1.1-billion-year-old porphyrins establish a marine ecosystem dominated by bacterial primary producers

Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes

The origin of eukaryotes was a key event in the history of life. Current leading hypotheses propose that a symbiosis between an asgardarchaeal host cell and an alphaproteobacterial endosymbiont represented a crucial step in eukaryotic origin and that metabolic cross-feeding between the partners provided the basis for their subsequent evolutionary integration. A major unanswered question is whether the metabolism of modern eukaryotes bears any vestige of this ancestral syntrophy. Here we systematically analyse the evolutionary origins of the eukaryotic gene repertoires mediating central carbon metabolism. Our phylogenetic and sequence analyses reveal that this gene repertoire is chimeric, with ancestral contributions from Asgardarchaeota and Alphaproteobacteria operating predominantly in glycolysis and the tricarboxylic acid cycle, respectively. Our analyses also reveal the extent to which this ancestral metabolic interplay has been remodelled via gene loss, transfer and subcellular retargeting in the >2 billion years since the origin of eukaryotic cells, and we identify genetic contributions from other prokaryotic sources in addition to the asgardarchaeal host and alphaproteobacterial endosymbiont. Our work demonstrates that, in contrast to previous assumptions, modern eukaryotic metabolism preserves information about the nature of the original asgardarchaeal-alphaproteobacterial interactions and supports syntrophy scenarios for the origin of the eukaryotic cell.

Hybrid Nanoplatforms Based on Photosensitizers and Metal/Covalent Organic Frameworks for Improved Cancer Synergistic Treatment Nano-Delivery Systems

Researchers have extensively investigated photosensitizer (PS) derivatives for various applications due to their superior photophysical and electrochemical properties. However, inherent problems, such as instability and self-quenching under physiological conditions, limit their biological applications. Metal-organic frameworks (MOFs) and covalent organic frameworks (COFs) represent two relatively new material types. These materials have high surface areas and permanent porosity, and they show a tremendous deal of potential for applications like these. This review summarizes key synthesis processes and highlights recent advancements in integrating PS-based COF and MOF nanocarriers for biomedical applications while addressing potential obstacles and prospects.

Polysphaeroides filiformis, a proterozoic cyanobacterial microfossil and implications for cyanobacteria evolution

Deciphering the fossil record of cyanobacteria is crucial to understand their role in the chemical and biological evolution of the early Earth. They profoundly modified the redox conditions of early ecosystems more than 2.4 Ga ago, the age of the Great Oxidation Event (GOE), and provided the ancestor of the chloroplast by endosymbiosis, leading the diversification of photosynthetic eukaryotes. Here, we analyze the morphology, ultrastructure, chemical composition, and metals distribution of Polysphaeroides filiformis from the 1040-1006 Ma Mbuji-Mayi Supergroup (DR Congo). We evidence trilaminar and bilayered ultrastructures for the sheath and the cell wall, respectively, and the preservation of Ni-tetrapyrrole moieties derived from chlorophyll in intracellular inclusions. This approach allows an unambiguous interpretation of P. filiformis as a branched and multiseriate photosynthetic cyanobacterium belonging to the family of Stigonemataceae. It also provides a possible minimum age for the emergence of multiseriate true branching nitrogen-fixing and probably heterocytous cyanobacteria.

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.

Recurrent photic zone euxinia limited ocean oxygenation and animal evolution during the Ediacaran

The Ediacaran Period (~635-539 Ma) is marked by the emergence and diversification of complex metazoans linked to ocean redox changes, but the processes and mechanism of the redox evolution in the Ediacaran ocean are intensely debated. Here we use mercury isotope compositions from multiple black shale sections of the Doushantuo Formation in South China to reconstruct Ediacaran oceanic redox conditions. Mercury isotopes show compelling evidence for recurrent and spatially dynamic photic zone euxinia (PZE) on the continental margin of South China during time intervals coincident with previously identified ocean oxygenation events. We suggest that PZE was driven by increased availability of sulfate and nutrients from a transiently oxygenated ocean, but PZE may have also initiated negative feedbacks that inhibited oxygen production by promoting anoxygenic photosynthesis and limiting the habitable space for eukaryotes, hence abating the long-term rise of oxygen and restricting the Ediacaran expansion of macroscopic oxygen-demanding animals.

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.

