We investigated the variability and phase relationship of two annually to subdecadally resolved sea surface temperature (SST) proxy records from the Mediterranean sapropel S5 deposited during the Last Interglacial. We compared our recently published alkenone-based SST record, considered to reliably represent surface temperature, with a newly generated record of archeal glycerol dialkyl glycerol tetraether (GDGTs). GDGT-based SST reconstruction in the Mediterranean Sea has been suggested to be affected by other parameters besides SST, and presumably represents subsurface temperature. Our investigation unveils notable differences between the two proxies; throughout most of the record, SST reconstructions derived from GDGTs and alkenones exhibit an anti-phase relationship in the multicentennial time band. This suggests that during sapropel deposition, centennial-scale alterations in the upper-ocean temperature gradient, plausibly due to water column stratification, influenced both compound classes. While we expect a direct, thermal driver for the alkenone ratio, the effect on the GDGT-based SST signal might have been mediated by ammonia oxidation rates that were positively correlated with changes in SST. A multidecadal comparison between GDGT- and alkenone-based SSTs reveals distinct behaviors of the two proxies under different oceanographic conditions, indicating that changing oceanographic and environmental dynamics significantly impacted short-term proxy variability. We demonstrate that during sapropel deposition in the Last Interglacial oceanographic, environmental and ecological factors played a crucial role in modulating the GDGT cyclization on both multidecadal and multicentennial time-scales, suggesting strong non-thermal forcing on GDGT-based SST reconstruction during Mediterranean sapropel deposition.

Marine sediments are a large reservoir of recalcitrant organic matter and host microbes at subsurface depths exceeding 2.4 kilometers and temperatures up to 120°C, yet the mechanisms supplying bioavailable substrates remain unclear. Here, we investigated 7.8-million-year-old sediment from IODP Site C0012 off the Nankai Trough, Japan, through incubations at 20°, 35°, 55°, and 85°C to simulate burial temperatures. Using 3D fluorescence spectroscopy and ultrahigh-resolution mass spectrometry, we tracked changes in dissolved organic matter (DOM). At 35°C, humic-like DOM was released alongside metal ions, exhibiting low bioavailability. At 55°C, abiotic decomposition of humic compounds generated smaller, more bioavailable DOM, promoting fermentation. At 85°C, large nitrogen-containing humic compounds decomposed, producing labile H2 and acetate mainly through abiotic processes, bypassing fermentation. Our findings show how abiotic thermal processes activate the refractory organic matter pool, advancing our understanding of long-term carbon sequestration in marine sediments and its implications for global carbon cycling.

For millions of years, the Mediterranean Sea has regularly experienced episodes of disrupted thermohaline circulation and increased primary productivity that resulted in a largely anoxic water column. These anoxic episodes are typically related to a more humid climate over Northern Africa and are captured in the sedimentary record as organic-rich sapropel layers. Given the excellent preservation of organic molecules in them, sapropels are extraordinary archives for the marine and continental ecosystems associated with the unique conditions that prevailed during their formation. We applied metagenomic environmental DNA (eDNA) analysis to recent sapropels (< 175 kyr) from the Eastern Mediterranean, including Sapropel S5 deposited during the Last Interglacial, and benchmarked obtained results with high resolution geochemical and molecular biomarker records. Ancient eDNA analysis enables reconstructions across all domains of life, including those components of the ecosystem that do not leave fossils or are not recorded in the fossil record. In the case of Mediterranean sapropels, this approach reveals information on both terrestrial and marine ecosystems. We provide detailed insight into vegetation changes in the Nile River Basin during the different, climatically diverse episodes of sapropel deposition. On the marine side, we reveal how water column ecology and major elemental cycles adapted to this massive ecosystem overhaul.

