Large enrichments in fatty acid 2H/1H ratios distinguish respiration from aerobic fermentation in yeast Saccharomyces cerevisiae.

Shifts in the hydrogen stable isotopic composition (2H/1H ratio) of lipids relative to water (lipid/water 2H-fractionation) at natural abundances reflect different sources of the central cellular reductant, NADPH, in bacteria. Here, we demonstrate that lipid/water 2H-fractionation (2εfattyacid/water) can also constrain the relative importance of key NADPH pathways in eukaryotes. We used the metabolically flexible yeast Saccharomyces cerevisiae, a microbial model for respiratory and fermentative metabolism in industry and medicine, to investigate 2εfattyacid/water. In chemostats, fatty acids from glycerol-respiring cells were >550‰ 2H-enriched compared to those from cells aerobically fermenting sugars via overflow metabolism, a hallmark feature in cancer. Faster growth decreased 2H/1H ratios, particularly in glycerol-respiring cells by 200‰. Variations in the activities and kinetic isotope effects among NADP+-reducing enzymes indicate cytosolic NADPH supply as the primary control on 2εfattyacid/water. Contributions of cytosolic isocitrate dehydrogenase (cIDH) to NAPDH production drive large 2H-enrichments with substrate metabolism (cIDH is absent during fermentation but contributes up to 20 percent NAPDH during respiration) and slower growth on glycerol (11 percent more NADPH from cIDH). Shifts in NADPH demand associated with cellular lipid abundance explain smaller 2εfattyacid/water variations (<30‰) with growth rate during fermentation. Consistent with these results, tests of murine liver cells had 2H-enriched lipids from slower-growing, healthy respiring cells relative to fast-growing, fermenting hepatocellular carcinoma. Our findings point to the broad potential of lipid 2H/1H ratios as a passive natural tracker of eukaryotic metabolism with applications to distinguish health and disease, complementing studies that rely on complex isotope-tracer addition methods.

Aquatic plant wax hydrogen and carbon isotopes in Greenland lakes record shifts in methane cycling during past Holocene warming.

Predicting changes to methane cycling in Arctic lakes is of global concern in a warming world but records constraining lake methane dynamics with past warming are rare. Here, we demonstrate that the hydrogen isotopic composition (δ2H) of mid-chain waxes derived from aquatic moss clearly decouples from precipitation during past Holocene warmth and instead records incorporation of methane in plant biomass. Trends in δ2Hmoss and δ13Cmoss values point to widespread Middle Holocene (11,700 to 4200 years ago) shifts in lake methane cycling across Greenland during millennia of elevated summer temperatures, heightened productivity, and lowered hypolimnetic oxygen. These data reveal ongoing warming may lead to increases in methane-derived C in many Arctic lakes, including lakes where methane is not a major component of the C cycle today. This work highlights a previously unrecognized mechanism influencing δ2H values of mid-chain wax and draws attention to the unquantified role of common aquatic mosses as a potentially important sink of lake methane across the Arctic.

Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil.

The rate at which microorganisms grow and reproduce is fundamental to our understanding of microbial physiology and ecology. While soil microbiologists routinely quantify soil microbial biomass levels and the growth rates of individual taxa in culture, there is a limited understanding of how quickly microbes actually grow in soil. For this work, we posed the simple question: what are the growth rates of soil microorganisms? In this study, we measure these rates in three distinct soil environments using hydrogen-stable isotope probing of lipids with 2H-enriched water. This technique provides a taxa-agnostic quantification of in situ microbial growth from the degree of 2H enrichment of intact polar lipid compounds ascribed to bacteria and fungi. We find that growth rates in soil are quite slow and correspond to average generation times of 14 to 45 d but are also highly variable at the compound-specific level (4 to 402 d), suggesting differential growth rates among community subsets. We observe that low-biomass microbial communities exhibit more rapid growth rates than high-biomass communities, highlighting that biomass quantity alone does not predict microbial productivity in soil. Furthermore, within a given soil, the rates at which specific lipids are being synthesized do not relate to their quantity, suggesting a general decoupling of microbial abundance and growth in soil microbiomes. More generally, we demonstrate the utility of lipid-stable isotope probing for measuring microbial growth rates in soil and highlight the importance of measuring growth rates to complement more standard analyses of soil microbial communities.