Discovering Nature's Fingerprints: Isotope Ratio Analysis on Bioanalytical Mass Spectrometers

For a generation or more, the mass spectrometry that developed at the frontier of molecular biology was worlds apart from isotope ratio mass spectrometry, a label-free approach done on optimized gas-source magnetic sector instruments. Recent studies show that electrospray-ionization Orbitraps and other mass spectrometers widely used in the life sciences can be fine-tuned for high-precision isotope ratio analysis. Since isotope patterns form everywhere in nature based on well-understood principles, intramolecular isotope measurements allow unique insights into a fascinating range of research topics. This Perspective introduces a wider readership to current topics in stable isotope research with the aim of discussing how soft-ionization mass spectrometry coupled with ultrahigh mass resolution can enable long-envisioned progress. We highlight novel prospects of observing isotopes in intact polar compounds and speculate on future directions of this adventure into the overlapping realms of biology, chemistry, and geology.

Hallmarks of anticancer and antimicrobial activities of corroles

Corroles provide a remarkable opportunity for the development of cancer theranostic agents among other porphyrinoids. While most transition metal corrole complexes are only therapeutic, post-transition metallocorroles also find their applications in bioimaging. Moreover, corroles exhibit excellent photo-physicochemical properties, which can be harnessed for antitumor and antimicrobial interventions. Nevertheless, these intriguing, yet distinct properties of corroles, have not attained sufficient momentum in cancer research. The current review provides a comprehensive summary of various cancer-relevant features of corroles ranging from their structural and photophysical properties, chelation, protein/corrole interactions, to DNA intercalation. Another aspect of the paper deals with the studies of corroles conducted in vitro and in vivo with an emphasis on medical imaging (optical and magnetic resonance), photo/sonodynamic therapies, and photodynamic inactivation. Special attention is also given to a most recent finding that shows the development of pH-responsive phosphorus corrole as a potent antitumor drug for organelle selective antitumor cytotoxicity in preclinical studies. Another biomedical application of corroles is also highlighted, signifying the application of water-soluble and completely lipophilic corroles in the photodynamic inactivation of microorganisms. We strongly believe that future studies will offer a greater possibility of utilizing advanced corroles for selective tumor targeting and antitumor cytotoxicity. In the line with future developments, an ideal pipeline is envisioned on grounds of cancer targeting nanoparticle systems upon decoration with tumor-specific ligands. Hence, we envision that a bright future lies ahead of corrole anticancer research and therapeutics.

Prediction of Structures of Compounds Encountered in Complex Organic Matter with Highly Flexible Alkyl Chains Using Ion Mobility-Mass Spectrometry

The chemical structure of an organic molecule has a direct influence on its three-dimensional conformation. One way to obtain information on this conformation is to use ion mobility spectrometry. This technique allows the separation of different isomers according to their collision cross section (CCS) with an inert gas. Smaller or more compact molecules will have lower collision cross section values than larger molecules. The CCS is an intrinsic ion parameter for a specific gas and is thus predictable. Today, calculations of rigid molecules are commonly performed to obtain additional structural information on an ion. However, calculations are more complex with very flexible molecules. In particular, molecules presenting long alkyl chains can yield a high number of conformers. Each conformer is then associated with a CCS value that is specific to it. We report, here, a methodology to predict CCS of flexible molecules. The used approach is based on automatic conformers research followed by geometry optimization and CCS calculations. Determination of theoretical and experimental CCS values for a rigid polycyclic aromatic hydrocarbons (PAHs) standard was used to calibrate the Mobcal software. Then, 13 standard molecules ranging from 4 to 19 carbon alkyl chains, including three long alkyl chain isomers of C₂₂H₃₈, were analyzed on a TWIMS-ToF and calculated using our methodology. CCS deviations between experimental and theoretical values were found to be less than 1.5% over the whole studied CCS range. This method was finally applied for structural analysis of petroleum compounds refractory to the hydro-denitrogenation process.

In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface

Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.

Biosignature stability in space enables their use for life detection on Mars

Two rover missions to Mars aim to detect biomolecules as a sign of extinct or extant life with, among other instruments, Raman spectrometers. However, there are many unknowns about the stability of Raman-detectable biomolecules in the martian environment, clouding the interpretation of the results. To quantify Raman-detectable biomolecule stability, we exposed seven biomolecules for 469 days to a simulated martian environment outside the International Space Station. Ultraviolet radiation (UVR) strongly changed the Raman spectra signals, but only minor change was observed when samples were shielded from UVR. These findings provide support for Mars mission operations searching for biosignatures in the subsurface. This experiment demonstrates the detectability of biomolecules by Raman spectroscopy in Mars regolith analogs after space exposure and lays the groundwork for a consolidated space-proven database of spectroscopy biosignatures in targeted environments.

