Genetics re-establish the utility of 2-methylhopanes as cyanobacterial biomarkers before 750 million years ago

Fossilized lipids offer a rare glimpse into ancient ecosystems. 2-Methylhopanes in sedimentary rocks were once used to infer the importance of cyanobacteria as primary producers throughout geological history. However, the discovery of hopanoid C-2 methyltransferase (HpnP) in Alphaproteobacteria led to the downfall of this molecular proxy. In the present study, we re-examined the distribution of HpnP in a new phylogenetic framework including recently proposed candidate phyla and re-interpreted a revised geological record of 2-methylhopanes based on contamination-free samples. We show that HpnP was probably present in the last common ancestor of cyanobacteria, while the gene appeared in Alphaproteobacteria only around 750 million years ago (Ma). A subsequent rise of sedimentary 2-methylhopanes around 600 Ma probably reflects the expansion of Alphaproteobacteria that coincided with the rise of eukaryotic algae-possibly connected by algal dependency on microbially produced vitamin B12. Our findings re-establish 2-methylhopanes as cyanobacterial biomarkers before 750 Ma and thus as a potential tool to measure the importance of oxygenic cyanobacteria as primary producers on early Earth. Our study illustrates how genetics can improve the diagnostic value of biomarkers and refine the reconstruction of early ecosystems.

Rapid encapsulation of true ferns and arborane/fernane compounds fossilised in siderite concretions supports analytical distinction of plant fossils

Fossilised true ferns (Pecopteris sp.) preserved in siderite concretions from the Mazon Creek Lagerstätte (Illinois) presented a unique opportunity to characterise the organic signatures of these late Carboniferous plants. Localised analyses of true fern fossils showed several highly abundant phytohopanoids and fernane/arborane derived aromatic products, which were present only negligibly within their siderite matrix, as well as from other types of fossilised plants. These terpenoids had been recognised in some extant ferns, but scarcely in sedimentary organic matter and their exact source remained ambiguous. The present fossil biomarker data confirms an ancient true fern origin. Furthermore, the excellent concretion preservation of a series of related terpenoid products provided a rare insight into their diagenetic formation. The benign properties of carbonate concretions could be exploited further for biomarker evidence of other fossilised organisms, with one important caveat being that biomarker signals attributed to isolated fossils be significantly distinct from background organic matter pervading the concretion matrix. For instance, hydrocarbon profiles of seed ferns (pteridosperms) and articulates (horsetails) also preserved in Mazon Creek concretions were indistinguishable from separate analysis of their concretion matrix, preventing biomarker recognition.

Early sea ice decline off East Antarctica at the last glacial-interglacial climate transition

Antarctic climate warming and atmospheric CO2 rise during the last deglaciation may be attributed in part to sea ice reduction in the Southern Ocean. Yet, glacial-interglacial Antarctic sea ice dynamics and underlying mechanisms are poorly constrained, as robust sea ice proxy evidence is sparse. Here, we present a molecular biomarker-based sea ice record that resolves the spring/summer sea ice variability off East Antarctica during the past 40 thousand years (ka). Our results indicate that substantial sea ice reduction culminated rapidly and contemporaneously with upwelling of carbon-enriched waters in the Southern Ocean at the onset of the last deglaciation but began at least ~2 ka earlier probably driven by an increasing local integrated summer insolation. Our findings suggest that sea ice reduction and associated feedbacks facilitated stratification breakup and outgassing of CO2 in the Southern Ocean and warming in Antarctica but may also have played a leading role in initializing these deglacial processes in the Southern Hemisphere.

Biological diversification linked to environmental stabilization following the Sturtian Snowball glaciation

The body fossil and biomarker records hint at an increase in biotic complexity between the two Cryogenian Snowball Earth episodes (ca. 661 million to ≤650 million years ago). Oxygen and nutrient availability can promote biotic complexity, but nutrient (particularly phosphorus) and redox dynamics across this interval remain poorly understood. Here, we present high-resolution paleoredox and phosphorus phase association data from multiple globally distributed drill core records through the non-glacial interval. These data are first correlated regionally by litho- and chemostratigraphy, and then calibrated within a series of global chronostratigraphic frameworks. The combined data show that regional differences in postglacial redox stabilization were partly controlled by the intensity of phosphorus recycling from marine sediments. The apparent increase in biotic complexity followed a global transition to more stable and less reducing conditions in shallow to mid-depth marine environments and occurred within a tolerable climatic window during progressive cooling after post-Snowball super-greenhouse conditions.

