Plant Secondary Metabolites—Missing Pieces in the Soil Organic Matter Puzzle of Boreal Forests

Processes underlying soil organic matter (SOM) transformations are meeting growing interest as SOM contains more carbon (C) than global vegetation and the atmosphere combined. Therefore, SOM is a crucial element of the C cycle, especially in ecosystems rich in organic matter, such as boreal forests. However, climate change may shift the fate of this SOM from C sink into C source, accelerating global warming. These processes require a better understanding of the involved mechanisms driving both the C cycle and the interlinked nitrogen (N) cycle. SOM transformations are balanced by a network of interactions between biological, chemical and physical factors. In this review, we discuss the findings of the most recent studies to the current state of knowledge about the main drivers in SOM transformations. We focus on plant-derived secondary metabolites, as their biochemical traits, especially interactions with soil microbial communities, organic N compounds and enzymes make them potential regulators of SOM decomposition. However, these regulatory abilities of plant-derived compounds are not fully explored.Peer reviewe

Tannins and Their Complex Interaction with Different Organic Nitrogen Compounds and Enzymes : Old Paradigms versus Recent Advances

Tannins, an abundant group of plant secondary compounds, raise interest in different fields of science, owing to their unique chemical characteristics. In chemical ecology, tannins play a crucial role in plant defense against pathogens, herbivores, and changing environmental conditions. In the food industry and in medicine, tannins are important because of their proven positive effect on human health and disease treatment, Such wide interests fueled studies on tannin chemistry, especially on their flagship ability to precipitate proteins. In this Review, we expand the basic knowledge on tannin chemistry to the newest insights from the field. We focus especially on tannin reactions with different non-protein organic N compounds, as well as the complex interactions of tannins with enzymes, resulting in either an increase or decrease in enzyme activity.Peer reviewe

Mechanisms of Carbon Sequestration in Highly Organic Ecosystems – Importance of Chemical Ecology

Abstract Organic matter decomposition plays a major role in the cycling of carbon (C) and nutrients in terrestrial ecosystems across the globe. Climate change accelerates the decomposition rate to potentially increase the release of greenhouse gases and further enhance global warming in the future. However, fractions of organic matter vary in turnover times and parts are stabilized in soils for longer time periods (C sequestration). Overall, a better understanding of the mechanisms underlying C sequestration is needed for the development of effective mitigation policies to reduce land-based production of greenhouse gases. Known mechanisms of C sequestration include the recalcitrance of C input, interactions with soil minerals, aggregate formation, as well as its regulation via abiotic factors. In this Minireview, we discuss the mechanisms behind C sequestration including the recently emerging significance of biochemical interactions between organic matter inputs that lead to C stabilization.Peer reviewe

Editorial: Sustainable and Climate-Smart Agriculture in the Boreal and Arctic Regions

Peer Reviewe

Fast and reliable method to estimate global DNA methylation in plants and fungi with high-pressure liquid chromatography (HPLC)-ultraviolet detection and even more sensitive one with HPLC-mass spectrometry

Abstract: DNA (Deoxyribonucleic acid) methylation is one of the epigenetic modifications of DNA, acting as a bridge between genotype and phenotype. Thus, disruption of DNA methylation pattern has tremendous consequences for organism development. Current methods to determine DNA methylation suffer from methodological drawbacks like high requirement of DNA and poor reproducibility of chromatograms. Here we provide a fast and reliable method using high-pressure liquid chromatography (HPLC)-ultraviolet (UV) detector and even more sensitive one with HPLC- mass spectrometry (MS) and we test this method with various plant and fungal DNA isolates. We optimized the preparation of the DNA degradation step to decrease background noise, we improved separation conditions to provide reliable and reproducible chromatograms and conditions to measure nucleotides in HPLC-MS. We showed that global DNA methylation level can be accurately and reproducibly measured with as little as 0.2 µM for HPLC-UV and 0.02 µM for HPLC-MS of methylated cytosine

Interaction between tannins and fungal necromass stabilizes fungal residues in boreal forest soils

See also the Commentary on this article by Hattenschwiler et al., 223: 5-7.Peer reviewe

Precise method to measure fungal and bacterial necromass using high pressure liquid chromatography with fluorescence detector adjusted to inorganic, organic and peat soils

