•Directly and simultaneously determining CL- and IPL-specific TEX86 and ring index values.•Greatly improved detection of IPLs and labile CLs.•Novel and comprehensive information on lipid fingerprints provided.Glycerol ether lipid distributions have been developed as proxies for reconstructing past environmental change or, in their intact polar form, for fingerprinting the viable microbial community composition. However, due to their structural complexity, full characterization of glycerol ether lipids requires separate protocols for the analysis of the polar head groups and the alkyl chain moieties in core ether lipids. As a consequence, the valuable relationship between core ether lipid composition and specific polar head groups is often lost; this limits understanding of the diversity of ether lipids and their utility as biogeochemical proxies. Here, we report a novel reversed phase liquid chromatography–electrospray ionization-mass spectrometry (RP-ESI-MS) protocol that enables the simultaneous analysis of polar head groups (e.g. phosphocholine, phosphoglycerol, phosphoinositol, hexose and dihexose) and alkyl moieties (e.g. alkyl moieties modified with different numbers of cycloalkyl moieties, hydroxyl and alkyl groups and double bonds) in crude lipid extracts without further preparation. The protocol greatly enhances detection of archaeal intact polar lipids (IPLs) and core lipids (CLs) with double bond- and hydroxyl group-bearing alkyl moieties. With these improvements, widely used ratios that describe relative distributions of the core lipids, such as TEX86 and ring index, can now be directly determined in specific intact polar lipids (IPL-specific TEX86 and ring index). Since IPLs are the putative precursors of the environmentally persistent core lipids, their detailed examination using this protocol can potentially provide new insights into diagenetic and biological mechanisms inherent to these proxies. In a series of 12 samples from diverse settings, core and IPL-specific TEX86 values followed the order: 2G-GDGTs > core GDGTs > 1G-GDGTs > 1G-GDGT-PI and the ring indices followed: 1G-GDGTs ≈ core GDGTs > 2G-GDGTs > 1G-GDGT-P1G > 2G-OH-GDGTs ≈ 1G-OH-GDGTs (1G, monoglycosyl; 2G, diglycosyl; P1G, phosphomonoglycosyl; GDGT, glycerol dialkyl glycerol tetraether).

The Yangtze River receives 37.5% of the municipal sewage of China, whose fate constitutes a major environmental and health concern. This study applied phytosterols, 5β(H)-stanols, tetrahymanol and 17α,21β(H)-C30-hopane to examine sewage and petroleum-derived organic pollutants, and assess their impact on the biogeochemistry of the lower river benthic environment. The results showed that significant contributions from sewage and petroleum pollutants were preserved in the riverbed. These potentially contributed to O2 depletion and apparently an anoxic environment in the riverbed, either directly or via an impact on primary productivity.Highlights► The Distributions of sedimentary biomarkers in the lower Yangtze River were investigated. ► Sewage and petroleum-derived pollutants were significant contributors to sedimentary organic matter in the lower river. ► Algal production was low in the lower river. ► Reducing, probably anoxic, conditions exist in parts of the riverbed, likely resulting from organic pollution.

Glycerol dialkyl glycerol tetraether (GDGT)-based proxies are increasingly used in modern carbon cycling and palaeoenvironmental investigations. It is therefore crucial to examine the robustness (sources, transport and degradation) of all GDGT-based proxies in continental margins, where sedimentation rates and extent of carbon cycling are high. We have analyzed the distributions of GDGTs in surface sediments from the Lower Yangtze River and East China Sea (ECS) shelf. The results revealed multiple sources and complex shelf processes that govern the distributions. The isoprenoid GDGT-inferred sea surface temperatures (SSTs) are robust and reflect the satellite-derived annual mean SSTs on the shallow ECS shelf, confirming an origin from surface water column-dwelling crenarchaeota. The input from methanogen-sourced, isoprenoid GDGTs is significant in the river surface sediments but they are almost absent from the ECS shelf. Branched GDGTs are also abundant in the river sediments, but ca. 95% are degraded in the Yangtze estuary, a much greater extent than observed for other terrigenous organic matter (OM) proxies. There is also evidence for production of branched GDGTs in the oxic ECS shelf water column and the anoxic sediments/waters of the Lower Yangtze River. As a result, branched GDGT-based proxies in the lower river and ECS surface sediments do not reflect the catchment environmental conditions. The effective degradation in the estuary and widespread aquatic contributions of branched GDGTs improves our understanding of how to use branched GDGT-based proxies in marginal seas.