Lost world of complex life and the late rise of the eukaryotic crown

Eukaryotic life appears to have flourished surprisingly late in the history of our planet. This view is based on the low diversity of diagnostic eukaryotic fossils in marine sediments of mid-Proterozoic age (around 1,600 to 800 million years ago) and an absence of steranes, the molecular fossils of eukaryotic membrane sterols^1,2. This scarcity of eukaryotic remains is difficult to reconcile with molecular clocks that suggest that the last eukaryotic common ancestor (LECA) had already emerged between around 1,200 and more than 1,800 million years ago. LECA, in turn, must have been preceded by stem-group eukaryotic forms by several hundred million years³. Here we report the discovery of abundant protosteroids in sedimentary rocks of mid-Proterozoic age. These primordial compounds had previously remained unnoticed because their structures represent early intermediates of the modern sterol biosynthetic pathway, as predicted by Konrad Bloch⁴. The protosteroids reveal an ecologically prominent 'protosterol biota' that was widespread and abundant in aquatic environments from at least 1,640 to around 800 million years ago and that probably comprised ancient protosterol-producing bacteria and deep-branching stem-group eukaryotes. Modern eukaryotes started to appear in the Tonian period (1,000 to 720 million years ago), fuelled by the proliferation of red algae (rhodophytes) by around 800 million years ago. This 'Tonian transformation' emerges as one of the most profound ecological turning points in the Earth's history.

Guts, gut contents, and feeding strategies of Ediacaran animals

The oldest animals appear in the fossil record among Ediacara biota communities. They prelude animal-dominated ecosystems of the Phanerozoic and may hold clues to the appearance of modern animal phyla in the Cambrian explosion. However, little is known about the phylogeny of the Ediacaran organisms and even less about their diet and feeding behavior.^1,2,3 An exception is mollusc-like Kimberella, for which a fossilized gut, feeding traces, and even potential coprolites have been found.^4,5 By contrast, Ediacaran organic-walled tubes, such as Sabellidites and Calyptrina, are thought to belong to tube worms comparable with modern Siboglinidae that have no gut but gain their nutrition from symbiotic bacteria.^6,7 Here, we examine the gut contents of Ediacaran animals using biomarker molecules. We show that 558-million-year (Ma)-old tube worm-like Calyptrina and mollusc-like Kimberella possessed a gut and shared a diet of green algae and bacteria. Despite their ancient age, sterol metabolism within the gut of both organisms was already comparable to extant invertebrates.⁸Dickinsonia, one of the key Ediacaran animals, show no traces of dietary molecules, indicating a different feeding mode and possible external digestion analogous to modern Placozoa. Lipid biomarkers uncover a range of feeding strategies in Ediacaran communities, highlighting true eumetazoan physiology of some Ediacaran animals.

Intracellular bound chlorophyll residues identify 1 Gyr-old fossils as eukaryotic algae

The acquisition of photosynthesis is a fundamental step in the evolution of eukaryotes. However, few phototrophic organisms are unambiguously recognized in the Precambrian record. The in situ detection of metabolic byproducts in individual microfossils is the key for the direct identification of their metabolisms. Here, we report a new integrative methodology using synchrotron-based X-ray fluorescence and absorption. We evidence bound nickel-geoporphyrins moieties in low-grade metamorphic rocks, preserved in situ within cells of a ~1 Gyr-old multicellular eukaryote, Arctacellularia tetragonala. We identify these moieties as chlorophyll derivatives, indicating that A. tetragonala was a phototrophic eukaryote, one of the first unambiguous algae. This new approach, applicable to overmature rocks, creates a strong new proxy to understand the evolution of phototrophy and diversification of early ecosystems.