Soil organic matter is the dominant pool of carbon (C) in terrestrial ecosystems. Recent advances in understanding of the mechanisms of C stabilization in the soil emphasize microbes as the main drivers. Special attention is placed on the accumulation of bacterial and fungal necromasses. This calls for development of fast and reliable methods to estimate microbial necromass in a various type of soils, including peat soils. Here we provide precise method to measure fungal and bacterial necromasses with high-pressure liquid chromatography-fluorescence detector (HPLC-FLD) and its comparison with gas chromatography method. Purity of the chromatographic peaks was confirmed with mass spectrometry. The HPLC-FLD method provides reliable results for mineral, organic and highly organic peat soils

Root presence modifies the long-term decomposition dynamics of fungal necromass and the associated microbial communities in a boreal forest

Recent studies have highlighted that dead fungal mycelium represents an important fraction of soil carbon (C) and nitrogen (N) inputs and stocks. Consequently, identifying the microbial communities and the ecological factors that govern the decomposition of fungal necromass will provide critical insight into how fungal organic matter (OM) affects forest soil C and nutrient cycles. Here, we examined the microbial communities colonising fungal necromass during a multiyear decomposition experiment in a boreal forest, which included incubation bags with different mesh sizes to manipulate both plant root and microbial decomposer group access. Necromass-associated bacterial and fungal communities were taxonomically and functionally rich throughout the 30 months of incubation, with increasing abundances of oligotrophic bacteria and root-associated fungi (i.e., ectomycorrhizal, ericoid mycorrhizal and endophytic fungi) in the late stages of decomposition in the mesh bags to which they had access. Necromass-associated beta-glucosidase activity was highest at 6 months, while leucine aminopeptidase peptidase was highest at 18 months. Based on an asymptotic decomposition model, root presence was associated with an initial faster rate of fungal necromass decomposition, but resulted in higher amounts of fungal necromass retained at later sampling times. Collectively, these results indicate that microbial community composition and enzyme activities on decomposing fungal necromass remain dynamic years after initial input, and that roots and their associated fungal symbionts result in the slowing of microbial necromass turnover with time.Peer reviewe

Uniqueness of tree stand composition and soil microbial communities are related across urban spruce-dominated forests

Context: Urban forest soils represent significant reservoirs of biodiversity in cities. Retaining this diversity under urban land-use change requires understanding on how species richness, community assembly and uniqueness of species assemblages are related to local forest characteristics and surrounding landscape structure. Objectives: Our aim was to assess the significance and relative importance of logging history, tree species composition and urbanization in shaping soil microbial communities across urban spruce-dominated forest landscapes. We investigated responses of microbial diversity from three complementary viewpoints: local diversity, community assembly patterns and community uniqueness. Methods: We collected soil bacterial and fungal metabarcoding data from 73 spruce-dominated forest sites distributed in three urban centers across southern Finland. We related these data to measurements of logging intensity, tree species composition and degree of urbanization. Results: Logging intensity, tree species composition and urbanization affected site-scale microbial diversity, but the effects varied between microbial groups. Only logging intensity had a significant imprint on microbial assembly, and this effect was restricted to bacteria. Relative uniqueness of microbial assemblages at the landscape-scale was coupled with the uniqueness of tree species composition in all microbial groups, and further affected by tree diversity in saprotrophic fungi and urbanization in ectomycorrhizal fungi. Conclusions: In the context of urban spruce-dominated forests, locally diverse tree stands are not necessarily the same as those that contribute the most to landscape-scale diversity. Identifying and preserving contrasting tree stand structures, which support distinctive soil microbial assemblages, may be the winning strategy in maintaining a wide range of soil microbial diversity

Automated geometric features evaluation method for normal foot skeleton model

Normal foot model is a geometric model of a healthy human foot. As the comparison of the processed feet requires a reference ideal healthy foot parameterization it was necessary to create such a model by defining skeleton geometric features and generating the feature set on a dataset population. Manual positioning of such number of landmarks is both a complex and time consuming task for a skilled radiologist, not to mention the total cost of such a procedure. Thus it was recommended to formulate an automated computer algorithm to perform this procedure with accuracy at a comparable level as the manual process. The following paper describes our approach based on automatic landmark positioning in a volumetric foot dataset. The proposed automated procedure is based on four main steps: manual landmark positioning on a reference dataset, registration of the reference dataset with the examined study, transformation of landmark positions from the reference dataset space into the examined dataset space, and calculation of the geometric features on the basis of landmarks positions. The results of our algorithm are presented and discussed in the context of pros and cons of the automated method itself as well as in the context of the generated normal foot model