Factors affecting consistency and accuracy in identifying modern macroperforate planktonic foraminifera

Planktonic foraminifera are widely used in biostratigraphic, palaeoceanographic and evolutionary studies, but the strength of many study conclusions could be weakened if taxonomic identifications are not reproducible by different workers. In this study, to assess the relative importance of a range of possible reasons for among-worker disagreement in identification, 100 specimens of 26 species of macroperforate planktonic foraminifera were selected from a core-top site in the subtropical Pacific Ocean. Twenty-three scientists at different career stages – including some with only a few days experience of planktonic foraminifera – were asked to identify each specimen to species level, and to indicate their confidence in each identification. The participants were provided with a species list and had access to additional reference materials. We use generalised linear mixed-effects models to test the relevance of three sets of factors in identification accuracy: participant-level characteristics (including experience), species-level characteristics (including a participant’s knowledge of the species) and specimen-level characteristics (size, confidence in identification). The 19 less experienced scientists achieve a median accuracy of 57 %, which rises to 75 % for specimens they are confident in. For the 4 most experienced participants, overall accuracy is 79 %, rising to 93 % when they are confident. To obtain maximum comparability and ease of analysis, everyone used a standard microscope with only 35× magnification, and each specimen was studied in isolation. Consequently, these data provide a lower limit for an estimate of consistency. Importantly, participants could largely predict whether their identifications were correct or incorrect: their own assessments of specimen-level confidence and of their previous knowledge of species concepts were the strongest predictors of accuracy

Boundary processes and neodymium cycling along the Pacific margin of West Antarctica

Neodymium (Nd) isotopes have been utilized as a tracer of water mass source in the modern ocean and in palaeoceanographic studies, though the oceanic cycling of Nd is not yet fully constrained. Recent studies have highlighted the importance of processes that occur near the seawater – sediment interface in altering the Nd isotopic composition of bottom waters. The two major observed processes “boundary exchange” and “benthic flux” have been suggested as playing an important role in setting water mass compositions, however, more studies are needed to constrain their chemical mechanism and the extent to which these processes set the composition of deep waters. The Antarctic continental margin is an important place to study these processes because Antarctic-sourced waters dominate the Southern Ocean and ventilate the global deep ocean. This study is the first to measure and compare seawater, porewater and sediment data from along the margin of Antarctica to examine the nature of potential boundary processes. We show that a process similar to boundary exchange seems to be occurring within porewaters, modifying porewater chemistry by shifting its Nd isotopic ratios to more radiogenic values without significantly increasing the concentration of dissolved Nd. We hypothesize that this shift results from partial dissolution of radiogenic detrital particles, such as smectite, amphibole and/or volcanic glass, while re-scavenging maintains low Nd concentrations. We infer the existence of benthic flux of porewaters to deep waters by examining chemical gradients in porewaters and show that it is much lower on the Antarctic Margin compared to other studies. Benthic flux appears to be slightly enhanced along the Antarctic Peninsula than in the Bellingshausen Sea due to partial degradation of organic matter and associated dissolution of Fe-Mn oxyhydroxides. Taken together, boundary processes do not significantly change the Nd isotopic composition of Antarctic margin seawater because while the porewaters have an altered Nd isotopic composition the Nd concentration of these porewaters is low compared to other settings

Integrating Suspended Sediment Flux in Large Alluvial River Channels: Application of a Synoptic Rouse‐Based Model to the Irrawaddy and Salween Rivers

A large portion of freshwater and sediment is exported to the ocean by a small number of major rivers. Many of these megarivers are subject to substantial anthropogenic pressures, which are having a major impact on water and sediment delivery to deltaic ecosystems. Due to hydrodynamic sorting, sediment grain size and composition vary strongly with depth and across the channel in large rivers, complicating flux quantification. To account for this, we modified a semi‐empirical Rouse model, synoptically predicting sediment concentration, grain‐size distribution, and organic carbon (%OC) concentration with depth and across the river channel. Using suspended sediment depth samples and flow velocity data, we applied this model to calculate sediment fluxes of the Irrawaddy (Ayeyarwady) and the Salween (Thanlwin), the last two free‐flowing megarivers in Southeast Asia. Deriving sediment‐discharge rating curves, we calculated an annual sediment flux of urn:x-wiley:jgrf:media:jgrf21236:jgrf21236-math-0001 Mt/year for the Irrawaddy and urn:x-wiley:jgrf:media:jgrf21236:jgrf21236-math-0002 Mt/year for the Salween, together exporting 46% as much sediment as the Ganges‐Brahmaputra system. The mean flux‐weighted sediment exported by the Irrawaddy is significantly coarser (D84 = 193 ± 13 μm) and OC‐poorer (0.29 ± 0.08 wt%) compared to the Salween (112 ± 27 μm and 0.59 ± 0.16 wt%, respectively). Both rivers export similar amounts of particulate organic carbon, with a total of urn:x-wiley:jgrf:media:jgrf21236:jgrf21236-math-0003 Mt C/year, 53% as much as the Ganges‐Brahmaputra. These results underline the global significance of the Irrawaddy and Salween rivers and warrant continued monitoring of their sediment flux, given the increasing anthropogenic pressures on these river basins