Geological alteration of Precambrian steroids mimics early animal signatures

The absence of unambiguous animal body fossils in rocks older than the late Ediacaran has rendered fossil lipids the most promising tracers of early organismic complexity. Yet much debate surrounds the various potential biological sources of putative metazoan steroids found in Precambrian rocks. Here we show that 26-methylated steranes-hydrocarbon structures currently attributed to the earliest animals-can form via geological alteration of common algal sterols, which carries important implications for palaeo-ecological interpretations and inhibits the use of such unconventional 'sponge' steranes for reconstructing early animal evolution.

Discovery of the oldest known biomarkers provides evidence for phototrophic bacteria in the 1.73 Ga Wollogorang Formation, Australia

The discovery of mid-Proterozoic (1.8-0.8 billion years ago, Ga) indigenous biomarkers is a challenge, since biologically informative molecules of such antiquity are commonly destroyed by metamorphism or overprinted by drilling fluids and other anthropogenic petroleum products. Previously, the oldest clearly indigenous biomarkers were reported from the 1.64 Ga Barney Creek Formation in the northern Australian McArthur Basin. In this study, we present the discovery of biomarker molecules from carbonaceous shales of the 1.73 Ga Wollogorang Formation in the southern McArthur Basin, extending the biomarker record back in time by ~90 million years. The extracted hydrocarbons illustrate typical mid-Proterozoic signatures with a large unresolved complex mixture, high methyl alkane/n-alkane ratios and the absence of eukaryotic steranes. Acyclic isoprenoids, saturated carotenoid derivatives, bacterial hopanes and aromatic hopanoids and steroids also were below detection limits. However, continuous homologous series of low molecular weight C₁₄ -C₁₉ 2,3,4- and 2,3,6-trimethyl aryl isoprenoids (AI) were identified, and C₂₀ -C₂₂ AI homologues were tentatively identified. Based on elevated abundances relative to abiogenic isomers, we interpret the 2,3,6-AI isomer series as biogenic molecules and the 2,3,4-AI series as possibly biogenic. The biological sources for the 2,3,6-AI series include carotenoids of cyanobacteria and/or green sulphur bacteria (Chlorobiaceae). The lower concentrated 2,3,4-AI series may be derived from purple sulphur bacteria (Chromatiaceae). These degradation products of carotenoids are the oldest known clearly indigenous molecules of likely biogenic origin.

Food sources for the Ediacara biota communities

The Ediacara biota represents the first complex macroscopic organisms in the geological record, foreshadowing the radiation of eumetazoan animals in the Cambrian explosion. However, little is known about the contingencies that lead to their emergence, including the possible roles of nutrient availability and the quality of food sources. Here we present information on primary producers in the Ediacaran based on biomarker molecules that were extracted from sediments hosting Ediacaran macrofossils. High relative abundances of algal steranes over bacterial hopanes suggest that the Ediacara biota inhabited nutrient replete environments with an abundance of algal food sources comparable to Phanerozoic ecosystems. Thus, organisms of the Ediacara biota inhabited nutrient-rich environments akin to those that later fuelled the Cambrian explosion.

Microbial assemblage and palaeoenvironmental reconstruction of the 1.38 Ga Velkerri Formation, McArthur Basin, northern Australia

The ca. 1.38 billion years (Ga) old Roper Group of the McArthur Basin, northern Australia, is one of the most extensive Proterozoic hydrocarbon-bearing units. Organic-rich black siltstones from the Velkerri Formation were deposited in a deep-water sequence and were analysed to determine their organic geochemical (biomarker) signatures, which were used to interpret the microbial diversity and palaeoenvironment of the Roper Seaway. The indigenous hydrocarbon biomarker assemblages describe a water column dominated by bacteria with large-scale heterotrophic reworking of the organic matter in the water column or bottom sediment. Possible evidence for microbial reworking includes a large unresolved complex mixture (UCM), high ratios of mid-chained and terminally branched monomethyl alkanes relative to n-alkanes-features characteristic of indigenous Proterozoic bitumen. Steranes, biomarkers for single-celled and multicellular eukaryotes, were below detection limits in all extracts analysed, despite eukaryotic microfossils having been previously identified in the Roper Group, albeit largely in organically lean shallower water facies. These data suggest that eukaryotes, while present in the Roper Seaway, were ecologically restricted and contributed little to export production. The 2,3,4- and 2,3,6-trimethyl aryl isoprenoids (TMAI) were absent or in very low concentration in the Velkerri Formation. The low abundance is primary and not caused by thermal destruction. The combination of increased dibenzothiophene in the Amungee Member of the Velkerri Formation and trace metal redox geochemistry suggests that degradation of carotenoids occurred during intermittent oxygen exposure at the sediment-water interface and/or the water column was rarely euxinic in the photic zone and likely only transiently euxinic at depth. A comparison of this work with recently published biomarker and trace elemental studies from other mid-Proterozoic basins demonstrates that microbial environments, water column geochemistry and basin redox were heterogeneous.

