Epigenetic stress memory in gymnosperms.

Gymnosperms are long-lived, cone-bearing seed plants that include some of the most ancient extant plant species. These relict land plants have evolved to survive in habitats marked by chronic or episodic stress. Their ability to thrive in these environments is partly due to their phenotypic flexibility, and epigenetic regulation likely plays a crucial part in this plasticity. We review the current knowledge on abiotic and biotic stress memory in gymnosperms and the possible epigenetic mechanisms underlying long-term phenotypic adaptations. We also discuss recent technological improvements and new experimental possibilities that likely will advance our understanding of epigenetic regulation in these ancient and hard-to-study plants.

Experimental herbivore exclusion, shrub introduction, and carbon sequestration in alpine plant communities.

BACKGROUND: Shrub cover in arctic and alpine ecosystems has increased in recent decades, and is predicted to further increase with climate change. Changes in shrub abundance may alter ecosystem carbon (C) sequestration and storage, with potential positive feedback on global C cycling. Small and large herbivores may reduce shrub expansion and thereby counteract the positive feedback on C cycling, but herbivore pressures have also changed in the alpine-arctic tundra; the increased shrub cover together with changes in herbivore pressure is leading to unpredictable changes in carbon sequestration and storage. In this study we investigate the importance of herbivory and shrub introduction for carbon sequestration in the short term. We measured standing biomass and daytime mid-growing season carbon fluxes in plots in a full factorial design where we excluded small and large mammalian herbivores and introduced Salix by planting Salix transplants. We used three study sites: one Empetrum-dominated heath, one herb- and cryptogam-dominated meadow, and one Salix-dominated shrub community in the low-alpine zone of the Dovre Mountains, Central Norway. RESULTS: After 2 years, significant treatment effects were recorded in the heath community, but not in the meadow and shrub communities. In the heath community cessation of herbivory increased standing biomass due to increased biomass of dwarf shrubs. Cessation of herbivory also reduced biomass of bryophytes and ecosystem respiration (ER). Except for an increase in biomass of deciduous shrubs caused by the Salix introduction, the only effect of Salix introduction was an increase in biomass of graminoids in the heath. CONCLUSIONS: Our short-term study demonstrated that herbivore exclusion had small but still significant effects on heath vegetation, whereas such effects were not apparent in the herb-and cryptogam-dominated meadow and the Salix-dominated shrub community. Following the treatments over more years is needed to estimate the long-term effects on community structure and the consequences for C sequestration in the three plant communities. Such data are important for predicting the impact of shrub expansion on C budgets from alpine regions.

Metabolomic analysis of extreme freezing tolerance in Siberian spruce (Picea obovata).

Siberian spruce (Picea obovata) is one of several boreal conifer species that can survive at extremely low temperatures (ELTs). When fully acclimated, its tissues can survive immersion in liquid nitrogen. Relatively little is known about the biochemical and biophysical strategies of ELT survival. We profiled needle metabolites using gas chromatography coupled with mass spectrometry (GC-MS) to explore the metabolic changes that occur during cold acclimation caused by natural temperature fluctuations. In total, 223 metabolites accumulated and 52 were depleted in fully acclimated needles compared with pre-acclimation needles. The metabolite profiles were found to develop in four distinct phases, which are referred to as pre-acclimation, early acclimation, late acclimation and fully acclimated. Metabolite changes associated with carbohydrate and lipid metabolism were observed, including changes associated with increased raffinose family oligosaccharide synthesis and accumulation, accumulation of sugar acids and sugar alcohols, desaturation of fatty acids, and accumulation of digalactosylglycerol. We also observed the accumulation of protein and nonprotein amino acids and polyamines that may act as compatible solutes or cryoprotectants. These results provide new insight into the mechanisms of freezing tolerance development at the metabolite level and highlight their importance in rapid acclimation to ELT in P. obovata.

Pair-wise multicomparison and OPLS analyses of cold-acclimation phases in Siberian spruce.

Analysis of metabolomics data often goes beyond the task of discovering biomarkers and can be aimed at recovering other important characteristics of observed metabolomic changes. In this paper we explore different methods to detect the presence of distinctive phases in seasonal-responsive changes of metabolomic patterns of Siberian spruce (Picea obovata) during cold acclimation occurred in the period from mid-August to January. Multivariate analysis, specifically orthogonal projection to latent structures discriminant analysis (OPLS-DA), identified time points where the metabolomic patterns underwent substantial modifications as a whole, revealing four distinctive phases during acclimation. This conclusion was re-examined by a univariate analysis consisting of multiple pair-wise comparisons to identify homogeneity intervals for each metabolite. These tests complemented OPLS-DA, clarifying biological interpretation of the classification: about 60% of metabolites found responsive to the cold stress indeed changed at one or more of the time points predicted by OPLS-DA. However, the univariate approach did not support the proposed division of the acclimation period into four phases: less than 10% of metabolites altered during the acclimation had homogeneous levels predicted by OPLS-DA. This demonstrates that coupling the classification found by OPLS-DA and the analysis of dynamics of individual metabolites obtained by pair-wise multicomparisons reveals a more correct characterization of biochemical processes in freezing tolerant trees and leads to interpretations that cannot be deduced by either method alone. The combined analysis can be used in other 'omics'-studies, where response factors have a causal dependence (like the time in the present work) and pair-wise multicomparisons are not conservative. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-011-0304-5) contains supplementary material, which is available to authorized users.