Past changes in the input/output, and internal cycling, of bioavailable nitrogen (N) in marine and lacustrine environments can be reconstructed by analyzing the N isotopic composition (delta N-15) of organic matter in the sedimentary record. To verify, and eliminate, potential biases of bulk sedimentary delta N-15 (delta N-15(bulk)) signatures by diagenetic alteration and external N inputs, we applied, for the first time, the diatom-bound N isotope (delta N-15(db)) paleo-proxy to lake sediments. By comparing delta N-15(bulk) and delta N-15(db) in a sedimentary record from eutrophic Lake Lugano (Switzerland), we demonstrate that changing redox conditions influence the degree of N-isotopic alteration of the bulk sediment, emphasizing the need for caution when interpreting delta N-15(bulk) in paleolimnological studies. Furthermore, in combining delta N-15(db) measurements with X-ray fluorescence scanning and state-of-the-art molecular biomarker analyses, we reconstruct nutrient cycling and paleoenvironmental conditions in the lake over the past similar to 125 yr. Coeval with the period of severe eutrophication in Lake Lugano in the 1960s, our proxy data indicate that export production, delta N-15(db), and the concentration of heterocyst glycolipids (a biomarker for N-2-fixing cyanobacteria) increased simultaneously. Together, these data suggest that the rise in delta N-15(db) is likely the result of enhanced water-column denitrification in response to increased phytoplankton productivity. We hypothesize that greater export production during eutrophication led to anoxic conditions in the hypolimnion as a result of enhanced organic matter remineralization, raising water-column denitrification. Enhanced N loss and remobilization of phosphorous (P) from the sediments under anoxic conditions lowered the N : P ratio in the lake, fostering cyanobacterial N-2 fixation in surface waters.

Marine sediments represent a major carbon reservoir on Earth. Dissolved organic matter (DOM) in pore waters accumulates products and intermediates of carbon cycling in sediments. The application of excitation-emission matrix spectroscopy (EEMs) in the analysis of subseafloor DOM samples is largely unexplored due to the redox-sensitive matrix of anoxic pore water. Therefore, this study aims to investigate the interference caused by the matrix on EEMs and propose a guideline to prepare pore water samples from anoxic marine sediments. The parameters determined by fluorescence spectra include 3D-index derived from EEMs after parallel factor analysis (PARAFAC), fluorescence index (FI) (contribution of terrigenous DOM), biological index (BIX) and humification index (HIX) derived from 2D emission spectra. First, we investigated the impacts of extensively-presented ions as typical electron acceptors, which are utilized by anaerobic microbes and stratified in marine sediments: Fe(II), Fe(III), Mn(II) and sulfide in anoxic pore water resulted in biases of fluorescent signals. We proposed threshold concentrations of these ions when the interference on EEMs occurred. Effective removal of sulfide from sulfide-rich samples could be achieved by flushing with N2 for 2 min. Second, the tests based on DOM standard were further verified using pristine samples from marine sediments. There was a significant change in the fluorescence spectra of DOM in anoxic sediments from the Rhône Delta. This study demonstrated that the change was caused by oxidation of the matrix rather than the intrinsic alteration of DOM. It was confirmed by extracted DOM via both EEMs analysis and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Slight oxidation of sulfur-containing compounds (e.g., sulfhydryl) and polyphenol-like compounds occurred. Finally, a sample preparation sequence is proposed for pore water from anoxic sediments. This method enables measurement with small volumes of the sample (e.g., 50 µL in this study) and ensures reliable data without the interference of the redox-sensitive matrix. This study provides access to the rapid analysis of DOM composition in marine sediments and can potentially open a window into examining the carbon cycling of the marine deep biosphere.

Using ancient environmental DNA (eDNA)[1][1] we reconstructed microbial and viral communities from the Kap København Formation in North Greenland[2][2]. We find pioneer microbial communities, along with likely dormant methanogens from the permafrost’s seed bank. Our findings reveal that at the time of the formation, the terrestrial input of the Kap København site originated from a palustrine wetland, suggesting non-permafrost conditions. During this time, detection of methanogenic archaea and carbon processing pathways suggests a moderate strengthening of methane emissions through the northward expansion of wetlands. Intriguingly, we discover a remarkable sequence similarity (>98%) between pioneer methanogens and present-day thawing permafrost counterparts. This suggests that not all microbes respond uniformly to environmental change over geological timescales, but that some microbial taxa’s adaptability and resilience remain constant over time. Our findings further suggest that the composition of microbial communities is changing prior to plant communities as a result of global warming.### Competing Interest StatementThe authors have declared no competing interest. [1]: #ref-1 [2]: #ref-2

AbstractThe exact drivers for the end-Permian mass extinction (EPME) remain controversial. Here we focus on a ~10,000 yr record from the marine type section at Meishan, China, preceding and covering the onset of the EPME. Analyses of polyaromatic hydrocarbons at sampling intervals representing 1.5–6.3 yr reveal recurrent pulses of wildfires in the terrestrial realm. Massive input pulses of soil-derived organic matter and clastic materials into the oceans are indicated by patterns of C2-dibenzofuran, C30 hopane and aluminum. Importantly, in the ~2,000 years preceding the main phase of the EPME, we observe a clearly defined sequence of wildfires, soil weathering, and euxinia provoked by the fertilization of the marine environment with soil-derived nutrients. Euxinia is indicated by sulfur and iron concentrations. Our study suggests that, in South China, centennial scale processes led to a collapse of the terrestrial ecosystem ~300 yr (120–480 yr; ± 2 s.d.) before the onset of the EPME and that this collapse induced euxinic conditions in the ocean, ultimately resulting in the demise of marine ecosystems.