Quantification of CO2 removal in a large-scale enhanced weathering field trial on an oil palm plantation in Sabah, Malaysia

Modeling studies show that large-scale deployment of enhanced rock weathering on croplands has the potential to reduce levels of atmospheric carbon dioxide by the end of the century. There is, however, a pressing need to verify model predictions through long-term field trials. Here we report results from the first 3 years of an ongoing enhanced weathering field trial, carried out on an oil palm plantation in Sabah, Malaysia. Crushed silicate rock was applied to three hydrologically isolated catchments, and three adjacent (paired) reference catchments were left untreated. The drawdown of atmospheric CO2 was quantified via the export of alkalinity in stream waters and changes in soil carbonate content. The amended and reference catchments were found to have a similar extent of CO2 drawdown via alkalinity export [respectively, 3.8 ± 0.8 (1 SD) and 3.7 ± 0.6 (1 SD) tCO2 ha−1] when all catchments were averaged over the study period (October 2018 to July 2021). However, differences were observed between the different catchment pairs (plots): two of the plots displayed a similar extent of CO2 removal for both the amended and reference catchments, but the third amended catchment had a higher extent of CO2 removal of ~1 tCO2 ha−1 relative to its adjacent reference catchment. The difference in CO2 removal rates determined for this plot can likely be attributed to increased weathering of silicate minerals in the amended catchment. Soil carbonate concentrations were on average < 0.2 wt% CaCO3, but we report a small increase of ~0.03 wt% CaCO3 in the top 30 cm of soil in the amended soils relative to the reference catchments. The magnitude of CO2 drawdown via alkalinity export determined for these agricultural catchments is around an order of magnitude higher than in natural forested catchments in Sabah and similar to that of basaltic catchments. We show that these high weathering rates are primarily driven by weathering of carbonate fertilizers. The data presented from this field trial provide vital contextual information on the real-world efficacy and practicalities associated with the implementation of enhanced weathering for atmospheric CO2 removal that will help to inform further trials as well as wider-scale deployment

Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results

The quality of gene expression microarray data has improved dramatically since the first arrays were introduced in the late 1990s. However, the reproducibility of data generated at multiple laboratory sites remains a matter of concern, especially for scientists who are attempting to combine and analyze data from public repositories. We have carried out a study in which a common set of RNA samples was assayed five times in four different laboratories using Affymetrix GeneChip arrays. We observed dramatic differences in the results across laboratories and identified batch effects in array processing as one of the primary causes for these differences. When batch processing of samples is confounded with experimental factors of interest it is not possible to separate their effects, and lists of differentially expressed genes may include many artifacts. This study demonstrates the substantial impact of sample processing on microarray analysis results and underscores the need for randomization in the laboratory as a means to avoid confounding of biological factors with procedural effects

Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results

The quality of gene expression microarray data has improved dramatically since the first arrays were introduced in the late 1990s. However, the reproducibility of data generated at multiple laboratory sites remains a matter of concern, especially for scientists who are attempting to combine and analyze data from public repositories. We have carried out a study in which a common set of RNA samples was assayed five times in four different laboratories using Affymetrix GeneChip arrays. We observed dramatic differences in the results across laboratories and identified batch effects in array processing as one of the primary causes for these differences. When batch processing of samples is confounded with experimental factors of interest it is not possible to separate their effects, and lists of differentially expressed genes may include many artifacts. This study demonstrates the substantial impact of sample processing on microarray analysis results and underscores the need for randomization in the laboratory as a means to avoid confounding of biological factors with procedural effects

Quantification of CO2 removal in a large-scale enhanced weathering field trial on an oil palm plantation in Sabah, Malaysia

