A Geochemical Characterization of Putative Biosignatures in Subseafloor Basalts

The discoveries of tubular alteration features of potential biological origin in subseafloor basalt glasses, ophiolites, and ancient greenstones has important implications for increasing our understanding of global biogeochemical cycling in hard-rock systems and the evolution of life on Earth, and for exploring other planets for signs of life. Given the technological challenges in accessing the modern subseafloor and the possibility that it could take thousands of years to form these features, at this point it is not possible to observe their formation in-situ, nor have they been successfully modeled in the lab. Thus, we must infer the formation and preservation mechanisms of these putative biosignatures from physical and chemical clues. We have used a number of micro-analytical techniques to geochemically characterize these features at the submicron scale. Using focused ion beam milling we prepared ultra-thin cross-sections of the tubules, which enabled high-resolution imaging and chemical analyses by transmission electron microscopy and electron-dispersive spectroscopy. These analyses revealed leached rims around the tubule margins, and partially crystalline Fe-bearing phyllosilicates infilling the tubules. In addition, we combined four different high-resolution synchrotron-based techniques, including X-ray fluorescence microprobe mapping, micro-diffraction, and absorption spectroscopy to determine the distribution and speciation of key major and trace elements. These studies revealed consistent patterns of Ca, Mg, Ti, Fe, Mn, S, and P distributions, metal oxidation, and authigenic precipitation of secondary phases, as well as identified possible biominerals and organic material. Put together, these results have provided insight into the processes involved in tubular alteration and mineralization. The formation mechanism involves initial incongruent dissolution of the glass potentially accompanied by the authigenic precipitation of biominerals, specifically Fe-oxides and sulfate. Successive stages of fluid flow then infill the tubules with a variety of Feand Ti-rich minerals, with concomitant partial to complete oxidation of the redox active elements. The consistency of these results across a 100Ma suite of subseafloor samples and one ophiolite sample implies that the alteration and mineralization patterns are consistent spatially and temporally. These results also add significant evidence to the argument for the biological formation of the tubules by revealing potential signs of microbial geochemical processing

Enigmatic persistence of dissolved organic matter in the ocean

Marine dissolved organic matter (DOM) contains more carbon than the combined stocks of Earth’s biota. Organisms in the ocean continuously release a myriad of molecules that become food for microheterotrophs, but, for unknown reasons, a residual fraction persists as DOM for millennia. In this Perspective, we discuss and compare two concepts that could explain this persistence. The long-standing ‘intrinsic recalcitrance’ paradigm attributes DOM stability to inherent molecular properties. In the ‘emergent recalcitrance’ concept, DOM is continuously transformed by marine microheterotrophs, with recalcitrance emerging on an ecosystems level. Both concepts are consistent with observations in the modern ocean, but they imply very different responses of the DOM pool to climate-related changes. To better understand DOM persistence, we propose a new overarching research strategy — the ecology of molecules — that integrates the concepts of intrinsic and emergent recalcitrance with the ecological and environmental context

Tracing the effect of nutrient and carbon supply on the biosynthesis and composition of lipids from marine microbes

The marine water column and the subsurface sediments remain among the least understood ecosystems on Earth. Particularly, microbial driven processes in marine environment, such as their activity, food-web strategies and ecological function within the marine realm are poorly understood. The aim of the presented research was to expand our knowledge on the microbial community structure and their lipid-based adaption mechanisms to nutrient limitation in the marine realm. To this end pure culture and environmental samples from different regions of the world were investigated using state-of-the-art analytical techniques. This dissertation provides important information on the biosynthesis of microbial lipids under energy limiting conditions, showing that microbes modify their lipid composition according to changing nutrient levels. Moreover, the detailed investigation of the proxy potential of selected microbial lipids, serves important information for future biomarker-based studies. Therefore, this dissertation increased the current knowledge of the microbial community and the physiologic mechanisms of microbes in the marine realm