Chemical, Thermal, and Radiation Resistance of an Iron Porphyrin: A Model Study of Biosignature Stability

Metal complexes of porphyrins and porphyrin-type compounds are ubiquitous in all three domains of life, with hemes and chlorophylls being the best-known examples. Their diagenetic transformation products are found as geoporphyrins, in which the characteristic porphyrin core structure is retained and which can be up to 1.1 billion years old. Because of this, and their relative ease of detection, metalloporphyrins appear attractive as chemical biosignatures in the search for extraterrestrial life. In this study, we investigated the stability of solid chlorido(2,3,7,8,12,13,17,18-octaethylporphyrinato)iron(III) [FeCl(oep)], which served as a model for heme-like molecules and iron geoporphyrins. [FeCl(oep)] was exposed to a variety of astrobiologically relevant extreme conditions, namely: aqueous acids and bases, oxidants, heat, and radiation. Key results are: (1) the [Fe(oep)]⁺ core is stable over the pH range 0.0-13.5 even at 80°C; (2) the oxidizing power follows the order ClO^- > H₂O₂ > ClO₃^- > HNO₃ > ClO₄^-; (3) in an inert atmosphere, the iron porphyrin is thermally stable to near 250°C; (4) at high temperatures, carbon dioxide gas is not inert but acts as an oxidant, forming carbon monoxide; (5) a decomposition layer is formed on ultraviolet irradiation and protects the [FeCl(oep)] underneath; (6) an NaCl/NaHCO₃ salt mixture has a protective effect against X-rays; and (7) no such effect is observed when [FeCl(oep)] is exposed to iron ion particle radiation. The relevance to potential iron porphyrin biosignatures on Mars, Europa, and Enceladus is discussed.

Characterization of the Halochromic Gloeocapsin Pigment, a Cyanobacterial Biosignature for Paleobiology and Astrobiology

Ultraviolet (UV)-screening compounds represent a substantial asset for the survival of cyanobacteria in extreme environments exposed to high doses of UV radiations on modern and early Earth. Among these molecules, the halochromic pigment gloeocapsin remains poorly characterized and studied. In this study, we identified a gloeocapsin-producing cultivable cyanobacteria: the strain Phormidesmis nigrescens ULC007. We succeeded to extract, to partially purify, and to compare the dark blue pigment from both the ULC007 culture and an environmental Gloeocapsa alpina dominated sample. FT-IR and Raman spectra of G. alpina and P. nigrescens ULC007 pigment extracts strongly suggested a common backbone structure. The high-pressure liquid chromatography-UV-MS/MS analysis of the ULC007 pigment extract allowed to narrow down the molecular formula of gloeocapsin to potentially five candidates within three classes of halochromic molecules: anthraquinone derivatives, coumarin derivatives, and flavonoids. With the discovery of gloeocapsin in P. nigrescens, the production of this pigment is now established for three lineages of cyanobacteria (including G. alpina, P. nigrescens, and Solentia paulocellulare) that belong to three distinct orders (Chroococcales, Pleurocapsales, Synechoccocales), inhabiting very diverse environments. This suggests that gloeocapsin production was a trait of their common ancestor or was acquired by lateral gene transfer. This work represents an important step toward the elucidation of the structure of this enigmatic pigment and its biosynthesis, and it potentially provides a new biosignature for ancient cyanobacteria. It also gives a glimpse on the evolution of UV protection strategies, which are relevant for early phototrophic life on Earth and possibly beyond.