Modeling studies show that large-scale deployment of enhanced rock weathering on croplands has the potential to reduce levels of atmospheric carbon dioxide by the end of the century. There is, however, a pressing need to verify model predictions through long-term field trials. Here we report results from the first 3 years of an ongoing enhanced weathering field trial, carried out on an oil palm plantation in Sabah, Malaysia. Crushed silicate rock was applied to three hydrologically isolated catchments, and three adjacent (paired) reference catchments were left untreated. The drawdown of atmospheric CO2 was quantified via the export of alkalinity in stream waters and changes in soil carbonate content. The amended and reference catchments were found to have a similar extent of CO2 drawdown via alkalinity export [respectively, 3.8 ± 0.8 (1 SD) and 3.7 ± 0.6 (1 SD) tCO2 ha−1] when all catchments were averaged over the study period (October 2018 to July 2021). However, differences were observed between the different catchment pairs (plots): two of the plots displayed a similar extent of CO2 removal for both the amended and reference catchments, but the third amended catchment had a higher extent of CO2 removal of ~1 tCO2 ha−1 relative to its adjacent reference catchment. The difference in CO2 removal rates determined for this plot can likely be attributed to increased weathering of silicate minerals in the amended catchment. Soil carbonate concentrations were on average < 0.2 wt% CaCO3, but we report a small increase of ~0.03 wt% CaCO3 in the top 30 cm of soil in the amended soils relative to the reference catchments. The magnitude of CO2 drawdown via alkalinity export determined for these agricultural catchments is around an order of magnitude higher than in natural forested catchments in Sabah and similar to that of basaltic catchments. We show that these high weathering rates are primarily driven by weathering of carbonate fertilizers. The data presented from this field trial provide vital contextual information on the real-world efficacy and practicalities associated with the implementation of enhanced weathering for atmospheric CO2 removal that will help to inform further trials as well as wider-scale deployment

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Global silicate weathering flux overestimated because of sediment–water cation exchange

Rivers carry the dissolved and solid products of silicate mineral weathering, a process that removes CO2 from the atmosphere and provides a key negative climate feedback over geological timescales. Here we show that in some river systems, a reactive exchange pool on river suspended particulate matter, bonded weakly to mineral surfaces, increases the mobile cation flux by 50%. The chemistry of both river waters and the exchange pool demonstrate exchange equilibrium, confirmed by Sr isotopes. Global silicate weathering fluxes are calculated based on riverine dissolved sodium (Na+) from silicate minerals. The large exchange pool supplies Na+ of non- silicate origin to the dissolved load, especially in catchments with widespread marine sediments, or where rocks have equilibrated with saline basement fluids. We quantify this by comparing the riverine sediment exchange pool and river water chemistry. In some basins, cation exchange could account for the majority of sodium in the river water, significantly reducing estimates of silicate weathering. At a global scale, we demonstrate that silicate weathering fluxes are over-estimated by 12-28%. This over-estimation is greatest in regions of high erosion and high sediment loads where the negative climate feedback has a maximum sensitivity to chemical weathering reactions. In the context of other recent findings that reduce the net CO2 consumption through chemical weathering, the magnitude of the continental silicate weathering fluxes and its implications for solid Earth CO2 degassing fluxes needs to be further investigated

Endoreplication Controls Cell Fate Maintenance

Cell-fate specification is typically thought to precede and determine cell-cycle regulation during differentiation. Here we show that endoreplication, also known as endoreduplication, a specialized cell-cycle variant often associated with cell differentiation but also frequently occurring in malignant cells, plays a role in maintaining cell fate. For our study we have used Arabidopsis trichomes as a model system and have manipulated endoreplication levels via mutants of cell-cycle regulators and overexpression of cell-cycle inhibitors under a trichome-specific promoter. Strikingly, a reduction of endoreplication resulted in reduced trichome numbers and caused trichomes to lose their identity. Live observations of young Arabidopsis leaves revealed that dedifferentiating trichomes re-entered mitosis and were re-integrated into the epidermal pavement-cell layer, acquiring the typical characteristics of the surrounding epidermal cells. Conversely, when we promoted endoreplication in glabrous patterning mutants, trichome fate could be restored, demonstrating that endoreplication is an important determinant of cell identity. Our data lead to a new model of cell-fate control and tissue integrity during development by revealing a cell-fate quality control system at the tissue level