The Indian monsoon system impacts over 1 billion people, and rainfall from its southwest monsoon is critical for agriculture. Cool sea surface temperatures (SSTs) in the Arabian Sea have been associated with reduced monsoon rainfall and vice versa, although this relationship is difficult to examine due to scarce and short instrumental records. We utilize laminated Pakistan Margin sediments to reconstruct southwest monsoon rainfall and Arabian Sea SSTs at sub‐annual to multi‐annual resolution for the twentieth century. We applied paired sub‐mm mapping techniques to intact sediment core surfaces to measure elemental abundances and lipid biomarkers. The first principal component of the elemental results (PC1) explains 47% of the elemental variance and is driven by detrital lithogenic elements K, Ti, and Fe. PC1 is positively correlated with homogeneous India June‐September rainfall departures from 1903 to 1928 and 1949–1970 on a multi‐annual scale. Correlations in the remaining timespans are either negative or absent, likely driven by a combination of dam and barrage construction on the Hub and Indus Rivers and negative rainfall departures. We propose PC1 as a proxy for southwest monsoon rainfall on multi‐annual timescales prior to ∼1930. A dampened annual SST cycle is resolved with the alkenone U37K′ ${\mathrm{U}}_{37}^{{\mathrm{K}}^{\prime }}$ paleothermometer, which also captures the interannual‐decadal trends of twentieth century Arabian Sea SSTs. We propose the crenarchaeol‐caldarchaeol tetraether index, sourced from planktonic Thaumarchaeota, as a delayed upwelling proxy for the western Arabian Sea. Our reconstructions corroborate the established relationship of reduced Arabian Sea upwelling leading to warmer SSTs and increased monsoon rainfall, and vice versa.

One of the most distinctive characteristics of archaea is their unique lipids. While the general nature of archaeal lipids has been linked to their tolerance to extreme conditions, little is known about the diversity of lipidic structures archaea are able to synthesize, which hinders the elucidation of the physicochemical properties of their cell membrane. In an effort to widen the known lipid repertoire of the piezophilic and hyperthermophilic model archaeon Thermococcus barophilus, we comprehensively characterized its intact polar lipid (IPL), core lipid (CL), and polar head group compositions using a combination of cutting-edge liquid chromatography and mass spectrometric ionization systems. We tentatively identified 82 different IPLs based on five distinct CLs and 10 polar head group derivatives of phosphatidylhexoses, including compounds reported here for the first time, e.g., di-N-acetylhexosamine phosphatidylhexose-bearing lipids. Despite having extended the knowledge on the lipidome, our results also indicate that the majority of T. barophilus lipids remain inaccessible to current analytical procedures and that improvements in lipid extraction and analysis are still required. This expanded yet incomplete lipidome nonetheless opens new avenues for understanding the physiology, physicochemical properties, and organization of the membrane in this archaeon as well as other archaea.

The relatively stable Holocene climate was preceded by a pronounced event of abrupt warming in the Northern Hemisphere, the termination of the Younger Dryas (YD) cold period 1 , 2 . Although this transition has been intensively studied, its imprint on low-latitude ocean temperature is still controversial and its effects on sub-annual to decadal climate variability remain poorly understood 1 , 3 , 4 . Sea surface temperature (SST) variability at these timescales in the tropical Atlantic is expected to intensify under current and future global warming and has considerable consequences for environmental conditions in Africa and South America, and for tropical Pacific climate 5 – 8 . Here we present a 100-µm-resolution record obtained by mass spectrometry imaging (MSI) of long-chain alkenones in sediments from the Cariaco Basin 9 – 11 and find that annually averaged SST remained stable during the transition into the Holocene. However, seasonality increased more than twofold and approached modern values of 1.6 °C, probably driven by the position and/or annual range of the Intertropical Convergence Zone (ITCZ). We further observe that interannual variability intensified during the early Holocene. Our results demonstrate that sub-decadal-scale SST variability in the tropical Atlantic is sensitive to abrupt changes in climate background, such as those witnessed during the most recent glacial to interglacial transition.

