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Isotopes in diatoms are increasingly used in palaeoenvironmental studies in both lacustrine and marine settings, enabling the reconstruction of a range of variables including temperature, precipitation, salinity, glacial discharge, carbon dynamics and biogeochemical cycling. This protocol details an optimised methodology for extracting diatoms for isotope analysis from sediment samples, using a range of chemical and density separation techniques that minimise sample loss and avoids the need for expensive equipment. Whilst designed for the extraction of diatoms for oxygen, silicon and carbon isotope analysis, additional stages are outlined for the analysis of other isotopes that are of increasing interest to the palaeo community (e.g., boron and zinc). The protocol also includes procedures for assessing sample purity, to ensure that analysed samples produce robust palaeoenvironmental reconstruction. Overall, the method aims to improve the quality of palaeoenvironmental research derived from isotopes in diatoms by maximising sample purity and the efficiency of the extraction process.

Lake Baikal has been experiencing limnological changes from recent atmospheric warming since the 1950s, with rising lake water temperatures, reduced ice cover duration and reduced lake surface-water mixing due to stronger thermal stratification. This study uses lake sediment cores to reconstruct recent changes (c. past 20 years) in Lake Baikal's pelagic diatom communities relative to previous 20th century diatom assemblage records collected in 1993 and 1994 at the same locations in the lake. Recent changes documented within the core-top diatom records agree with predictions of diatom responses to warming at Lake Baikal. Sediments in the south basin of the lake exhibit clear temporal changes, with the most rapid occurring in the 1990's with shifts towards higher abundances of the cosmopolitan Synedra acus and a decline in endemic species, mainly Cyclotella minuta and Stephanodiscus meyerii and to a lesser extent Aulacoseira baicalensis and Aulacoseira skvortzowii. The north basin, in contrast, shows no evidence of recent diatom response to lake warming despite marked declines in north basin ice cover in recent decades. This study also shows no diatom-inferred evidence of eutrophication from deep water sediments. However, due to the localised impacts seen in areas of Lake Baikal's shoreline from nutrient pollution derived from inadequate sewage treatment, urgent action is vital to prevent anthropogenic pollution extending into the open waters.

The high-latitude oceans are key areas of carbon and heat exchange between the atmosphere and the ocean. As such, they are a focus of both modern oceanographic and palaeoclimate research. However, most palaeoclimate proxies that could provide a long-term perspective are based on calcareous organisms, such as foraminifera, that are scarce or entirely absent in deep-sea sediments south of 50∘ S in the Southern Ocean and north of 40∘ N in the North Pacific. As a result, proxies need to be developed for the opal-based organisms (e.g. diatoms) found at these high latitudes, which dominate the biogenic sediments recovered from these regions. Here we present a method for the analysis of the boron (B) content and isotopic composition (δ11B) of diatom opal. We apply it for the first time to evaluate the relationship between seawater pH, δ11B and B concentration ([B]) in the frustules of the diatom Thalassiosira weissflogii, cultured across a range of carbon dioxide partial pressure (pCO2) and pH values. In agreement with existing data, we find that the [B] of the cultured diatom frustules increases with increasing pH (Mejía et al., 2013). δ11B shows a relatively well defined negative trend with increasing pH, completely distinct from any other biomineral previously measured. This relationship not only has implications for the magnitude of the isotopic fractionation that occurs during boron incorporation into opal, but also allows us to explore the potential of the boron-based proxies for palaeo-pH and palaeo-CO2 reconstruction in high-latitude marine sediments that have, up until now, eluded study due to the lack of suitable carbonate material.

