Calibrating aquatic microfossil proxies with regression-tree ensembles : Cross-validation with modern chironomid and diatom data

Peer reviewe

Warm summers and rich biotic communities during N-Hemisphere deglaciation

Detailed studies on fossil remains of plants or animals in glacial lake sediments are rare. As a result, environmental conditions right at the moment of deglaciation of the large N-Hemisphere ice-sheets remain largely unknown. Here we study three deglacial phases of the Fennoscandian Ice Sheet as a unique, repeated element in a long sediment record preserved at Sokli in northern Finland. We summarize extensive multi-proxy data (diatoms, phytoliths, chironomids, pollen, spores, non-pollen palynomorphs, macrofossils, lithology, loss-on-ignition, C/N) obtained on glacial lake sediments dated to the early Holocene (ca. 10 kyr BP), early MIS 3 (ca. 50 kyr BP) and early MIS 5a (ca. 80 kyr BP). In contrast to the common view of an unproductive ice-marginal environment, our study reconstructs rich ecosystems both in the glacial lake and along the shores with forest on recently deglaciated land. Higher than present-day summer temperatures are reconstructed based on a large variety of aquatic taxa. Rich biota developed due to the insolation-induced postglacial warming and high nutrient levels, the latter resulting from erosion of fresh bedrock and sediment, leaching of surface soils, decay of plant material under shallow water conditions, and sudden decreases in lake volume. Aquatic communities responded quickly to deglaciation and warm summers and reflect boreal conditions, in contrast to the terrestrial ecosystem which responded with some delay probably due to time required for slow soil formation processes. Birch forest is reconstructed upon deglaciation of the large LGM ice-sheet and shrub tundra following the probably faster melting smaller MIS 4 and MIS 5b ice-sheets. Our study shows that glacial lake sediments can provide valuable palaeo-environmental data, that aquatic biota and terrestrial vegetation rapidly accommodated to new environmental conditions during deglaciation, and that glacial lake ecosystems, and the carbon stored in their sediments, should be included in earth system modeling.Peer reviewe

Sequencing cell-type-specific transcriptomes with SLAM-ITseq.

Analysis of cell-type-specific transcriptomes is vital for understanding the biology of tissues and organs in the context of multicellular organisms. In this Protocol Extension, we combine a previously developed cell-type-specific metabolic RNA labeling method (thiouracil (TU) tagging) and a pipeline to detect the labeled transcripts by a novel RNA sequencing (RNA-seq) method, SLAMseq (thiol (SH)-linked alkylation for the metabolic sequencing of RNA). By injecting a uracil analog, 4-thiouracil, into transgenic mice that express cell-type-specific uracil phosphoribosyltransferase (UPRT), an enzyme required for 4-thiouracil incorporation into newly synthesized RNA, only cells expressing UPRT synthesize thiol-containing RNA. Total RNA isolated from a tissue of interest is then sequenced with SLAMseq, which introduces thymine to cytosine (T>C) conversions at the sites of the incorporated 4-thiouracil. The resulting sequencing reads are then mapped with the T>C-aware alignment software, SLAM-DUNK, which allows mapping of reads containing T>C mismatches. The number of T>C conversions per transcript is further analyzed to identify which transcripts are synthesized in the UPRT-expressing cells. Thus, our method, SLAM-ITseq (SLAMseq in tissue), enables cell-specific transcriptomics without laborious FACS-based cell sorting or biochemical isolation of the labeled transcripts used in TU tagging. In the murine tissues we assessed previously, this method identified ~5,000 genes that are expressed in a cell type of interest from the total RNA pool from the tissue. Any laboratory with access to a high-throughput sequencer and high-power computing can adapt this protocol with ease, and the entire pipeline can be completed in <5 d.This work was supported by grants from Cancer Research UK (C13474/A18583, C6946/A14492) and the Wellcome Trust (104640/Z/14/Z, 092096/Z/10/Z) to E.A.M.; and a grant from the European Research Council (ERC-StG-338252 miRLIFE) to S.L.A. The IMP is generously supported by Boehringer Ingelheim. W.M. was supported by the Nakajima Foundation and St John’s College Benefactors’ Scholarship. K.G. was supported by a Swiss National Foundation postdoc mobility fellowship

ADVANCED CUTTINGS TRANSPORT STUDY

This is the second quarterly progress report for Year-4 of the ACTS Project. It includes a review of progress made in: (1) Flow Loop construction and development and (2) research tasks during the period of time between October 1, 2002 and December 30, 2002. This report presents a review of progress on the following specific tasks. (a) Design and development of an Advanced Cuttings Transport Facility Task 3: Addition of a Cuttings Injection/Separation System, Task 4: Addition of a Pipe Rotation System. (b) New research project (Task 9b): ''Development of a Foam Generator/Viscometer for Elevated Pressure and Elevated Temperature (EPET) Conditions''. (d) Research project (Task 10): ''Study of Cuttings Transport with Aerated Mud Under Elevated Pressure and Temperature Conditions''. (e) Research on three instrumentation tasks to measure: Cuttings concentration and distribution in a flowing slurry (Task 11), Foam texture while transporting cuttings. (Task 12), and Viscosity of Foam under EPET (Task 9b). (f) New Research project (Task 13): ''Study of Cuttings Transport with Foam under Elevated Pressure and Temperature Conditions''. (g) Development of a Safety program for the ACTS Flow Loop. Progress on a comprehensive safety review of all flow-loop components and operational procedures. (Task 1S). (h) Activities towards technology transfer and developing contacts with Petroleum and service company members, and increasing the number of JIP members

ADVANCED CUTTINGS TRANSPORT STUDY

This is the first quarterly progress report for Year-4 of the ACTS Project. It includes a review of progress made in: (1) Flow Loop construction and development and (2) research tasks during the period of time between July 1, 2002 and Sept. 30, 2002. This report presents a review of progress on the following specific tasks: (a) Design and development of an Advanced Cuttings Transport Facility Task 3: Addition of a Cuttings Injection/Separation System, Task 4: Addition of a Pipe Rotation System, (b) New Research project (Task 9b): ''Development of a Foam Generator/Viscometer for Elevated Pressure and Elevated Temperature (EPET) Conditions'', (d) Research project (Task 10): ''Study of Cuttings Transport with Aerated Mud Under Elevated Pressure and Temperature Conditions'', (e) Research on three instrumentation tasks to measure: Cuttings concentration and distribution in a flowing slurry (Task 11), Foam texture while transporting cuttings (Task 12), Viscosity of Foam under EPET (Task 9b). (f) Development of a Safety program for the ACTS Flow Loop. Progress on a comprehensive safety review of all flow-loop components and operational procedures. (Task 1S). (g) Activities towards technology transfer and developing contacts with Petroleum and service company members, and increasing the number of JIP members

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

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 8500 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'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