Ancient steroids establish the Ediacaran fossil Dickinsonia as one of the earliest animals

The enigmatic Ediacara biota (571 million to 541 million years ago) represents the first macroscopic complex organisms in the geological record and may hold the key to our understanding of the origin of animals. Ediacaran macrofossils are as "strange as life on another planet" and have evaded taxonomic classification, with interpretations ranging from marine animals or giant single-celled protists to terrestrial lichens. Here, we show that lipid biomarkers extracted from organically preserved Ediacaran macrofossils unambiguously clarify their phylogeny. Dickinsonia and its relatives solely produced cholesteroids, a hallmark of animals. Our results make these iconic members of the Ediacara biota the oldest confirmed macroscopic animals in the rock record, indicating that the appearance of the Ediacara biota was indeed a prelude to the Cambrian explosion of animal life.

Snowball Earth climate dynamics and Cryogenian geology-geobiology

Geological evidence indicates that grounded ice sheets reached sea level at all latitudes during two long-lived Cryogenian (58 and ≥5 My) glaciations. Combined uranium-lead and rhenium-osmium dating suggests that the older (Sturtian) glacial onset and both terminations were globally synchronous. Geochemical data imply that CO₂ was 10² PAL (present atmospheric level) at the younger termination, consistent with a global ice cover. Sturtian glaciation followed breakup of a tropical supercontinent, and its onset coincided with the equatorial emplacement of a large igneous province. Modeling shows that the small thermal inertia of a globally frozen surface reverses the annual mean tropical atmospheric circulation, producing an equatorial desert and net snow and frost accumulation elsewhere. Oceanic ice thickens, forming a sea glacier that flows gravitationally toward the equator, sustained by the hydrologic cycle and by basal freezing and melting. Tropical ice sheets flow faster as CO₂ rises but lose mass and become sensitive to orbital changes. Equatorial dust accumulation engenders supraglacial oligotrophic meltwater ecosystems, favorable for cyanobacteria and certain eukaryotes. Meltwater flushing through cracks enables organic burial and submarine deposition of airborne volcanic ash. The subglacial ocean is turbulent and well mixed, in response to geothermal heating and heat loss through the ice cover, increasing with latitude. Terminal carbonate deposits, unique to Cryogenian glaciations, are products of intense weathering and ocean stratification. Whole-ocean warming and collapsing peripheral bulges allow marine coastal flooding to continue long after ice-sheet disappearance. The evolutionary legacy of Snowball Earth is perceptible in fossils and living organisms.

Cryogenian evolution of stigmasteroid biosynthesis

Sedimentary hydrocarbon remnants of eukaryotic C₂₆-C₃₀ sterols can be used to reconstruct early algal evolution. Enhanced C₂₉ sterol abundances provide algal cell membranes a density advantage in large temperature fluctuations. Here, we combined a literature review with new analyses to generate a comprehensive inventory of unambiguously syngenetic steranes in Neoproterozoic rocks. Our results show that the capacity for C₂₉ 24-ethyl-sterol biosynthesis emerged in the Cryogenian, that is, between 720 and 635 million years ago during the Neoproterozoic Snowball Earth glaciations, which were an evolutionary stimulant, not a bottleneck. This biochemical innovation heralded the rise of green algae to global dominance of marine ecosystems and highlights the environmental drivers for the evolution of sterol biosynthesis. The Cryogenian emergence of C₂₉ sterol biosynthesis places a benchmark for verifying older sterane signatures and sets a new framework for our understanding of early algal evolution.

