No abstract

Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the phylum Thaumarchaeota. Here, we comprehensively describe the core and intact polar lipid (IPL) inventory of ten ammonia-oxidising thaumarchaeal cultures representing all four characterized phylogenetic clades. IPLs of these thaumarchaeal strains are generally similar and consist of membrane-spanning, glycerol dibiphytanyl glycerol tetraethers with monoglycosyl, diglycosyl, phosphohexose and hexose-phosphohexose headgroups. However, the relative abundances of these IPLs and their core lipid compositions differ systematically between the phylogenetic subgroups, indicating high potential for chemotaxonomic distinction of thaumarchaeal clades. Comparative lipidomic analyses of 19 euryarchaeal and crenarchaeal strains suggested that the lipid methoxy archaeol is synthesized exclusively by Thaumarchaeota and may thus represent a diagnostic lipid biomarker for this phylum. The unprecedented diversity of the thaumarchaeal lipidome with 118 different lipids suggests that membrane lipid composition and adaptation mechanisms in Thaumarchaeota are more complex than previously thought and include unique lipids with as yet unresolved properties.

Subterranean estuaries extend inland into density-stratified coastal carbonate aquifers containing a surprising diversity of endemic animals (mostly crustaceans) within a highly oligotrophic habitat. How complex ecosystems (termed anchialine) thrive in this globally distributed, cryptic environment is poorly understood. Here, we demonstrate that a microbial loop shuttles methane and dissolved organic carbon (DOC) to higher trophic levels of the anchialine food web in the Yucatan Peninsula (Mexico). Methane and DOC production and consumption within the coastal groundwater correspond with a microbial community capable of methanotrophy, heterotrophy, and chemoautotrophy, based on characterization by 16S rRNA gene amplicon sequencing and respiratory quinone composition. Fatty acid and bulk stable carbon isotope values of cave-adapted shrimp suggest that carbon from methanotrophic bacteria comprises 21% of their diet, on average. These findings reveal a heretofore unrecognized subterranean methane sink and contribute to our understanding of the carbon cycle and ecosystem function of karst subterranean estuaries.

Atmospheric contributions of methane from Arctic wetlands during the Holocene are dynamic and linked to climate oscillations. However, long-term records linking climate variability to methane availability in Arctic wetlands are lacking. We present a multi-proxy *12,000 year paleoecological reconstruction of intermittent methane availability from a radiocarbon-dated sediment core (LQ-West) taken from a shallow tundra lake (Qalluuraq Lake) in Arctic Alaska. Specifically, stable carbon isotopic values of photosynthetic biomarkers and methane are utilized to estimate the proportional contribution of methane-derived carbon to lake-sediment-preserved benthic (chironomids) and pelagic (cladocerans) components over the last *12,000 years. These results were compared to temperature, hydrologic, and habitat reconstructions from the same site using chironomid assemblage data, oxygen isotopes of chironomid head capsules, and radiocarbon ages of plant macrofossils. Cladoceran ephippia from *4,000 cal year BP sediments have d 13 C values that range from *-39 to -31%, suggesting peak methane carbon assimilation at that time. These low d 13 C values coincide with an apparent decrease in effective moisture and development of a wetland that included Sphagnum subsecundum. Incorporation of methane-derived carbon by This is one of 18 papers published in a special issue edited by Darrell Kaufman and dedicated to reconstructing Holocene climate and environmental change from Arctic lake sediments. chironomids and cladocerans decreased from *2,500 to 1,500 cal year BP, coinciding with a temperature decrease. Live-collected chironomids with a radiocarbon age of 1,640 cal year BP, and fossil chironomids from 1,500 cal year BP in the core illustrate that 'old' carbon has also contributed to the development of the aquatic ecosystem since *1,500 cal year BP. The relatively low d 13 C values of aquatic invertebrates (as low as -40.5%) provide evidence of methane incorporation by lake invertebrates, and suggest intermittent climate-linked methane release from the lake throughout the Holocene.

Glycerol ether lipids have been developed as proxies to reconstruct past environmental changes or in their intact polar form to fingerprint the viable microbial community composition. However, due to the structural complexity, the 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 our understanding of the diversity of ether lipids and their utilities as biogeochemical proxies. Here, we report a novel reverse-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. This protocol greatly enhances the 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 distribution of the core lipid, such as the TEX 86 and ring index, can now be directly determined in specific intact polar lipids (IPL-specific TEX 86 and ring index). Since IPLs are the putative precursors of the environmentally persistent core lipids, their detailed examination by 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 TEX 86 values follow the order: 2G-GDGTs > core GDGTs > 1G-GDGTs > 1G-GDGT-PI; and the ring indices follow: 1G-GDGTs ≈ core GDGTs > 2G-GDGTs > 1G-GDGT