treatment, the light treatment enhanced ozone-induced cell death in leaves. The distinct responses from ozone versus high light treatments show that plants can activate stress signaling pathways in a highly precise manner.

Surfactin lipopeptide is an eco-friendly microbially synthesized bioproduct that holds considerable potential in therapeutics (antibiofilm) as well as in agriculture (antifungal). In the present study, production of surfactin by a marine strain Bacillus velezensis MS20 was carried out, followed by physico-chemical characterization, anti-biofilm activity, plant growth promotion, and quantitative Reverse Transcriptase—Polymerase Chain Reaction (q RT-PCR) studies. From the results, it was inferred that MS20 was found to produce biosurfactant (3,300 mg L–1) under optimized conditions. From the physicochemical characterization [Thin layer chromatography (TLC), Fourier Transform Infrared (FTIR) Spectroscopy, Liquid Chromatography/Mass Spectroscopy (LC/MS), and Polymerase Chain Reaction (PCR) amplification] it was revealed to be surfactin. From bio-assay and scanning electron microscope (SEM) images, it was observed that surfactin (MIC 50 μg Ml–1) has appreciable bacterial aggregation against clinical pathogens Pseudomonas aeruginosa MTCC424, Escherichia coli MTCC43, Klebsiella pneumoniae MTCC9751, and Methicillin resistant Staphylococcus aureus (MRSA) and mycelial condensation property against a fungal phytopathogen Rhizoctonia solani. In addition, the q-RTPCR studies revealed 8-fold upregulation (9.34 ± 0.11-fold) of srfA-A gene compared to controls. Further, treatment of maize crop (infected with R. solani) with surfactin and MS20 led to the production of defense enzymes. In conclusion, concentration and synergy of a carbon source with inorganic/mineral salts can ameliorate surfactin yield and, application wise, it has antibiofilm and antifungal activities. In addition, it induced systemic resistance in maize crop, which makes it a good candidate to be employed in sustainable agricultural practices.

Iron superoxide dismutase 1 (FSD1) was recently characterized as a plastidial, cytoplasmic, and nuclear enzyme with osmoprotective and antioxidant functions. However, the current knowledge on its role in oxidative stress tolerance is ambiguous. Here, we characterized the role of FSD1 in response to methyl viologen (MV)-induced oxidative stress in Arabidopsis thaliana. In accordance with the known regulation of FSD1 expression, abundance, and activity, the findings demonstrated that the antioxidant function of FSD1 depends on the availability of Cu2+ in growth media. Arabidopsis fsd1 mutants showed lower capacity to decompose superoxide at low Cu2+ concentrations in the medium. Prolonged exposure to MV led to reduced ascorbate levels and higher protein carbonylation in fsd1 mutants and transgenic plants lacking a plastid FSD1 pool as compared to the wild type. MV induced a rapid increase in FSD1 activity, followed by a decrease after 4 h long exposure. Genetic disruption of FSD1 negatively affected the hydrogen peroxide-decomposing ascorbate peroxidase in fsd1 mutants. Chloroplastic localization of FSD1 is crucial to maintain redox homeostasis. Proteomic analysis showed that the sensitivity of fsd1 mutants to MV coincided with decreased abundances of ferredoxin and photosystem II light-harvesting complex proteins. These mutants have higher levels of chloroplastic proteases indicating an altered protein turnover in chloroplasts. Moreover, FSD1 disruption affects the abundance of proteins involved in the defense response. Collectively, the study provides evidence for the conditional antioxidative function of FSD1 and its possible role in signaling.