Chemistry and Analysis of Organic Compounds in Dinosaurs

This review provides an overview of organic compounds detected in non-avian dinosaur fossils to date. This was enabled by the development of sensitive analytical techniques. Non-destructive methods and procedures restricted to the sample surface, e.g., light and electron microscopy, infrared (IR) and Raman spectroscopy, as well as more invasive approaches including liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), time-of-flight secondary ion mass spectrometry, and immunological methods were employed. Organic compounds detected in samples of dinosaur fossils include pigments (heme, biliverdin, protoporphyrin IX, melanin), and proteins, such as collagens and keratins. The origin and nature of the observed protein signals is, however, in some cases, controversially discussed. Molecular taphonomy approaches can support the development of suitable analytical methods to confirm reported findings and to identify further organic compounds in dinosaur and other fossils in the future. The chemical properties of the various organic compounds detected in dinosaurs, and the techniques utilized for the identification and analysis of each of the compounds will be discussed.

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.

The occurrence of 2-methylhopanoids in modern bacteria and the geological record

The 2-methylhopanes (2-MeHops) are molecular fossils of 2-methylbacteriohopanepolyols (2-MeBHPs) and among the oldest biomarkers on Earth. However, these biomarkers' specific sources are currently unexplained, including whether they reflect an expansion of marine cyanobacteria. Here, we study the occurrence of 2-MeBHPs and the genes involved in their synthesis in modern bacteria and explore the occurrence of 2-MeHops in the geological record. We find that the gene responsible for 2-MeBHP synthesis (hpnP) is widespread in cyano- and ⍺-proteobacteria, but absent or very limited in other classes/phyla of bacteria. This result is consistent with the dominance of 2-MeBHP in cyano- and ⍺-proteobacterial cultures. The review of their geological occurrence indicates that 2-MeHops are found from the Paleoproterozoic onwards, although some Precambrian samples might be biased by drilling contamination. During the Phanerozoic, high 2-MeHops' relative abundances (index >15%) are associated with climatic and biogeochemical perturbations such as the Permo/Triassic boundary and the Oceanic Anoxic Events. We analyzed the modern habitat of all hpnP-containing bacteria and find that the only one species coming from an undisputed open marine habitat is an ⍺-proteobacterium acting upon the marine nitrogen cycle. Although organisms can change their habitat in response to environmental stress and evolutionary pressure, we speculate that the high sedimentary 2-MeHops' occurrence observed during the Phanerozoic reflect ⍺-proteobacteria expansion and marine N-cycle perturbations in response to climatic and environmental change.

ExoMars Mars Organic Molecule Analyzer (MOMA) Laser Desorption/Ionization Mass Spectrometry (LDI-MS) Analysis of Phototrophic Communities from a Silica-Depositing Hot Spring in Yellowstone National Park, USA

The Mars Organic Molecule Analyzer (MOMA) is a key scientific instrument on the ExoMars Rover mission. MOMA is designed to detect and characterize organic compounds, over a wide range of volatility and molecular weight, in samples obtained from up to 2 m below the martian surface. Thorough analog sample studies are required to best prepare to interpret MOMA data collected on Mars. We present here the MOMA characterization of Mars analog samples, microbial streamer communities composed primarily of oxygenic and anoxygenic phototrophs, collected from an alkaline silica-depositing hot spring in Yellowstone National Park, Wyoming, USA. Samples of partly mineralized microbial streamers and their total lipid extract (TLE) were measured on a MOMA Engineering Test Unit (ETU) instrument by using its laser desorption/ionization mass spectrometry (LDI-MS) mode. MOMA LDI-MS detected a variety of lipids and pigments such as chlorophyll a, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, diacylglycerols, and β-carotene in the TLE sample. Only chlorophyll a was detected in the untreated streamer samples when using mass isolation, which was likely due to the higher background signal of this sample and the relative high ionization potential of the chlorophyll a compared with other compounds in unextracted samples. The results add to the LDI-MS sample characterization database and demonstrate the benefit of using mass isolation on the MOMA instrument to reveal the presence of complex organics and potential biomarkers preserved in a natural sample. This will also provide guidance to in situ analysis of surface samples during Mars operations.