Deep Carbon Observatory: A Decade of Discovery

The Deep Carbon Observatory launched in 2009 with an ambitious plan to understand how carbon inside Earth—deep carbon—contributes to and affects the global carbon cycle. Carbon is one of the most important elements of our planet: carbon-based fuels provide much of our energy; carbon is an essential element of life; and excess carbon in our atmosphere presents one of the greatest planetary challenges of our time. The amount of carbon in the easily accessible surface environment, however, is only a tiny fraction of the carbon in Earth. Before DCO, remarkably little was known about the physical, chemical, and biological properties of Earth’s deep carbon.Alfred P. Sloan Foundatio

Glycerol ether lipids in sediments: sources, diversity and implications

Glycerol ether lipids are prominent membrane constituents in Archaea and Bacteria that are characterized by high potential for preservation in geological settings.During the past decade they were increasingly used in molecular proxies. For example,selected glycerol dialkyl glycerol tetraethers (GDGT) are used in ratios such as the TEX86 and BIT index for reconstructing past sea surface temperature (SST) and terrestrial input, respectively. However, the distribution and structural diversity of glycerol ether lipids in marine sediments has not yet been fully explored. In order to obtain a better understanding of the origin and fate of these lipids and to evaluate the potential impact on molecular proxies, a globally distributed set of samples was analyzed in this PhD thesis project. More than forty novel compounds were revealed and it could be shown that the diversity of glycerol ether lipids in marine sediments is much higher than previously recognized. Among the studied lipids, isoprenoid GDGTs were shown as the most dominant component in all analyzed sediments with over 70% of total ether lipids. A comparison of the lipid composition of core and intact polar isoprenoid GDGTs pointed to a potential impact of live benthic archaea and their intact lipids on the application of the TEX86 SST proxy. The same study suggested that recycling of fossil GDGTs from planktonic archaea by the benthic archaeal community could be an important process. In a set of peat sediments, two intact polar lipids of the orphan branched GDGTs were for the first time observed. These branched GDGTs that constitute the BIT index have in their intact form glucuronosyl and glucosyl headgroups. The two compounds accounted for 4-7% of total IPLs, suggesting that their producers represent a sizeable but not dominant component of the microbial community. The identification of these intact polar precursors of these orphan lipids provides important constraints for the search of their microbial sources. The presence of newly identified glycerol ether lipids with distinctive structures and ubiquitous distribution in all analyzed marine sediments provided potential phylogenetic biomarkers and a large reservoir for novel molecular proxies to be developed. A series of novel ether core lipids coexisting with corresponding isoprenoid GDGTs was identified in all analyzed sediments. The first series of compounds,accounting on average for 7% of total ether lipids, was identified as glycerol dibiphytanol diethers (GDDs) and is considered to represent either biosynthetic intermediates or degradation products of GDGTs. A second series was identified as hydroxylated GDGTs based on nuclear magnetic resonance (NMR) and mass spectral interpretation. Accordingly, a series of unknown IPLs that had been previously reported as a major component in samples of archaeal cultures, sediments, and the water column were then recognized to be glycosidic hydroxy-GDGTs. The widespread occurrence of IPLs of hydroxy-GDGTs suggests an important contribution of specific archaeal species with high activity in a wide range of geological settings. Several other groups of novel compounds were also tentatively identified based on interpretation of mass spectra. Specifically, extended H-shaped GDGTs, hybrid isoprenoid/branched GDGTs, and overly and sparsely branched GDGTs are characterized with a common feature of methylation series, containing compounds with one -CH2- unit difference between each other. It is expected that the information encoded in the distribution of the novel lipids can be used to develop molecular proxies indicating past environmental factors such as temperature and salinity and/or information pertaining to the composition and activity of extant microbial communities. An overall distribution of detected glycerol ether lipids in marine subsurface sediments was shown by the estimated relative abundance of 11 structural groups, and therefore reflects a general composition of ether lipid producing microbes contributing to the sedimentary record

Co-Existence and niche differentiation of sulfur oxidizing bacteria in marine environments