In perennial fruit and berry crops of the Rosaceae family, flower initiation occurs in late summer or autumn after downregulation of a strong repressor TERMINAL FLOWER1 (TFL1), and flowering and fruiting takes place the following growing season. Rosaceous fruit trees typically form two types of axillary shoots, short flower-bearing shoots called spurs and long shoots that are, respectively, analogous to branch crowns and stolons in strawberry. However, regulation of flowering and shoot architecture differs between species, and environmental and endogenous controlling mechanisms have just started to emerge. In woodland strawberry (Fragaria vesca L.), long days maintain vegetative meristems and promote stolon formation by activating TFL1 and GIBBERELLIN 20-OXIDASE4 (GA20ox4), respectively, while silencing of these factors by short days and cool temperatures induces flowering and branch crown formation. We characterized flowering responses of 14 accessions of seven diploid Fragaria species native to diverse habitats in the northern hemisphere and selected two species with contrasting environmental responses, Fragaria bucharica Losinsk. and Fragaria nilgerrensis Schlecht. ex J. Gay for detailed studies together with Fragaria vesca. Similar to F. vesca, short days at 18°C promoted flowering in F. bucharica, and the species was induced to flower regardless of photoperiod at 11°C after silencing of TFL1. F. nilgerrensis maintained higher TFL1 expression level and likely required cooler temperatures or longer exposure to inductive treatments to flower. We also found that high expression of GA20ox4 was associated with stolon formation in all three species, and its downregulation by short days and cool temperature coincided with branch crown formation in F. vesca and F. nilgerrensis, although the latter did not flower. F. bucharica, in contrast, rarely formed branch crowns, regardless of flowering or GA20ox4 expression level. Our findings highlighted diploid Fragaria species as rich sources of genetic variation controlling flowering and plant architecture, with potential applications in breeding of Rosaceous crops.

The pressure to increase forest and land carbon stocks simultaneously with increasing forest based biomass harvest for energy and materials emphasizes the need for dedicated analyses of impacts and possible trade-offs between these different mitigation options including also forest related biophysical factors, surface albedo and the formation of biogenic Secondary Organic Aerosols (SOA). We analyzed the change in global radiative forcing (RF) due to changes in these climatic agents as affected by the change in state of Finnish forests under increased or decreased harvest scenarios from a baseline. We also included avoided emissions due to wood material and energy substitution. Increasing harvests from baseline (65% of Current Annual Increment) decreased the total carbon sink (carbon in trees, soil and harvested wood products) at least for 50 years. When we coupled this change in carbon with other biosphere responses, surface albedo and aerosols, decreasing harvests from the baseline produced the largest cooling effect during 50 years. Accounting also for the avoided emissions due to increased wood use, the RF responses of the two lowest harvest scenarios were within uncertainty range. Our results show that the effects of forest management on SOA formation should be included in the analyses trying to deduce the net climate impact of forest use. The inclusion of the rarely considered SOA effects enforces the view that the lower the harvest, the more climatic cooling boreal forests provide. These results should act as a caution mark for policy makers who are emphasizing the increased utilization of forest biomass for short-living products and bioenergy as an efficient measure to mitigate climate change.

The incidence, distribution, and variation of simple sequence repeats (SSRs) in viruses is instrumental in understanding the functional and evolutionary aspects of repeat sequences. Full-length genome sequences retrieved from NCBI were used for extraction and analysis of repeat sequences using IMEx software. We have also developed two MATLAB-based tools for extraction of gene locations from GenBank in tabular format and simulation of this data with SSR incidence data. Present study encompassing 147 Mycobacteriophage genomes revealed 25,284 SSRs and 1,127 compound SSRs (cSSRs) through IMEx. Mono-to hexa-nucleotide motifs were present. The SSR count per genome ranged from 78 (M100) to 342 (M58) while cSSRs incidence ranged from 1 (M138) to 17 (M28, M73). Though cSSRs were present in all the genomes, their frequency and SSR to cSSR conversion percentage varied from 1.08 (M138 with 93 SSRs) to 8.33 (M116 with 96 SSRs). In terms of localization, the SSRs were predominantly localized to coding regions (similar to 78%). Interestingly, genomes of around 50 kb contained a similar number of SSRs/cSSRs to that in a 110 kb genome, suggesting functional relevance for SSRs which was substantiated by variation in motif constitution between species with different host range. The three species with broad host range (M97, M100, M116) have around 90% of their mono-nucleotide repeat motifs composed of G or C and only M16 has both A and T mononucleotide motifs. Around 20% of the di-nucleotide repeat motifs in the genomes exhibiting a broad host range were CT/TC, which were either absent or represented to a much lesser extent in the other genomes.