Postdiagenetic Bacterial Transformation of Nickel and Vanadyl Sedimentary Porphyrins of Organic-Rich Shale Rock (Fore-Sudetic Monocline, Poland)

Nickel and vanadyl porphyrins belong to the so-called fossil geo- or sedimentary porphyrins. They occur in different types of organic matter-rich sediments but mostly occur in crude oils and their source rocks, oil shales, coals, and oil sands. In this study, we aimed to understand the process of bacterial transformation of geoporphyrins occurring in the subsurface shale rock (Fore-Sudetic Monocline, SW Poland). We studied these transformations in rock samples directly obtained from the field; in rock samples treated with bacterial strain isolated from shale rock (strain LM27) in the laboratory; and using synthetic nickel and vanadyl porphyrins treated with LM27. Our results demonstrate the following: (i) cleavage and/or degradation of aliphatic and aromatic substituents of porphyrins; (ii) degradation of porphyrin (tetrapyrrole) ring; (iii) formation of organic compounds containing 1, 2, or 3 pyrrole rings; (iv) formation of nickel- or vanadium-containing organic compounds; and (v) mobilization of nickel and vanadium. Our results also showed that the described bacterial processes change the composition and content of geoporphyrins, composition of extractable organic matter, as well as nickel and vanadium content in shale rock.

The enigmatic Placozoa part 1: Exploring evolutionary controversies and poor ecological knowledge

The placozoan Trichoplax adhaerens is a tiny hairy plate and more simply organized than any other living metazoan. After its original description by F.E. Schulze in 1883, it attracted attention as a potential model for the ancestral state of metazoan organization, the "Urmetazoon". Trichoplax lacks any kind of symmetry, organs, nerve cells, muscle cells, basal lamina, and extracellular matrix. Furthermore, the placozoan genome is the smallest (not secondarily reduced) genome of all metazoan genomes. It harbors a remarkably rich diversity of genes and has been considered the best living surrogate for a metazoan ancestor genome. The phylum Placozoa presently harbors three formally described species, while several dozen "cryptic" species are yet awaiting their description. The phylogenetic position of placozoans has recently become a contested arena for modern phylogenetic analyses and view-driven claims. Trichoplax offers unique prospects for understanding the minimal requirements of metazoan animal organization and their corresponding malfunctions.

Vertical structure of the bacterial diversity in meromictic Fayetteville Green Lake

The permanently stratified water columns in euxinic meromictic lakes produce niche environments for phototrophic sulfur oxidizers and diverse sulfur metabolisms. While Green Lake (Fayetteville, New York, NY) is known to host a diverse community of ecologically important sulfur bacteria, analyses of its microbial communities, to date, have been largely based on pigment analysis and smaller datasets from Sanger sequencing techniques. Here, we present the results of next-generation sequencing of the eubacterial community in the context of the water column geochemistry. We observed abundant purple and green sulfur bacteria, as well as anoxygenic photosynthesis-capable cyanobacteria within the upper monimolimnion. Amidst the phototrophs, we found other sulfur-cycling bacteria including sulfur disproportionators and chemotrophic sulfur oxidizers, further detailing our understanding of the sulfur cycle and microbial ecology of euxinic, meromictic lakes.

Cyanobacteria and biogeochemical cycles through Earth history

Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis, transforming the biology and chemistry of our planet. Genomic and evolutionary studies have revolutionized our understanding of early oxygenic phototrophs, complementing and dramatically extending inferences from the geologic record. Molecular clock estimates point to a Paleoarchean origin (3.6-3.2 billion years ago, bya) of the core proteins of Photosystem II (PSII) involved in oxygenic photosynthesis and a Mesoarchean origin (3.2-2.8 bya) for the last common ancestor of modern cyanobacteria. Nonetheless, most extant cyanobacteria diversified after the Great Oxidation Event (GOE), an environmental watershed ca. 2.45 bya made possible by oxygenic photosynthesis. Throughout their evolutionary history, cyanobacteria have played a key role in the global carbon cycle.

Chemistry of porphyrins in fossil plants and animals

Porphyrins are macrocyclic tetrapyrrole derivatives that are widely distributed in nature. They are often complexed with a metal ion located in the center of the ring system and may be modified by various substituents including additional rings, or by ring opening, which leads to a plethora of different functions. Due to their extended conjugated aromatic ring system, porphyrins absorb light in the visible range and therefore show characteristic colors. Well-known natural porphyrins include the red-colored heme present in hemoglobin, which is responsible for blood oxygen transport, and the chlorophylls in some bacteria and in plants which are utilized for photosynthesis. Porphyrins are mostly lipophilic pigments that display relatively high chemical stability. Therefore, they can even survive hundreds of millions of years. The present review article provides an overview of natural porphyrins, their chemical structures, and properties. A special focus is put on porphyrins discovered in the fossil record. Examples will be highlighted, and information on their chemical analysis will be provided. We anticipate that the development of novel analytical methods with increased sensitivity will prompt new discoveries of porphyrins in fossils.