Paleoecology of Neoproterozoic hypersaline environments: Biomarker evidence for haloarchaea, methanogens, and cyanobacteria

While numerous studies have examined modern hypersaline ecosystems, their equivalents in the geologic past, particularly in the Precambrian, are poorly understood. In this study, biomarkers from ~820 million year (Ma)-old evaporites from the Gillen Formation of the mid-Neoproterozoic Bitter Springs Group, central Australia, are investigated to elucidate the antiquity and paleoecology of halophiles. The sediments were composed of alternating laminae of dolomitized microbial mats and up to 90% anhydrite. Solvent extraction of these samples yielded thermally well-preserved hydrocarbon biomarkers. The regularly branched C₂₅ isoprenoid 2,6,10,14,18-pentamethylicosane, the tail-to-tail linked C₃₀ isoprenoid squalane, and breakdown products of the head-to-head linked C₄₀ isoprenoid biphytane, were particularly abundant in the most anhydrite-rich sediments and mark the oldest current evidence for halophilic archaea. Linear correlations between isoprenoid concentrations (normalized to n-alkanes) and the anhydrite/dolomite ratio reveal microbial consortia that fluctuated with changing salinity levels. Halophilic archaea were the dominant organisms during periods of high salinity and gypsum precipitation, while bacteria were prevalent during stages of carbonate formation. The irregularly branched C₂₅ isoprenoid 2,6,10,15,19-pentamethylicosane (PMI), with a central tail-to-tail link, was also abundant during periods of elevated salinity, highlighting the activity of methanogens. By contrast, the irregularly branched C₂₀ isoprenoid 2,6,11,15-tetramethylhexadecane (crocetane) was more common in dolomite-rich facies, revealing that an alternate group of archaea was active during less saline periods. Elevated concentrations of isotopically depleted heptadecane (n-C₁₇ ) revealed the presence of cyanobacteria under all salinity regimes. The combination of biomarkers in the mid-Neoproterozoic Gillen Formation resembles lipid compositions from modern hypersaline cyanobacterial mats, pointing to a community composition that remained broadly constant since at least the Neoproterozoic. However, as a major contrast to most modern hypersaline environments, the Gillen evaporites did not yield any evidence for algae or other eukaryotes.

Local paleoenvironmental controls on the carbon-isotope record defining the Bitter Springs Anomaly

Large magnitude (>10‰) carbon-isotope (δ¹³ C) excursions recorded in carbonate-bearing sediments are increasingly used to monitor environmental change and constrain the chronology of the critical interval in the Neoproterozoic stratigraphic record that is timed with the first appearance and radiation of metazoan life. The ~10‰ Bitter Springs Anomaly preserved in Tonian-aged (1000-720 Ma) carbonate rocks in the Amadeus Basin of central Australia has been offered as one of the best preserved examples of a primary marine δ¹³ C excursion because it is regionally reproducible and δ¹³ C values covary in organic and carbonate carbon arguing against diagenetic exchange. However, here we show that δ¹³ C values defining the excursion coincide with abrupt lithofacies changes between regularly cyclic grainstone and microbial carbonates, and desiccated red bed mudstones with interbedded evaporite and dolomite deposits, recording local environmental shifts from restricted marine conditions to alkaline lacustrine and playa settings that preserve negative (-4‰) and positive (+6‰) δ¹³ C values, respectively. The stratigraphic δ¹³ C pattern in both organic and carbonate carbon recurs within the basin in a similar way to associated sedimentary facies, reflecting the linkage of local paleoenvironmental conditions and δ¹³ C values. These local excursions may be time transgressive or record a relative sea-level influence manifest through exposure of sub-basins isolated by sea-level fall below shallow sills, but are independent of secular seawater variation. As the shallow intracratonic setting of the Bitter Springs Formation is typical of other Neoproterozoic carbonate successions used to construct the present δ¹³ C seawater record, it identifies the potential for local influences on δ¹³ C excursions that are neither diagenetic nor representative of the global exogenic cycle.