In the context of gradual Cenozoic cooling, the timing of the onset of significant Northern Hemisphere glaciation 2.7 million years ago is consistent with Milankovitch's orbital theory, which posited that ice sheets grow when polar summertime insolation and temperature are low. However, the role of moisture supply in the initiation of large Northern Hemisphere ice sheets has remained unclear. The subarctic Pacific Ocean represents a significant source of water vapour to boreal North America, but it has been largely overlooked in efforts to explain Northern Hemisphere glaciation. Here we present alkenone unsaturation ratios and diatom oxygen isotope ratios from a sediment core in the western subarctic Pacific Ocean, indicating that 2.7 million years ago late-summer sea surface temperatures in this ocean region rose in response to an increase in stratification. At the same time, winter sea surface temperatures cooled, winter floating ice became more abundant and global climate descended into glacial conditions. We suggest that the observed summer warming extended into the autumn, providing water vapour to northern North America, where it precipitated and accumulated as snow, and thus allowed the initiation of Northern Hemisphere glaciation. Cool effects of warmth The onset of glaciation in the Northern Hemisphere during the Late Cenozoic ice age, 2.7 million years ago, was one of the most dramatic climate shifts on record, but its causes are not yet clear. Changes in North Atlantic circulation that were once thought to be a factor are now known to have occurred long before the glaciation. New palaeoceanographic data, combined with the results of a climate model, indicate that changes in the subarctic North Pacific may have driven this climate transition. A stronger seasonality in the North Pacific, the major source of atmospheric water vapour upstream of the North American continent, seems to have initiated Northern Hemisphere glaciation by inducing warming in late summer and autumn thus increasing the amount of water available to fall as snow.

The causes for rising temperatures along the Antarctic Peninsula over the past few thousand years have been debated. Analyses of diatom geochemistry and assemblage ecology from Palmer Deep off the western margin of the Antarctic Peninsula reveal that atmospheric processes have dominated glacial ice discharge during the late Holocene. The causes for rising temperatures along the Antarctic Peninsula during the late Holocene have been debated, particularly in light of instrumental records of warming over the past decades 1 . Suggested mechanisms range from upwelling of warm deep waters onto the continental shelf in response to variations in the westerly winds 2 , to an influence of El Niño–Southern Oscillation on sea surface temperatures 3 . Here, we present a record of Holocene glacial ice discharge, derived from the oxygen isotope composition of marine diatoms from Palmer Deep along the west Antarctic Peninsula continental margin. We assess atmospheric versus oceanic influences on glacial discharge at this location, using analyses of diatom geochemistry to reconstruct atmospherically forced glacial ice discharge and diatom assemblage 4 ecology to investigate the oceanic environment. We show that two processes of atmospheric forcing—an increasing occurrence of La Niña events 5 and rising levels of summer insolation—had a stronger influence during the late Holocene than oceanic processes driven by southern westerly winds and upwelling of upper Circumpolar Deepwater. Given that the evolution of El Niño–Southern Oscillation under global warming is uncertain 6 , its future impacts on the climatically sensitive system of the Antarctic Peninsula Ice Sheet remain to be established.

[This corrects the article DOI: 10.1371/journal.pone.0208765.].

The Mid-Pleistocene Transition (MPT) is characterised by cooling and lengthening glacial cycles from 600–1200 ka, thought to be driven by reductions in glacial CO 2 in particular from ~900 ka onwards. Reduced high latitude upwelling, a process that retains CO 2 within the deep ocean over glacials, could have aided drawdown but has so far not been constrained in either hemisphere over the MPT. Here, we find that reduced nutrient upwelling in the Bering Sea, and North Pacific Intermediate Water expansion, coincided with the MPT and became more persistent at ~900 ka. We propose reduced upwelling was controlled by expanding sea ice and North Pacific Intermediate Water formation, which may have been enhanced by closure of the Bering Strait. The regional extent of North Pacific Intermediate Water across the subarctic northwest Pacific would have contributed to lower atmospheric CO 2 and global cooling during the MPT. The causes of Mid-Pleistocene Transition global cooling 1 million years ago are still unknown. Here, the authors find the subarctic North Pacific became stratified during these glaciations due to closure of the Bering Strait, which would have removed CO 2 from the atmosphere and caused global cooling.

Radiolarian silicon isotopes (δ30Sirad) hold significant potential as a proxy for constraining past silicon cycling in seawater. However, the extent to which δ30Sirad signatures in sediments accurately represent the isotopic signals of the overlying water column remains unclear, particularly under the influence of radiolarian shell dissolution during sinking and burial in the sediment record. This study presents the first comparative analysis of δ30Sirad compositions and the radiolarian assemblage community using water column and surface sediment samples collected from the South China Sea (SCS). The results indicate that δ30Sirad values range from 1.56 ‰–1.83 ‰ (mean = 1.74 ‰) in the water column and from 1.61 ‰–1.85 ‰ (mean = 1.73 ‰) in surface sediments, with the fractionation factor for δ30Sirad varying from −0.33 ‰ to −0.92 ‰ (mean = −0.58 ‰). δ30Sirad signatures in the water column are primarily contributed to by radiolarians from the 0–100 m water depth layer. No significant discrepancies in δ30Sirad values were observed between plankton and sediment samples at each sampling station, as evidenced by the paired t test (p = 0.75), implying that dissolution has a minimal impact on δ30Sirad during the transfer of radiolarian shells to the sediment record. This finding may be enhanced by the dominance of more dissolution-resistant Spumellaria and Nassellaria taxa (> 99 % relative abundance) within the radiolarian community, coupled with the scarcity or absence of the readily dissolvable radiolarian taxa in the analysed samples. This study demonstrates the faithful preservation of the δ30Sirad signature and its potential for studying past changes in the marine silicon cycle.

