Bacterial Tetraether Lipids in Lacustrine Environments Implications for their use as Paleoclimate Proxies Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch- Naturwissenschaftlichen Fakultät der Universität Basel von Thomas Yuuki Weber aus Deutschland Basel 2018 Originaldokument gespeichert auf dem Dokumenten- server der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Moritz Lehmann (Fakultätsverantwortlicher), Dr. Helge Niemann (Dissertationsleiter), und Prof. Dr. Timothy Eglinton, ETH Zürich (Korreferent). Basel, den 21.03.2017 Prof. Dr. Martin Spiess, Dekan Summary 1 Summary Anthropogenic global warming poses a long-term threat to human society. The reliable predic- tion of future climate evolution, however, not only builds upon our understanding of present-day processes, but also requires profound knowledge of Earth system responses on timescales exceeding the range of instrumental observations. Current numerical simulations steadily grow in complexity, increasing the need for high-quality paleoclimate data as a means of model evaluation, especially from the spatially heterogeneous terrestrial realm. One promising approach for the reconstruction of past continental temperatures is based on organic-geochemical analyses of bacterial tetraether lipids (i.e., branched GDGTs), which are prevalent in the environment, and show systematic compositional changes with ambient temperature. Several studies established quantitative relationships between atmospheric T and brGDGT distribution in modern lake sediments, yet, application of these transfer functions to different limnological settings does not always yield robust paleotemperature estimates. Attempts for further improvement of the brGDGT proxy are currently hindered by the fact that the vast majority of brGDGT-producing microbes are still unidentified, and the ecophysiological mechanisms behind the apparent T response are unknown. In order to shed light on the ecology and lifestyle of these microbes in lacustrine systems, we investigated a variety of recent lake sediments from the Swiss and Italian Alps, as well as suspended- and sinking biomass from the permanently stratified north basin of Lake Lugano (Southern Switzerland), by a combination of stable isotope-, geochemical-, and molecular biological methods. Almost 50 % of the investigated lake deposits contained an as yet unknown brGDGT isomer that was not detectable in soils collected from the catchments, which provided unprecedented molecular evidence for brGDGT biosynthesis within lacustrine systems. This compound was also abundantly present in hypoxic and anoxic deep water of Lake Lugano. Strikingly, however, it was completely absent from the overlying oxic waters, implying an exclusive origin from microbes adapted to low dissolved oxygen concentrations. In contrast, concentration profiles and stable carbon isotope data show that another structural brGDGT isomer is dominantly synthesized by bacteria inhabiting oxygenated waters, attesting to a vertical differentiation of the brGDGT-producing microbial commu- nity. In order to constrain the identity of the source organisms, we investigated prokaryotic diversity by sequencing of ribosomal DNA, with special emphasis on members of the phylum Acidobacteria — the only group known thus far to produce brGDGTs. Indeed, members of different acidobacteria subdivisions showed a depth differentiation that is reminiscent of the concentration gradients found for individual brGDGT lipids, with a number of uncultured representatives exclusively occurring in the anoxic water column. 2 Summary Summary 3 In Lake Lugano, we further studied the vertical transport of brGDGTs by deploying three sediment traps, (i) at the base of the thermocline, (ii) at the redox transition zone, and (iii) 90 m within the anoxic water body. The brGDGT content of settling organic particles increased successively from the upper towards the lower trap, attesting to pronounced hypolimnetic in-situ production under both, oxic and hypoxic/anoxic conditions. Subsequent laboratory experiments showed quick uptake of isotopically labeled organic C into brGDGTs from surface water, and a ~100-fold abundance increase within six weeks, demonstrating a high potential for aerobic brGDGT production by heterotrophic bacteria. Surprisingly, however, a corresponding anoxic incubation with biomass from the bottom waters of Lake Lugano did not result in measurable label uptake, suggesting that anaerobic brGDGT production may be limited to the redox transition zone (RTZ) where alternative electron acceptors such as nitrate are still present. Our work in Lake Lugano also revealed a steep decline in the natural 13C content of brGDGTs 13 13 (δ CbrGDGT) at the RTZ, most likely related to the cycling of C-depleted organic compounds derived from the oxidation of methane. This is consistent with the fact that in the majority of the investigated lakes, brGDGTs were substantially depleted in 13C (up to 10 ‰) compared to the bulk of sedimen- 13 13 tary organic C (δ CTOC). Indeed, we found significantly lower δ CbrGDGT values in meso-eutrophic lakes that exhibit bottom water anoxia, than in oligotrophic and fully-oxygenated settings, which is best explained by the co-occurrence of methane-oxidizing- and brGDGT-producing bacteria in the vicinity of the RTZ. The 36 lakes investigated in this study span an altitudinal air temperature difference of ~10 °C. However, the correlation between mean annual air temperature (MAT) at the lake sites and commonly applied brGDGT proxy indices in the surface sediments was poor (R2=0.1), contradicting previ- ously reported data from lakes of other regions. In light of the important role of deep water-derived brGDGTs in lake sediments we show here, we reason that the brGDGT–MAT relationship in our data set is likely compromised by the variable contribution of brGDGTs from terrestrial, shallow-, and deep water pools, each of which carry distinct temperature imprints. Specialized lipid extraction techniques are required for the recovery of GDGTs from living biomass. We tested three commonly used protocols on suspended particulate matter from Lake Lugano, and found substantial extraction biases affecting the intact polar lipid (IPL) fraction of brGDGTs. Up to 90 % of the IPL pool were not accessible by means of normal ultrasonic solvent extraction, nor were they recovered with the widely applied, phosphate-buffered ‘modified Bligh-Dyer’ protocol. Near complete IPL recovery was, however, only achieved after substitution of the P-buffer with a solution of 5% trichloroacetic acid. Our results therefore suggest that previous studies may have substantially underestimated the ‘living fraction’ of brGDGTs and its contribution to the total lipid pool. 4 Summary Summary 5 Table of contents Chapter 1 ................................................................................................................................................................................................................7 1.1. Rationale ...................................................................................................................................................................................................7 1.2. Introduction .................................................................................................................................................................................... .10 1.3. Research objectives ............................................................................................................................................................... .28 1.4. Methods ................................................................................................................................................................................................ .29 1.5. Publication outline ................................................................................................................................................................. .32 1.6. References ......................................................................................................................................................................................... .35 Chapter 2 ......................................................................................................................................................................................................... .53 productionIdentification and carbon isotope composition of a novel branched GDGT isomer in lake sediments: Evidence for lacustrine branched GDGT Chapter 3 ........................................................................................................................................................................................................... .75 Incomplete recovery of intact polar glycerol dialkyl glycerol tetraethers (GDGTs) from lacustrine suspended ...................................................................................................................................... biomass .96 3.1. Supplementary information Chapter 4 .......................................................................................................................................................................................................101 Redox-dependent niche differentiation of tetraether producing bacteria: Evidence for multiple branched GDGT ..................................................................................................................................