Carbon isotope evidence for the global physiology of Proterozoic cyanobacteria

Ancestral cyanobacteria are assumed to be prominent primary producers after the Great Oxidation Event [≈2.4 to 2.0 billion years (Ga) ago], but carbon isotope fractionation by extant marine cyanobacteria (α-cyanobacteria) is inconsistent with isotopic records of carbon fixation by primary producers in the mid-Proterozoic eon (1.8 to 1.0 Ga ago). To resolve this disagreement, we quantified carbon isotope fractionation by a wild-type planktic β-cyanobacterium (Synechococcus sp. PCC 7002), an engineered Proterozoic analog lacking a CO₂-concentrating mechanism, and cyanobacterial mats. At mid-Proterozoic pH and pCO₂ values, carbon isotope fractionation by the wild-type β-cyanobacterium is fully consistent with the Proterozoic carbon isotope record, suggesting that cyanobacteria with CO₂-concentrating mechanisms were apparently the major primary producers in the pelagic Proterozoic ocean, despite atmospheric CO₂ levels up to 100 times modern. The selectively permeable microcompartments central to cyanobacterial CO₂-concentrating mechanisms ("carboxysomes") likely emerged to shield rubisco from O₂ during the Great Oxidation Event.

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.

Niche expansion for phototrophic sulfur bacteria at the Proterozoic-Phanerozoic transition

Carotenoid pigments afford valuable clues about the chemistry and biology of both modern and ancient aquatic environments. This study reveals that fossil aromatic carotenoids—long considered biomarkers for anoxygenic, phototrophic sulfur bacteria and their physiological requirement for hydrogen sulfide and illumination—can also be biosynthesized by oxygen-producing cyanobacteria. Cyanobacterial aromatic carotenoids, which are distinct in their chemical structures and occurrence patterns, are the most commonly encountered compounds in Proterozoic marine settings as well as in lakes from more recent eras. In contrast, carotenoids diagnostic for green sulfur bacteria of the family Chlorobiaceae became both prevalent and abundant in marine paleoenvironments beginning in the Phanerozoic Eon. This expansion occurs as marine sulfate inventories increased toward the end of the Proterozoic Eon.

Fossilized carotenoid hydrocarbons provide a window into the physiology and biochemistry of ancient microbial phototrophic communities for which only a sparse and incomplete fossil record exists. However, accurate interpretation of carotenoid-derived biomarkers requires detailed knowledge of the carotenoid inventories of contemporary phototrophs and their physiologies. Here we report two distinct patterns of fossilized C₄₀ diaromatic carotenoids. Phanerozoic marine settings show distributions of diaromatic hydrocarbons dominated by isorenieratane, a biomarker derived from low-light-adapted phototrophic green sulfur bacteria. In contrast, isorenieratane is only a minor constituent within Neoproterozoic marine sediments and Phanerozoic lacustrine paleoenvironments, for which the major compounds detected are renierapurpurane and renieratane, together with some novel C₃₉ and C₃₈ carotenoid degradation products. This latter pattern can be traced to cyanobacteria as shown by analyses of cultured taxa and laboratory simulations of sedimentary diagenesis. The cyanobacterial carotenoid synechoxanthin, and its immediate biosynthetic precursors, contain thermally labile, aromatic carboxylic-acid functional groups, which upon hydrogenation and mild heating yield mixtures of products that closely resemble those found in the Proterozoic fossil record. The Neoproterozoic–Phanerozoic transition in fossil carotenoid patterns likely reflects a step change in the surface sulfur inventory that afforded opportunities for the expansion of phototropic sulfur bacteria in marine ecosystems. Furthermore, this expansion might have also coincided with a major change in physiology. One possibility is that the green sulfur bacteria developed the capacity to oxidize sulfide fully to sulfate, an innovation which would have significantly increased their capacity for photosynthetic carbon fixation.