Early sponges and toxic protists: possible sources of cryostane, an age diagnostic biomarker antedating Sturtian Snowball Earth

The period 800-717 million years (Ma) ago, in the lead-up to the Sturtian Snowball glaciation, saw an increase in the diversity of eukaryotic microfossils. To afford an independent and complementary view of this evolutionary period, this study presents the distribution of eukaryotic biomarkers from three pre-Sturtian successions across the supercontinent Rodinia: the ca. 780 Ma Kanpa Formation of the Western Australian Officer Basin, the ca. 800-740 Ma Visingsö Group of Sweden, and the 740 Ma Chuar Group in Arizona, USA. The distribution of eukaryotic steranes is remarkably similar in the three successions but distinct from all other known younger and older sterane assemblages. Cholestane was the only conventional structure, while indigenous steranes alkylated in position C-24, such as ergostane, stigmastane, dinosterane and isopropylcholestane, and n-propylcholestane, were not observed. This sterane distribution appears to be age diagnostic for the pre-Sturtian Neoproterozoic. It attests to the distinct evolutionary state of pre-Snowball eukaryotes, pointing to a taxonomic disparity that was still lower than in the Ediacaran (635-541 Ma). All three basins also show the presence of a new C28 sterane that was tentatively identified as 26-methylcholestane, here named cryostane. The only known extant organisms that can methylate sterols in the 26-position are demosponges. This assignment is plausible as molecular clocks place the appearance of the earliest animals into the pre-Sturtian Neoproterozoic. The unusual 26-methylsterol may have protected sponges, but also other eukaryotes, against their own membranolytic toxins. Some protists release lytic toxins to deter predators and kill eukaryotic prey. As conventional membrane sterols can be the site of attack for these toxins, sterols with unusual side-chain modification protect the cell. This interpretation of cryostane supports fossil evidence of predation in the Chuar Group and promotes hypotheses about the proliferation of eukaryophagy in the lead-up to the Cryogenian.

Reappraisal of hydrocarbon biomarkers in Archean rocks

Hopanes and steranes found in Archean rocks have been presented as key evidence supporting the early rise of oxygenic photosynthesis and eukaryotes, but the syngeneity of these hydrocarbon biomarkers is controversial. To resolve this debate, we performed a multilaboratory study of new cores from the Pilbara Craton, Australia, that were drilled and sampled using unprecedented hydrocarbon-clean protocols. Hopanes and steranes in rock extracts and hydropyrolysates from these new cores were typically at or below our femtogram detection limit, but when they were detectable, they had total hopane (<37.9 pg per gram of rock) and total sterane (<32.9 pg per gram of rock) concentrations comparable to those measured in blanks and negative control samples. In contrast, hopanes and steranes measured in the exteriors of conventionally drilled and curated rocks of stratigraphic equivalence reach concentrations of 389.5 pg per gram of rock and 1,039 pg per gram of rock, respectively. Polycyclic aromatic hydrocarbons and diamondoids, which exceed blank concentrations, exhibit individual concentrations up to 80 ng per gram of rock in rock extracts and up to 1,000 ng per gram of rock in hydropyrolysates from the ultraclean cores. These results demonstrate that previously studied Archean samples host mixtures of biomarker contaminants and indigenous overmature hydrocarbons. Therefore, existing lipid biomarker evidence cannot be invoked to support the emergence of oxygenic photosynthesis and eukaryotes by ∼ 2.7 billion years ago. Although suitable Proterozoic rocks exist, no currently known Archean strata lie within the appropriate thermal maturity window for syngenetic hydrocarbon biomarker preservation, so future exploration for Archean biomarkers should screen for rocks with milder thermal histories.

A framework for the extraction and interpretation of organic molecules in speleothem carbonate

RATIONALE

The organic content of speleothem calcite is a well-recognized component of their chemical composition. To date, the techniques for interpretation of this material include UV fluorescence, FTIR spectroscopy and biomarker analysis using gas chromatography/mass spectroscopy (GC/MS). However, investigation of the minute concentrations of molecules in speleothems demands careful sampling and laboratory controls.

METHODS

To be certain extracted molecules were encapsulated at the time of speleothem growth and do not represent contamination, we submitted three pieces of speleothem calcite to a rigorous extraction procedure. Based on sequential digestion and analysis by GC/MS, we measured concentration profiles of individual compounds with increasing distance from sample surfaces.