Reduced sulfur compounds and sulfur-oxidizing prokaryotes (SOP) are widely distributed in the marine environment. Diverse microbial lineages thrive on the oxidation of reduced sulfur. They co-exist successfully by the adaptive radiation into different physiological and ecological niches. However, the factors determining this differentiation and SOP distribution are largely unknown. Environmental factors, like pH, temperature and salinity, as well as the physiological capabilities of different SOPs for sulfur-oxidation and carbon assimilation likely govern the niche-differentiation. Therefore, as part of multiple collaborative studies, I studied the influence of substrate quality and availability on structuring sulfur-oxidizing microbial communities in different marine habitats. First, the role of elemental sulfur (S0), in particular cyclooctasulfur (S8), as substrate for SOPs in marine benthic habitats was examined (Chapter II). We observed a specific association between Sulfurimonas/Sulfurovum-related Epsilonproteobacteria and S0/S8 regardless of the habitat. We propose that substrate quality effects SOP diversity and niche differentiation, and the capability to oxidize S8 probably provides a competitive advantage to the Sulfurimonas/Sulfurovum-group. Moreover, we investigated the diversity and distribution SOPs along gradients of a sulfide, oxygen and light in a highly sulfidic marine karst lake (Lake Rogoznica, Chapter III). The comprehensive analysis of microbial diversity revealed a community shift from phototrophic to chemotrophic sulfur oxidation during holomixis and tight coupling between sulfide and oxygen concentration and the sulfur-oxidizing microbial community in Lake Rogoznica. In two further studies, we explored different aspects of carbon assimilation in hydrothermally influenced habitats dominated by thiotrophic Sulfurimonas/Sulfurovum-related Epsilonproteobacteria. We demonstrated the effects of temperature and/or substrate flux on carbon-isotope fractionation during CO2 assimilation in environmental samples (Chapter IV). Furthermore, we showed that these and other hydrothermal vent associated thiotrophs do not incorporate acetate (Chapter V), despite their heterotrophic potential. Other microorganisms, not involved in oxidative sulfur cycling at hydrothermal vents, showed high activity and growth after the input of organic substrate. In summary, this thesis contributes to the general understanding of microbial ecology in sulfur-rich environments by provides novel insights into diversity and niche in sulfur-oxidizing microbial communities

PHOSPHOLIPID FATTY ACIDS AS BIOMASS PROXIES AND THEIR USE IN CHARACTERIZING DEEP TERRESTRIAL SUBSURFACE MICROBIAL COMMUNITIES

Understanding the distribution, abundances and metabolic activities of microbial life in the subsurface is fundamental to our understanding of the role microbes play in many areas of inquiry such as terrestrial biogeochemical cycling and the search for extraterrestrial life. The deep terrestrial subsurface is known to harbor microbial life at depths of up to several kilometers where, in some cases, organisms live independently from the photosphere and atmosphere. Ancient fracture fluids trapped within the crystalline basement of the Canadian Precambrian Shield have been shown to be preserved on geologic timescales (millions to billions of years). Significant challenges exist when probing the deep terrestrial subsurface including the low biomass abundance, heterogeneous distribution of biomass, and the potential for matrix effects during sampling and analysis. This Master’s thesis project has two main parts. The first study utilizes phospholipid fatty acid (PLFA) analysis to determine the extent of mineral matrices on the effectiveness of PLFA extraction and analysis from deep terrestrial subsurface samples. This was done by creating a bacterial dilution series of known concentration to inoculate one of two mineral matrices, granite or bentonite. This study revealed the presence of significant influence of mineral matrices on PLFA extraction and demonstrated the unreliability of PLFA-based biomass conversion factors with respect to complex microbial communities. The second study in this thesis combine PLFA analysis with stable carbon isotope analysis to characterize microbial communities associated with fracture fluids with mean residence times of ~1.4 Ga from boreholes located ~2.4km below the surface in Kidd Creek Mine, in Timmins, Ontario. Characterizing communities in subsurface systems has large implications for the search for life on other planets and moons, acting as an analogue environment. Large volumes of water from two boreholes, 12261 and 12299, were passively filtered for 6-12 months to collect microbial biomass. Borehole adjacent biofilms were also collected along with mine service water, which served as a control. All samples had significant biomass associated with them but were distinct in PLFA fingerprint and δ13C – PLFA signatures indicating the presence of three distinct microbial communities living in association with the fracture fluids and gases. These results have implications for the potential existence of ancient deep subsurface communities that have survived geologic time in isolation, in particular with relation to the subsurface of Mars, as well as give us insight into life on the early Earth.ThesisMaster of Science (MSc