Analytical developments have been crucial for the advancement of molecular biomarker research in the Earth sciences. In this chapter, we focus on two areas where recent technological developments have profoundly impacted the use and relevance of molecular organic biomarkers: (1) the increase in spatial resolution heralded by imaging techniques, which results in biomarker-based paleoenvironmental reconstruction with unprecedented temporal resolution; and (2) the accurate, simultaneous characterization of a wide range of compounds in complex matrices enabled by ultra-high-resolution mass spectrometry.

Mass spectrometry imaging (MSI) in sedimentary archives can produce records of molecular proxies at μm-scale resolution. For example, in annually varved sediments of the Santa Barbara Basin, such a fine resolution allows deciphering sub-annual distributions of archaeal tetraether lipids, haptophyte-derived alkenones, and sterols. Herein, we reported the establishment of an untargeted data processing workflow aimed at dissecting the MSI datasets and extracting information beyond that obtained by targeted analysis of known molecular proxies. The combination of MSI and the untargeted workflow not only increases the spatial resolution for molecular stratigraphy but also dramatically broadens the number and diversity of molecular signals evaluated, enabling us to discover unique molecular signatures imprinted by various biogeochemical processes. We applied the proposed workflow to two MSI datasets that were both measured on the uppermost ∼10 cm of the Santa Barbara Basin sediments while covering different mass ranges. Two matrices of 18625×293 and 18963×323 (number of spectra × number of peaks) were, respectively, extracted after peak alignment using bin-wise kernel density estimation and subsequent peak picking by peak prominence filtering combined with geochemical context-based filtering. Feature extraction by non-negative matrix factorization revealed in total 15 stable molecular clusters with distinct spatial distributions in the sediments. Each cluster typically comprised several to dozens of compounds, with the majority of compounds in each cluster likely belonging to similar chemical taxonomies. Some of these clusters can be linked to specific biogeochemical processes. For example, chlorin-like compounds are possibly related to diatom production, alkenones are related to coccolithophorid production, and steranes and long-chain fatty acids likely represent terrigenous input. Supervised learning from these data mining results further extracted molecular signatures with proxy potential that appear to be linked to specific environmental conditions inferred from historical oceanographic data. However, generalizability to other sedimentary settings will require further investigation.

The Last Interglacial (~129,000–116,000 years ago) is the most recent geologic period with a warmer-than-present climate. Proxy-based temperature reconstructions from this interval can help contextualize natural climate variability in our currently warming world, especially if they can define changes on decadal timescales. Here, we established a ~4.800-year-long record of sea surface temperature (SST) variability from the eastern Mediterranean Sea at 1–4-year resolution by applying mass spectrometry imaging of long-chain alkenones to a finely laminated organic-matter-rich sapropel deposited during the Last Interglacial. We observe the highest amplitude of decadal variability in the early stage of sapropel deposition, plausibly due to reduced vertical mixing of the highly stratified water column. With the subsequent reorganization of oceanographic conditions in the later stage of sapropel deposition, when SST forcing resembled the modern situation, we observe that the maximum amplitude of reconstructed decadal variability did not exceed the range of the recent period of warming climate. The more gradual, centennial SST trends reveal that the maximal centennial scale SST increase in our Last Interglacial record is below the projected temperature warming in the twenty-first century.

Varved sediments from the center of the Santa Barbara Basin (SBB) off southern California are a valuable archive for high-resolution climate reconstruction. Using mass spectrometry imaging of lipid biomarkers, this study examines interactions of perennial upwelling strength and oxygen-driven redox conditions at the sediment-water interface from 1900 CE to 2009. In the SBB, variations in upwelling are recorded by isoprenoidal tetraethers from planktonic archaea, while the redox-sensitive C-29 stanol/stenol ratio reflects oxygen content in the bottom water and surficial sediment. The changing coherence of these two proxies allows investigation of the interplay between upwelling, bioproductivity and redox conditions, and their dependence on SBB source water composition during the 20th century. Prior to a large-scale oceanographic regime shift observed in the North Pacific in the 1970s, both proxies are positively correlated: periods of enhanced upwelling promoted mixing, resulting in increased oxygen availability at the sediment-water interface; conversely periods of reduced upwelling favored development of oxygen-depleted water at depth. In the wake of the basin-wide regime shift, changing oceanographic conditions led to a reduction in the southward flowing California Current and a stronger influence of the poleward California Undercurrent, which increased stratification and the supply of warm, oxygen-poor tropical water in the subsurface. As a result, oxygen availability in SBB bottom waters was predominantly regulated by upwelling-induced productivity and subsequent oxygen-consuming remineralization of organic matter.