RESULTS

Declining concentrations toward interior extracts identified cholesterol, phthalates, and n-alkanes as surface contaminants. In contrast, iodo organic compounds had homogeneous concentration profiles and were also significantly above laboratory background levels, consistent with an indigenous origin. However, further laboratory testing demonstrated that iodo organics were produced by the reaction of iodine derived from the speleothem with solvent additives and other impurities of the extraction procedure. Sitosterol and some fatty acids demonstrated distributions which were probably indigenous to the speleothem archive, thus recording environmental conditions commensurate with time of growth.

CONCLUSIONS

We do not aim to provide an environmental interpretation of extracted molecules, but highlight the caution necessary before doing so. We ultimately establish a framework for differentiating between organic constituents that are introduced to the speleothems during storage, handling and as artifacts of extraction, and those encapsulated in situ at the time of growth.

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

This study describes reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries from surface waters of Lake Tyrrell (LT), a hypersaline lake in NW Victoria, Australia. Lineage-specific probes were designed using the assembled genomes to visualize these novel archaea, which were highly abundant in the 0.1-0.8 μm size fraction of lake water samples. Gene content and inferred metabolic capabilities were highly dissimilar to all previously identified hypersaline microbial species. Distinctive characteristics included unique amino acid composition, absence of Gvp gas vesicle proteins, atypical archaeal metabolic pathways and unusually small cell size (approximately 0.6 μm diameter). Multi-locus phylogenetic analyses demonstrated that these organisms belong to a new major euryarchaeal lineage, distantly related to halophilic archaea of class Halobacteria. Consistent with these findings, we propose creation of a new archaeal class, provisionally named 'Nanohaloarchaea'. In addition to their high abundance in LT surface waters, we report the prevalence of Nanohaloarchaea in other hypersaline environments worldwide. The simultaneous discovery and genome sequencing of a novel yet ubiquitous lineage of uncultivated microorganisms demonstrates that even historically well-characterized environments can reveal unexpected diversity when analyzed by metagenomics, and advances our understanding of the ecology of hypersaline environments and the evolutionary history of the archaea.

Unravelling ancient microbial history with community proteogenomics and lipid geochemistry

Our window into the Earth's ancient microbial past is narrow and obscured by missing data. However, we can glean information about ancient microbial ecosystems using fossil lipids (biomarkers) that are extracted from billion-year-old sedimentary rocks. In this Opinion article, we describe how environmental genomics and related methodologies will give molecular fossil research a boost, by increasing our knowledge about how evolutionary innovations in microorganisms have changed the surface of planet Earth.

Reassessing the first appearance of eukaryotes and cyanobacteria

The evolution of oxygenic photosynthesis had a profound impact on the Earth's surface chemistry, leading to a sharp rise in atmospheric oxygen between 2.45 and 2.32 billion years (Gyr) ago and the onset of extreme ice ages. The oldest widely accepted evidence for oxygenic photosynthesis has come from hydrocarbons extracted from approximately 2.7-Gyr-old shales in the Pilbara Craton, Australia, which contain traces of biomarkers (molecular fossils) indicative of eukaryotes and suggestive of oxygen-producing cyanobacteria. The soluble hydrocarbons were interpreted to be indigenous and syngenetic despite metamorphic alteration and extreme enrichment (10-20 per thousand) of (13)C relative to bulk sedimentary organic matter. Here we present micrometre-scale, in situ (13)C/(12)C measurements of pyrobitumen (thermally altered petroleum) and kerogen from these metamorphosed shales, including samples that originally yielded biomarkers. Our results show that both kerogen and pyrobitumen are strongly depleted in (13)C, indicating that indigenous petroleum is 10-20 per thousand lighter than the extracted hydrocarbons. These results are inconsistent with an indigenous origin for the biomarkers. Whatever their origin, the biomarkers must have entered the rock after peak metamorphism approximately 2.2 Gyr ago and thus do not provide evidence for the existence of eukaryotes and cyanobacteria in the Archaean eon. The oldest fossil evidence for eukaryotes and cyanobacteria therefore reverts to 1.78-1.68 Gyr ago and approximately 2.15 Gyr ago, respectively. Our results eliminate the evidence for oxygenic photosynthesis approximately 2.7 Gyr ago and exclude previous biomarker evidence for a long delay (approximately 300 million years) between the appearance of oxygen-producing cyanobacteria and the rise in atmospheric oxygen 2.45-2.32 Gyr ago.