Root and butt rot caused by members of the Heterobasidion annosum species complex is the most economically important disease of conifer trees in boreal forests. Wood decay in the infected trees dramatically decreases their value and causes considerable losses to forest owners. Trees vary in their susceptibility to Heterobasidion infection, but the genetic determinants underlying the variation in the susceptibility are not well-understood. We performed the identification of Norway spruce genes associated with the resistance to Heterobasidion parviporum infection using genome-wide exon-capture approach. Sixty-four clonal Norway spruce lines were phenotyped, and their responses to H. parviporum inoculation were determined by lesion length measurements. Afterwards, the spruce lines were genotyped by targeted resequencing and identification of genetic variants (SNPs). Genome-wide association analysis identified 10 SNPs located within 8 genes as significantly associated with the larger necrotic lesions in response to H. parviporum inoculation. The genetic variants identified in our analysis are potential marker candidates for future screening programs aiming at the differentiation of disease-susceptible and resistant trees.

Climate changes, exemplified by increased temperatures and CO2 concentration, pose a global threat to forest health. Of particular concern are pests and pathogens, with a warming climate altering their distributions and evolutionary capacity, while impairing the ability of some plants to respond to infections. Progress in understanding and mitigating such effects is currently hindered by a lack of empirical research. Norway spruce (Picea abies) is one of the most economically important tree species in northern Europe, and is considered highly vulnerable to changes in climate. It is commonly infected by the fungus Endoconidiophora polonica, and we hypothesized that damage caused to trees will increase under future climate change predictions. To test this hypothesis an in vivo greenhouse experiment was conducted to evaluate the effects of a changed growing environment on E. polonica infected Norway spruce seedlings, comparing ambient conditions to predicted temperatures and CO2 levels in Finland for the years 2030 and 2100. In total, 450 seedlings were randomized amongst the three treatments, with 25 seedlings from each allocated to inoculation with one of five different fungal strains or mock-inoculation. Seedlings were monitored throughout the thermal growing season for mortality, and lesion length and depth indices were measured at the experiment conclusion. Disease severity (mortality and lesions) was consistently greater in fungal-inoculated than mock-inoculated seedlings. However, substantial differences were observed among fungal strains in response to climate scenarios. For example, although overall seedling mortality was highest under the most distant (and severe) climate change expectations, of the two fungal strains with the highest mortality counts (referred to as F4 and F5), one produced greater mortality under the 2030 and 2100 scenarios than ambient conditions, whereas climate scenario had no effect on the other. This study contributes to a limited body of empirical research on the effects of projected climate changes on forestry pathosystems, and is the first to investigate interactions between Norway spruce and E. polonica. The results indicate the potential for future climate changes to alter the impact of forest pathogens with implications for productivity, while highlighting the need for a strain-specific level of understanding of the disease agents.

Flowering time control integrates endogenous as well as environmental signals to promote flower development. The pathways and molecular networks involved are complex and integrate many modes of signal transduction. In plants ubiquitin mediated protein degradation pathway has been proposed to be as important mode of signaling as phosphorylation and transcription. To systematically study the role of ubiquitin signaling in the molecular regulation of flowering we have taken a genomic approach to identify flower related Ubiquitin Proteasome System components. As a large and versatile gene family the RING type ubiquitin E3 ligases were chosen as targets of the genomic screen. To this end the complete list of Arabidopsis RING E3 ligases were retrieved and verified in the Arabidopsis genome v11. Their differential expression was used for their categorization into flower organs or developmental stages. Known regulators of flowering time or floral organ development were identified in these categories through literature search and representative mutants for each category were purchased for functional characterization by growth and morphological phenotyping. To this end, a workflow was developed for high throughput phenotypic screening of growth, morphology and flowering of nearly a thousand Arabidopsis plants in one experimental round.