Sub-decadal to annual climate oscillations are particularly relevant to human climate perception, including such well-known phenomena as the seasonal monsoons and El Niño-Southern Oscillation (ENSO). To assess the variability of these oscillations in the past, proxies for climate parameters that are influenced by these oscillations (e.g., temperature, precipitation) and geologic materials with a temporal resolution able to record them are both needed. However, even in settings where these two criteria are met, the sample size needed for laboratory analysis can limit temporal resolution. We utilize a novel mass spectrometry imaging technique to measure and map distributions of climate-relevant biomarkers (e.g., GDGTs, alkenones) from intact sediment core surfaces in sub-mm increments, unlocking the ability to reconstruct sub-annual paleoclimate. These same sediment sample surfaces are analyzed with micro-XRF mapping to enable congruent examination of complementary elemental- and biomarker-derived paleoenvironmental proxies at ultra-high spatial resolution, both down-core and along-lamination. We applied our biomarker and elemental mapping techniques to annually-laminated Pakistan Margin (northeastern Arabian Sea) sediment core SO90-58KG, spanning 1790-1993 CE. Laminated Pakistan Margin marine sediments are excellent archives of past climate and oceanographic conditions that are influenced by the summer (Southwest) and winter (Northeast) monsoons of India. We measured alkenones and GDGTs at 200 µm resolution, and elemental abundances at 50 µm resolution. Reconstructed sea surface temperatures (SSTs) were calculated from alkenone (UK'37) and GDGT (CCaT) ratios, respectively, with sample resolution up to four points per year. Principal component analysis was applied to the elemental measurements. The first principal component (PC1) is associated with siliciclastic elements (Al, Si, K, Ti, Fe), and is used as a proxy for sub-annual precipitation-driven river runoff. Reconstructed SSTs for both biomarker proxies contain congruent trends, and align with the annual range of instrumental measurements (23 to 30 °C). The annual cycles in SST, with low temperatures driven by mixing during the winter monsoon, are prominent in the time series and highly significant in their power spectra. Using this annual cycle in SST and our paired elemental measurements, we determine the season(s) of river runoff. PC1 is typically highest when SST is low, suggesting runoff/deposition usually occurs during the winter monsoon, consistent with precipitation from westerly storms. However, some years contain PC1 peaks that occur in-phase with warm SSTs, suggesting expansion of summer monsoon rainfall west of Karachi during these years. This work demonstrates the cutting edge of high-resolution paleoclimate science, and provides new insights into the variability of the Indian monsoon from its sensitive western edge.

Microbial mats from alkaline hot springs in the Yellowstone National Park are ideal natural laboratories to study photosynthetic life under extreme conditions, as well as the nuanced interactions of oxygenic and anoxygenic phototrophs. They represent distinctive examples of chlorophototroph (i.e., chlorophyll or bacteriochlorophyll-based phototroph) diversity, and several novel phototrophs have been first described in these systems, all confined in space, coexisting and competing for niches defined by parameters such as light, oxygen, or temperature. In a novel approach, we employed mass spectrometry imaging of chloropigments, quinones, and intact polar lipids (IPLs) to describe the spatial distribution of different groups of chlorophototrophs along the ~ 1 cm thick microbial mat at 75 µm resolution and in the top ~ 1.5 mm green part of the mat at 25 µm resolution. We observed a fine-tuned sequence of oxygenic and anoxygenic chlorophototrophs with distinctive biomarker signatures populating the microbial mat. The transition of oxic to anoxic conditions is characterized by an accumulation of biomarkers indicative of anoxygenic phototrophy. It is also identified as a clear boundary for different species and ecotypes, which adjust their biomarker inventory, particularly the interplay of quinones and chloropigments, to prevailing conditions. Colocalization of the different biomarker groups led to the identification of characteristic IPL signatures and indicates that glycosidic diether glycerolipids are diagnostic for anoxygenic phototrophs in this mat system. The zoom-in into the upper green part further reveals how oxygenic and anoxygenic phototrophs share this microenvironment and informs on subtle, microscale adjustments in lipid composition of Synechococcus spp.