Production of diverse brGDGTs by Acidobacterium Solibacter usitatus in response to temperature, pH, and O2 provides a culturing perspective on brGDGT proxies and biosynthesis.

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids that are frequently employed as paleoenvironmental proxies because of the strong empirical correlations between their relative abundances and environmental temperature and pH. Despite the ubiquity of brGDGTs in modern and paleoenvironments, the source organisms of these enigmatic compounds have remained elusive, requiring paleoenvironmental applications to rely solely on observed environmental correlations. Previous laboratory and environmental studies have suggested that the globally abundant bacterial phylum of the Acidobacteria may be an important brGDGT producer in nature. Here, we report on experiments with a cultured Acidobacterium, Solibacter usitatus, that makes a large portion of its cellular membrane (24 ± 9% across all experiments) out of a structurally diverse set of tetraethers including the common brGDGTs Ia, IIa, IIIa, Ib, and IIb. Solibacter usitatus was grown across a range of conditions including temperatures from 15 to 30°C, pH from 5.0 to 6.5, and O2 from 1% to 21%, and demonstrated pronounced shifts in the degree of brGDGT methylation across these growth conditions. The temperature response in culture was in close agreement with trends observed in published environmental datasets, supporting a physiological basis for the empirical relationship between brGDGT methylation number and temperature. However, brGDGT methylation at lower temperatures (15 and 20°C) was modulated by culture pH with higher pH systematically increasing the degree of methylation. In contrast, pH had little effect on brGDGT cyclization, supporting the hypothesis that changes in bacterial community composition may underlie the link between cyclization number and pH observed in environmental samples. Oxygen concentration likewise affected brGDGT methylation highlighting the potential for this environmental parameter to impact paleotemperature reconstruction. Low O2 culture conditions further resulted in the production of uncommon brGDGT isomers that could be indicators of O2 limitation. Finally, the production of brGTGTs (trialkyl tetraethers) in addition to the previously discovered iso-C15-based mono- and diethers in S. usitatus suggests a potential biosynthetic pathway for brGDGTs that uses homologs of the archaeal tetraether synthase (Tes) enzyme for tetraether synthesis from diethers.

Pronounced summer warming in northwest Greenland during the Holocene and Last Interglacial.

Projections of future rates of mass loss from the Greenland Ice Sheet are highly uncertain because its sensitivity to warming is unclear. Geologic reconstructions of Quaternary interglacials can illustrate how the ice sheet responded during past warm periods, providing insights into ice sheet behavior and important tests for data-model comparisons. However, paleoclimate records from Greenland are limited: Early Holocene peak warmth has been quantified at only a few sites, and terrestrial sedimentary records of prior interglacials are exceptionally rare due to glacial erosion during the last glacial period. Here, we discuss findings from a lacustrine archive that records both the Holocene and the Last Interglacial (LIG) from Greenland, allowing for direct comparison between two interglacials. Sedimentary chironomid assemblages indicate peak July temperatures 4.0 to 7.0 °C warmer than modern during the Early Holocene maximum in summer insolation. Chaoborus and chironomids in LIG sediments indicate July temperatures at least 5.5 to 8.5 °C warmer than modern. These estimates indicate pronounced warming in northwest Greenland during both interglacials. This helps explain dramatic ice sheet thinning at Camp Century in northwest Greenland during the Early Holocene and, for the LIG, aligns with controversial estimates of Eemian warming from ice core data retrieved in northern Greenland. Converging geologic evidence for strong LIG warming is challenging to reconcile with inferred Greenland Ice Sheet extent during the LIG, and the two appear incompatible in many models of ice sheet evolution. An increase in LIG snowfall could help resolve this problem, pointing to the need for hydroclimate reconstructions from the region.