High‐Throughput DNA sequencing of ancient wood

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management.     

The Net Landscape Carbon Balance—Integrating terrestrial and aquatic carbon fluxes in a managed boreal forest landscape in Sweden

The boreal biome exchanges large amounts of carbon (C) and greenhouse gases (GHGs) with the atmosphere and thus significantly affects the global climate. A managed boreal landscape consists of various sinks and sources of carbon dioxide (CO₂), methane (CH₄), and dissolved organic and inorganic carbon (DOC and DIC) across forests, mires, lakes, and streams. Due to the spatial heterogeneity, large uncertainties exist regarding the net landscape carbon balance (NLCB). In this study, we compiled terrestrial and aquatic fluxes of CO₂, CH₄, DOC, DIC, and harvested C obtained from tall‐tower eddy covariance measurements, stream monitoring, and remote sensing of biomass stocks for an entire boreal catchment (~68 km²) in Sweden to estimate the NLCB across the land–water–atmosphere continuum. Our results showed that this managed boreal forest landscape was a net C sink (NLCB = 39 g C m^?2 year^?1) with the landscape–atmosphere CO₂ exchange being the dominant component, followed by the C export via harvest and streams. Accounting for the global warming potential of CH₄, the landscape was a GHG sink of 237 g CO₂‐eq m^?2 year^?1, thus providing a climate‐cooling effect. The CH₄ flux contribution to the annual GHG budget increased from 0.6% during spring to 3.2% during winter. The aquatic C loss was most significant during spring contributing 8% to the annual NLCB. We further found that abiotic controls (e.g., air temperature and incoming radiation) regulated the temporal variability of the NLCB whereas land cover types (e.g., mire vs. forest) and management practices (e.g., clear‐cutting) determined their spatial variability. Our study advocates the need for integrating terrestrial and aquatic fluxes at the landscape scale based on tall‐tower eddy covariance measurements combined with biomass stock and stream monitoring to develop a holistic understanding of the NLCB of managed boreal forest landscapes and to better evaluate their potential for mitigating climate change.     

A high‐resolution approach for the spatiotemporal analysis of forest canopy space using terrestrial laser scanning data

Forest canopies and tree crown structures are of high ecological importance. Measuring canopies and crowns by direct inventory methods is time‐consuming and of limited accuracy. High‐resolution inventory tools, in particular terrestrial laser scanning (TLS), is able to overcome these limitations and obtain three‐dimensional (3D) structural information about the canopy with a very high level of detail. The main objective of this study was to introduce a novel method to analyze spatiotemporal dynamics in canopy occupancy at the individual tree and local neighborhood level using high‐resolution 3D TLS data. For the analyses, a voxel grid approach was applied. The tree crowns were modeled through the combination of two approaches: the encasement of all crown points with a 3D α‐shape, which was then converted into a voxel grid, and the direct voxelization of the crown points. We show that canopy occupancy at individual tree level can be quantified as the crown volume occupied only by the respective tree or shared with neighboring trees. At the local neighborhood level, our method enables the precise determination of the extent of canopy space filling, the identification of tree–tree interactions, and the analysis of complementary space use. Using multitemporal TLS data recordings, this method allows the precise detection and quantification of changes in canopy occupancy through time. The method is applicable to a wide range of investigations in forest ecology research, including the study of tree diversity effects on forest productivity or growing space analyses for optimal tree growth. Due to the high accuracy of this novel method, it facilitates the precise analyses even of highly plastic individual tree crowns and, thus, the realistic representation of forest canopies. Moreover, our voxel grid framework is flexible enough to allow for the inclusion of further biotic and abiotic variables relevant to complex analyses of forest canopy dynamics.     

Micro Flow-Through Thermocycler with Simple Meandering Channel with Symmetric Temperature Zones for Disposable PCR-Devices in Microscope Slide Format

Chip-based flow-through PCR implements the PCR as a continuous process for nucleic acid analytics. The sample is transported in a winding channel through temperature zones required for denaturation, annealing and extension. Main fields of application are the monitoring of continuous processes for rapid identification of contaminants and quality control as well as high throughput screening of cells or microorganisms. A modular arrangement with five heating zones for flow-through PCR is discussed and evaluated. The special heater arrangement allows the implementation of up to 40 cycles on the footprint of a microscope slide, which is placed on top ofa 5 zones heating plate. Liquid/liquid two phase flow of PCR reaction mixture and mineral oil have been applied to create a segmented flow process scheme. In that way, the developed system may provide flow-through PCR as a unit operation for the droplet based microfluidics platform. The single use of disposable devices is commonly preferred due to the sensitivity of the PCR process to contaminations. All-glass microfluidic chips and disposable chip devices, made from polycarbonate as a replication with identically geometry, have been fabricated and tested. For the first time, microchannel geometries with nearly circular profile developed by all-glass technology have been transferred to mass fabrication by injection compression molding. Both devices have been successfully applied for the detection of the tumor suppressor gene p53. Although product yield and selectivity of the amplification process do not depend on the chip material, a well defined, reliable segmented flow regime could only be realized in the all-glass chip.     

Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis

Histone deacetylases have central functions in regulating stress defenses and development in plants. However, the knowledge about the deacetylase functions is largely limited to histones, although these enzymes were found in diverse subcellular compartments. In this study, we determined the proteome‐wide signatures of the RPD3/HDA1 class of histone deacetylases in Arabidopsis. Relative quantification of the changes in the lysine acetylation levels was determined on a proteome‐wide scale after treatment of Arabidopsis leaves with deacetylase inhibitors apicidin and trichostatin A. We identified 91 new acetylated candidate proteins other than histones, which are potential substrates of the RPD3/HDA1‐like histone deacetylases in Arabidopsis, of which at least 30 of these proteins function in nucleic acid binding. Furthermore, our analysis revealed that histone deacetylase 14 (HDA14) is the first organellar‐localized RPD3/HDA1 class protein found to reside in the chloroplasts and that the majority of its protein targets have functions in photosynthesis. Finally, the analysis of HDA14 loss‐of‐function mutants revealed that the activation state of RuBisCO is controlled by lysine acetylation of RuBisCO activase under low‐light conditions.     

Comparison of Bird Communities in Primary vs. Young Secondary Tropical Montane Cloud Forest in Guatemala

Cloud forests in central Guatemala are fragmented and decreasing in area due to slash-and-burn agricultural activities. We studied bird species composition, abundance, guild composition, and site tenacity of a 102 ha plot located in a cloud forest region of the Sierra Yalijux in Guatemala, half of which was primary forest and half young secondary forest (<7-years-old). Of the 100 species present 14 were restricted to the Endemic Bird Area ‘Northern Central American highlands’ (i.e. 66% of a total of 21 endemics). Five of the 100 analysed species, including one of the restricted-range species (Troglodytes rufociliatus), had a significantly different abundance in primary and secondary forests. Theoretical analysis suggests that seven species out of a community comprised of 141 bird species are already extirpated and only three out of the 14 present restricted-range species might survive the current state of deforestation. Insectivores were the dominant guild on the plot in terms of numbers of species, followed by omnivores, frugivores and granivores. However, in terms of individuals, omnivores made up nearly half of the bird individuals in primary forest, but declined by 44% in secondary forest, whereas granivores more than doubled in this habitat type. Numbers of species per guild were not significantly different between habitats, while numbers of individuals per guild were significantly different. In general, individuals per species are significantly different in the two habitats. Results suggest that most of the species that are currently surviving in the remnant forests of the Sierra Yalijux might be fairly well adapted to a range of forest conditions, but that populations of a number of restricted-range species might be small. Even generalists species like the Common Bush Tanager (Chlorospingus ophthalmicus) are less abundant in secondary vegetation than in primary forest of the study plot.     

Insights into the feeding ecology of the Seychelles Black Parrot Coracopsis barklyi using two monitoring approaches

Feeding ecology is an important factor for the survival of a species and knowledge of its parameters is a prerequisite for successful conservation work. In this study we describe the feeding ecology of the endemic Seychelles Black Parrot Coracopsis barklyi on Praslin, Seychelles, the only island on which this parrot is resident. We compared two methods to evaluate feeding choices: incidental observations and feeding walks on 25 transects in all habitat types. Black parrots fed on 46 different species, bringing the total number of known food plants to 53 species. They predominantly consumed endemic and native species (58% of observed feeding bouts), mainly their fruit pulp (in 68% of feeding bouts), followed by buds (15%) and seeds (37%) with occasional observations of leaves, bark and scale insects. The incidental method rendered many more observed bouts than the transect approach and the ratios of consumed species differed between methods but the transect results are regarded as more representative. The incidental method is not suitable for quantitative conclusions but complements the transect method, providing information about rarely occurring feeding events.     

Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: Part I. Experimental observations

An experimental set-up for acquiring metabolite and transient (13)C-labeling data in mammalian cells is presented. An efficient sampling procedure was established for hepatic cells cultured in six-well plates as a monolayer attached to collagen, which allowed simultaneous quenching of metabolism and extraction of the intracellular intermediates of interest. Extracellular concentrations of glucose, amino acids, lactate, pyruvate, and urea were determined by GC-MS procedures and were used for estimation of metabolic uptake and excretion rates. Sensitive LC-MS and GC-MS methods were used to quantify the intracellular intermediates of tricarboxylic acid cycle, glycolysis, and pentose phosphate pathway and for the determination of isotopomer fractions of the respective metabolites. Mass isotopomer fractions were determined in a transient (13)C-labeling experiment using (13)C-labeled glucose as substrate. The absolute amounts of intracellular metabolites were obtained from a non-labeled experiment carried out in exactly the same way as the (13)C-labeling experiment, except that the media contained naturally labeled glucose only. Estimation of intracellular metabolic fluxes from the presented data is addressed in part II of this contribution.