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are membrane‐spanning lipids synthesized by bacteria in numerous substrates. The degree of methylation of the five methyl brGDGTs in both soils and lake sediments, described by the MBT′5Me index, is empirically related to surface atmospheric temperature. This relationship in lakes is generally assumed to reflect lake surface temperatures captured by brGDGT production in the water column and exported to lake sediments, and the MBT′5Me index has been applied to brGDGTs in lake sediment successions to reconstruct changes in temperature through time. We analyzed the relationship between MBT′5Me and the isomerization of brGDGTs (IR6Me) in globally distributed surficial lake sediments and demonstrated that the relationship, and calibrations, of MBT′5Me and temperature in middle and high latitude lakes are sensitive to incompletely understood factors related to IR6Me. IR6Me does not appear to track a non‐thermal influence of brGDGT methylation in tropical lakes, but this could change as the data set is expanded. We address ongoing challenges in the application of the MBT′5Me paleothermometer in middle and high latitude lakes with new MBT′5Me‐temperature calibrations based on grouping lakes by IR6Me. We demonstrate how IR6Me can distinguish samples with a significant non‐thermal influence on MBT′5Me by targeting anomalously warm temperatures during the Last Glacial Maximum from newly analyzed piston and gravity core samples from Lake Baikal, Russia. Plain Language Summary Branched glycerol dialkyl glycerol tetraethers are fats used by bacteria to build their cell walls. Bacteria build their cell walls with different kinds of brGDGTs in response to ambient temperature. BrGDGTs are often preserved in lake sediments, making them a useful tool for reconstructing past climate. While working on samples from Lake Baikal, Russia, we noticed unexpectedly warm temperatures during the last ice age estimated from brGDGTs. These warm temperatures coincided with unusually high relative amounts of 6‐methyl brGDGTs. This observation spurred the analysis of a large data set of published globally distributed lake brGDGT data. We found that samples from middle and high latitude lakes with relatively more 6‐methyl brGDGTs tended to have higher than expected brGDGT‐estimated temperatures. We use our findings to refine the equations that relate brGDGT distributions to surface air temperature in middle and high latitude lake sediments. Key Points A non‐thermal effect on brGDGT paleotemperature estimates in lakes is identified by the isomer ratio IR6Me The calibration of MBT′5Me to temperature in middle and high latitude lakes is strengthened if samples with IR6Me > 0.4 are excluded IR6Me does not appear to identify non‐thermal effects on tropical lake samples, but this could change as the data set is expanded

Late Miocene climate evolution provides an opportunity to assess Earth’s climate sensitivity to carbon cycle perturbation under warmer-than-modern conditions. Despite its relevance for understanding the climate system, the driving mechanisms underlying profound climate and carbon cycle changes – including the enigmatic Late Miocene cooling from 7 to 5.4 million years ago – remain unclear. Here, we present magnetic and geochemical paleoceanographic proxies from a hydrogenetic ferromanganese crust retrieved in the northwestern Pacific Ocean. Our results indicate a striking 50% surge in deep ocean phosphorus concentrations occurred 7 – 4 million years ago, synchronous with enhanced deep ocean oxygen consumption. Employing a global biogeochemical model, we show that increased continental phosphorus weathering, without a concurrent rise in silicate weathering, contributed to the decline in atmospheric CO 2 and associated cooling over the Late Miocene. This suggests a prominent decoupling of phosphorus and silicate weathering during a major carbon cycling event over the last 10 million years. West Pacific ferromanganese crust provides new insights to Late Miocene Cooling associated with the increased continental phosphorus weathering.