The treasure vault can be opened: large-scale genome skimming works well using herbarium and silica gel dried material

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications

Global maps of soil temperature.

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km <sup>2</sup> resolution for 0-5 and 5-15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km <sup>2</sup> pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (-0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world\u27s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Past surface conditions and speleogenesis as inferred from cave sediments in the Great Cave of Șălitrari Mountain (SW Romania)

Abstract In one of the passages in the Great Cave of Șălitrari Mountain the floor is completely covered by an alluvial deposit at least 6 m in thickness, ranging from boulders, and cobbles, to sand and clay, topped by a layer of dry bat guano. Sediment and mineral samples collected from six profiles underwent broad analyses to determine their petrological and mineralogical makeup, grain-size distribution, and paleoclimatic significance. The complicated facies alternation suggests frequent changes in the former stream’s hydrological parameters, with frequent flooding, leading to the hypothesis that the climate was somewhat wetter than today. Both the mineralogical composition of the sediment (ranging from quartz, mica, gypsum, phosphates, and calcite to garnet, zircon, titanite, olivine, serpentine, tourmaline, sphalerite, pyrite/chalcopyrite, and feldspars) and the petrological composition of the larger clasts (limestone, sandstone, mudstone, granitoids, serpentinite, amphibolite, diorite, gneiss, quartzite, microconglomerate, and schist) ascribe the potential source rocks to an area with contrasting lithologies, such as amphibolites, felsic and basic metaigneous, and metasedimentary rocks, mixed with a variety of detritic rocks. These rock types are not entirely comprised by the catchment area of the modern Presacina Brook, thus implying that due either to hydrological conditions, or to changes in the base level caused by river down cutting or active tectonics, the former source area was much more extensive. Based on morphological and sedimentological criteria, the cave started under pipe-full flow conditions, and further evolved during a prolonged and complex vadose phase. Evidence to support the existence of hypogene conditions is also present. Once the underground stream left the cave and most of the sediment was removed, speleothem precipitation was initiated. In this contribution we put forward evidence that argue for an extra-basinal origin of some of the alluvial sediments, an uncommon fact documented in few cave environments so far

The Romanian Grassland Database (RGD): historical background, current status and future perspectives

This report describes the Romanian Grassland Database (RGD), registered under EU-RO-008 in the Global Index of Vegetation-Plot Databases (GIVD). This collaborative initiative aims at collecting all available vegetation-plot data (relevés) of grasslands and other open habitats from the territory of Romania and providing them for science, nationally and internationally, e.g. via the European Vegetation Archive (EVA) and the global database “sPlot”. It mainly contains data from wet, mesic, dry, saline, alpine and rocky grasslands, but also some other vegetation types like heathlands, mires, ruderal, segetal, aquatic and cryptogam-dominated vegetation. The currently 21,685 relevés have mainly been digitised from literature sources (90%), while the rest comes from individual unpublished sources (10%). We report on the background and history of RGD, explain its “Data Property and Governance Rules” under which data are contributed and retrieved and outline how RGD can contribute to research in the fields of vegetation ecology, macroecology and conservation

ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications

International audienc

Early stage litter decomposition across biomes

peer reviewedThrough litter decomposition enormous amounts of carbon is emitted to the atmosphere. Numerous large-scale decomposition experiments have been conducted focusing on this fundamental soil process in order to understand the controls on the terrestrial carbon transfer to the atmosphere. However, previous studies were mostly based on site-specific litter and methodologies, adding major uncertainty to syntheses, comparisons and metaanalyses across different experiments and sites. In the TeaComposition initiative, the potential litter decomposition is investigated by using standardized substrates (Rooibos and Green tea) for comparison of litter mass loss at 336 sites (ranging from −9 to +26 °C MAT and from 60 to 3113mm MAP) across different ecosystems. In this study we tested the effect of climate (temperature and moisture), litter type and land-use on early stage decomposition (3 months) across nine biomes. We show that litter quality was the predominant controlling factor in early stage litter decomposition, which explained about 65% of the variability in litter decomposition at a global scale. The effect of climate, on the other hand, was not litter specific and explained b0.5% of the variation for Green tea and 5% for Rooibos tea, and was of significance only under unfavorable decomposition conditions (i.e. xeric versus mesic environments).When the data were aggregated at the biome scale, climate played a significant role on decomposition of both litter types (explaining 64% of the variation for Green tea and 72% for Rooibos tea).No significant effect of land-use on early stage litter decompositionwas notedwithin the temperate biome. Our results indicate that multiple drivers are affecting early stage littermass loss with litter quality being dominant. In order to be able to quantify the relative importance of the different drivers over time, long-term studies combined with experimental trials are needed