Sporulenes, heptaprenyl metabolites from Bacillus subtilis spores

Sporulene, a C₃₅-terpenoid hydrocarbon with an unusual pentacyclic structure, is produced by Bacillus subtilis during sporulation.

Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea

The disappearance of iron formations from the geological record approximately 1.8 billion years (Gyr) ago was the consequence of rising oxygen levels in the atmosphere starting 2.45-2.32 Gyr ago. It marks the end of a 2.5-Gyr period dominated by anoxic and iron-rich deep oceans. However, despite rising oxygen levels and a concomitant increase in marine sulphate concentration, related to enhanced sulphide oxidation during continental weathering, the chemistry of the oceans in the following mid-Proterozoic interval (approximately 1.8-0.8 Gyr ago) probably did not yet resemble our oxygen-rich modern oceans. Recent data indicate that marine oxygen and sulphate concentrations may have remained well below current levels during this period, with one model indicating that anoxic and sulphidic marine basins were widespread, and perhaps even globally distributed. Here we present hydrocarbon biomarkers (molecular fossils) from a 1.64-Gyr-old basin in northern Australia, revealing the ecological structure of mid-Proterozoic marine communities. The biomarkers signify a marine basin with anoxic, sulphidic, sulphate-poor and permanently stratified deep waters, hostile to eukaryotic algae. Phototrophic purple sulphur bacteria (Chromatiaceae) were detected in the geological record based on the new carotenoid biomarker okenane, and they seem to have co-existed with communities of green sulphur bacteria (Chlorobiaceae). Collectively, the biomarkers support mounting evidence for a long-lasting Proterozoic world in which oxygen levels remained well below modern levels.

Phylogenetic and biochemical evidence for sterol synthesis in the bacterium Gemmata obscuriglobus

Sterol biosynthesis is viewed primarily as a eukaryotic process, and the frequency of its occurrence in bacteria has long been a subject of controversy. Two enzymes, squalene monooxygenase and oxidosqualene cyclase, are the minimum necessary for initial biosynthesis of sterols from squalene. In this work, 19 protein gene sequences for eukaryotic squalene monooxygenase and 12 protein gene sequences for eukaryotic oxidosqualene cyclase were compared with all available complete and partial prokaryotic genomes. The only unequivocal matches for a sterol biosynthetic pathway were in the proteobacterium, Methylococcus capsulatus, in which sterol biosynthesis is known, and in the planctomycete, Gemmata obscuriglobus. The latter species contains the most abbreviated sterol pathway yet identified in any organism. Analysis shows that the major sterols in Gemmata are lanosterol and its uncommon isomer, parkeol. There are no subsequent modifications of these products. In bacteria, the sterol biosynthesis genes occupy a contiguous coding region and possibly comprise a single operon. Phylogenetic trees constructed for both enzymes show that the sterol pathway in bacteria and eukaryotes has a common ancestry. It is likely that this contiguous reading frame was exchanged between bacteria and early eukaryotes via lateral gene transfer or endosymbiotic events. The primitive sterols produced by Gemmata suggest that this genus could retain the most ancient remnants of the sterol biosynthetic pathway.

Archean molecular fossils and the early rise of eukaryotes

Molecular fossils of biological lipids are preserved in 2700-million-year-old shales from the Pilbara Craton, Australia. Sequential extraction of adjacent samples shows that these hydrocarbon biomarkers are indigenous and syngenetic to the Archean shales, greatly extending the known geological range of such molecules. The presence of abundant 2alpha-methylhopanes, which are characteristic of cyanobacteria, indicates that oxygenic photosynthesis evolved well before the atmosphere became oxidizing. The presence of steranes, particularly cholestane and its 28- to 30-carbon analogs, provides persuasive evidence for the existence of eukaryotes 500 million to 1 billion years before the extant fossil record indicates that the lineage arose.