Leaf Optical Properties (LOPs) convey information relating to temporally dynamic photosynthetic activity and biochemistry. LOPs are also sensitive to variability in anatomically related traits such as Specific Leaf Area (SLA), via the interplay of intra-leaf light scattering and absorption processes. Therefore, variability in such traits, which may demonstrate little plasticity over time, potentially disrupts remote sensing estimates of photosynthesis or biochemistry across space. To help to disentangle the various factors that contribute to the variability of LOPs, we defined baseline variation as variation in LOPs that occurs across space, but not time. Next we hypothesized that there were two main controls of potentially disruptive baseline spatial variability of photosynthetically-related LOPs at our boreal forest site: light environment and species. We measured photosynthetically-related LOPs in conjunction with morphological, biochemical, and photosynthetic leaf traits during summer and across selected boreal tree species and vertical gradients in light environment. We then conducted a detailed correlation analysis to disentangle the spatial factors that control baseline variability of leaf traits and, resultantly, LOPs. Baseline spatial variability of the Photochemical Reflectance Index (PRI) was strongly influenced by species and to a lesser extent light environment. Baseline variability of spectral fluorescence derived LOPs was less influenced by species; however at longer near-infrared wavelengths, light environment was an important control. In summary, remote sensing of chlorophyll fluorescence has good potential to detect variation in photosynthetic performance across space in boreal forests given reduced sensitivity to species related baseline variability in comparison to the PRI. Our results also imply that spatially coarse remote sensing observations are potentially unrepresentative of the full scope of natural variation that occurs within a boreal forest.

The pull of water from the soil to the leaves causes water in the transpiration stream to be under negative pressure decreasing the water potential below zero. The osmotic concentration also contributes to the decrease in leaf water potential but withmuch lesser extent. Thus, the surface tension force is approximately balanced by a force induced by negative water potential resulting in concavely curved water-air interfaces in leaves. The lowered water potential causes a reduction in the equilibrium water vapor pressure in internal (sub-stomatal/ intercellular) cavities in relation to that over water with the potential of zero, i.e., over the flat surface. The curved surface causes a reduction also in the equilibrium vapor pressure of dissolved CO2, thus enhancing its physical solubility to water. Although the water vapor reduction is acknowledged by plant physiologists its consequences for water vapor exchange at low water potential values have received very little attention. Consequences of the enhanced CO2 solubility to a leaf water-carbon budget have not been considered at all before this study. We use theoretical calculations and modeling to show how the reduction in the vapor pressures affects transpiration and carbon assimilation rates. Our results indicate that the reduction in vapor pressures of water and CO2 could enhance plant water use efficiency up to about 10% at a leaf water potential of -2 MPa, and much more when water potential decreases further. The low water potential allows for a direct stomatal water vapor uptake from the ambient air even at sub-100% relative humidity values. This alone could explain the observed rates of foliar water uptake by e.g., the coastal redwood in the fog belt region of coastal California provided the stomata are sufficiently open. The omission of the reduction in the water vapor pressure causes a bias in the estimates of the stomatal conductance and leaf internal CO2 concentration based on leaf gas exchange measurements. Manufactures of leaf gas exchange measurement systems should incorporate leaf water potentials in measurement set-ups.

Timothy is a perennial forage grass grown commonly in Boreal regions. This study explored the effect of vernalization and photoperiod (PP) on flowering and growth characteristics and how this related to changes in expression of three flowering related genes in accessions from different geographic origin. Large variation was found in accessions in their vernalization and PP responses. In southern accessions vernalization response or requirement was not observed, the heading date remained unchanged, and plants flowered without vernalization. On the contrary, northern types had obligatory requirement for vernalization and long PP, but the tiller elongation did not require vernalization at 16-h PP. Longer vernalization or PP treatments reduced the genotypical differences in flowering. Moreover, the vernalization saturation progressed stepwise from main tiller to lateral tillers, and this process was more synchronized in southern accessions. The expression of PpVRN1 was associated with vernalization while PpVRN3 accumulated at long PP. A crucial role for PpVRN3 in the transition to flowering was supported as in southern accession the transcript accumulated in non-vernalized plants after transfer to 16-h PP, and the apices transformed to generative stage. Differences in vernalization requirements were associated with variation in expression levels of PpVRN1 and PpVRN3, with higher expression levels in southern type. Most divergent transcript accumulation of PpMADS10 was found under different vernalization conditions. These differences between accessions can be translated into agronomic traits, such as the tiller composition of canopy, which affects the forage yield. The southern types, with minimal vernalization response, have fast re-growth ability and rapidly decreasing nutritive value, whereas northern types grow slowly and have better quality. This information can be utilized in breeding for new cultivars for longer growing seasons at high latitudes.