Isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) are biomarkers of archaea, but improvement is needed for more precise analysis of intact polar lipid (IPL)-iGDGTs. Here, we present a multiple reaction monitoring (MRM) method for IPL-iGDGTs using reversed phase liquid chromatography (RP-LC) and triple quadrupole mass spectrometry equipped with electrospray ionization (RP-LC–ESI-MRM). The MRM mode showed much greater sensitivity and lower detection limits than the commonly used selected ion monitoring (SIM) mode. Furthermore, the MRM mode had better stability and repeatability than the SIM mode. Thus, the RP-LC–ESI-MRM method can allow efficient fingerprinting of archaeal IPL-iGDGTs, particularly when they are in trace abundance in natural environments.

•Nitrososphaera spp. are the dominant archaeal population producing crenarchaeol in Chongming Island soil.•GDGT-1, GDGT-3, crenarchaeol and its isomer correlated with pH change in the soil.•A thaumarchaeota index (TI) is proposed as a proxy for past pH change in soil.Crenarchaeol is a unique glycerol dialkyl glycerol tetraether (GDGT) lipid specific to Thaumarchaeota, which play an important role in the global C and N cycles. GDGTs from Thaumarchaeota have been used to develop proxies for paleoclimate or paleoenvironment studies in aquatic environments. However, our understanding of their response to environmental change in soil remains poor. We addressed this question by investigating the change in archaeal lipid composition and community structure in the context of other environmental variables over a period of 12 months in a subtropical soil from Chongming Island, China. The results showed that Nitrososphaera spp. were the dominant archaeal population producing crenarchaeol in the soil. The relative abundance of GDGTs with one and three cyclopentane moieties, and crenarchaeol and its isomer in the core lipid (CL) fraction correlated with seasonal pH change in the soil. We therefore propose a molecular fossil proxy, the thaumarchaeota index (TI), which significantly related to pH in not only Chongming Island soil (R2 0.56, RMSE 0.14, P < 0.05), but also global soils (R2 0.51, RMSE 1.39, P < 0.001) and five thaumarchaeotal enrichments (R2 0.99, RMSE 0.04, P < 0.001). This suggests that TI could be a useful proxy for soil pH, which may corroborate the use of the bacterial GDGT proxy for soil pH, the cyclisation ratio of branched tetraethers (CBT).

Highlights•Multi-paleotemperature records were generated in the southern Okinawa Trough.•Core top sample approximated the SST extending to the mixed layer in warmer seasons.•Drop of SST during the B-A corresponds to the timing of the Antarctic Cold Reversal.•Low SST during the HS1 and YD corresponds to the millennial-scale cold signals.Three paleotemperature records (foraminiferal Mg/Ca, TEX86 and UK′37) were generated for the past 17.3 ka in the southern Okinawa Trough (OT) using a sediment core (OKT-3) taken at a water depth of 1792 m. Temperature estimates based on the inorganic and organic indices for the OKT-3 core top sample approximated modern sea surface temperature (SST) and extended to the mixed layer (<50 m) in warmer seasons. Reconstructed SSTs from OKT-3 gradually increased towards the top of the core with lower values occurring during Heinrich Stadial 1 (HS1) and the Younger Dryas (YD). These values coincided with the glacial–interglacial cycles established by the Globigerinoides ruber δ18O curve. Notably, SSTs decreased during the BØlling-AllerØd (B-A) but warming occurred before and after the B-A, from approximately 16 to 14 ka and 12.5 to 10 ka. The SST cooling during the B-A corresponded to the timing of the Antarctic Cold Reversal (ACR), which is thought to be connected with melt water pulse 1a (MWP1a). The cooling was also concurrent with the spread of millennial-scale cold signals to the OT during the HS1 and YD periods, when widespread melt and collapse of Northern Hemisphere ice sheets occurred along with reduced Atlantic Meridional Overturning Circulation (AMOC) and a southward shift of the Intertropical Convergence Zone (ITCZ). The last deglaciation, which began approximately 16–15 ka BP in the OT, might mark the time when the Kuroshio Current (KC) began to strengthen.