Free and kerogen-bound biomarkers from late Tonian sedimentary rocks record abundant eukaryotes in mid-Neoproterozoic marine communities

Lipid biomarker assemblages preserved within the bitumen and kerogen phases of sedimentary rocks from the ca. 780-729 Ma Chuar and Visingsö Groups facilitate paleoenvironmental reconstructions and reveal fundamental aspects of emerging mid-Neoproterozoic marine communities. The Chuar and Visingsö Groups were deposited offshore of two distinct paleocontinents (Laurentia and Baltica, respectively) during the Tonian Period, and the rock samples used had not undergone excessive metamorphism. The major polycyclic alkane biomarkers detected in the rock bitumens and kerogen hydropyrolysates consist of tricyclic terpanes, hopanes, methylhopanes, and steranes. Major features of the biomarker assemblages include detectable and significant contribution from eukaryotes, encompassing the first robust occurrences of kerogen-bound regular steranes from Tonian rocks, including 21-norcholestane, 27-norcholestane, cholestane, ergostane, and cryostane, along with a novel unidentified C₃₀ sterane series from our least thermally mature Chuar Group samples. Appreciable values for the sterane/hopane (S/H) ratio are found for both the free and kerogen-bound biomarker pools for both the Chuar Group rocks (S/H between 0.09 and 1.26) and the Visingsö Group samples (S/H between 0.03 and 0.37). The more organic-rich rock samples generally yield higher S/H ratios than for organic-lean substrates, which suggests a marine nutrient control on eukaryotic abundance relative to bacteria. A C₂₇ sterane (cholestane) predominance among total C₂₆ -C₃₀ steranes is a common feature found for all samples investigated, with lower amounts of C₂₈ steranes (ergostane and crysotane) also present. No traces of known ancient C₃₀ sterane compounds; including 24-isopropylcholestanes, 24-n-propylcholestanes, or 26-methylstigmastanes, are detectable in any of these pre-Sturtian rocks. These biomarker characteristics support the view that the Tonian Period was a key interval in the history of life on our planet since it marked the transition from a bacterially dominated marine biosphere to an ocean system which became progressively enriched with eukaryotes. The eukaryotic source organisms likely encompassed photosynthetic primary producers, marking a rise in red algae, and consumers in a revamped trophic structure predating the Sturtian glaciation.

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.

The impact of marine nutrient abundance on early eukaryotic ecosystems

The rise of eukaryotes to ecological prominence represents one of the most dramatic shifts in the history of Earth's biosphere. However, there is an enigmatic temporal lag between the emergence of eukaryotic organisms in the fossil record and their much later ecological expansion. In parallel, there is evidence for a secular increase in the availability of the key macronutrient phosphorus (P) in Earth's oceans. Here, we use an Earth system model equipped with a size-structured marine ecosystem to explore relationships between plankton size, trophic complexity, and the availability of marine nutrients. We find a strong dependence of planktonic ecosystem structure on ocean nutrient abundance, with a larger ocean nutrient inventory leading to greater overall biomass, broader size spectra, and increasing abundance of large Zooplankton. If existing estimates of Proterozoic marine nutrient levels are correct, our results suggest that increases in the ecological impact of eukaryotic algae and trophic complexity in eukaryotic ecosystems were directly linked to restructuring of the global P cycle associated with the protracted rise of surface oxygen levels. Our results thus suggest an indirect but potentially important mechanism by which ocean oxygenation may have acted to shape marine ecological function during late Proterozoic time.

Exploring cycad foliage as an archive of the isotopic composition of atmospheric nitrogen

Molecular nitrogen (N₂ ) constitutes the majority of Earth's modern atmosphere, contributing ~0.79 bar of partial pressure (pN₂ ). However, fluctuations in pN₂ may have occurred on 10⁷ -10⁹  year timescales in Earth's past, perhaps altering the isotopic composition of atmospheric nitrogen. Here, we explore an archive that may record the isotopic composition of atmospheric N₂ in deep time: the foliage of cycads. Cycads are ancient gymnosperms that host symbiotic N₂ -fixing cyanobacteria in modified root structures known as coralloid roots. All extant species of cycads are known to host symbionts, suggesting that this N₂ -fixing capacity is perhaps ancestral, reaching back to the early history of cycads in the late Paleozoic. Therefore, if the process of microbial N₂ fixation records the δ¹⁵ N value of atmospheric N₂ in cycad foliage, the fossil record of cycads may provide an archive of atmospheric δ¹⁵ N values. To explore this potential proxy, we conducted a survey of wild cycads growing in a range of modern environments to determine whether cycad foliage reliably records the isotopic composition of atmospheric N₂ . We find that neither biological nor environmental factors significantly influence the δ¹⁵ N values of cycad foliage, suggesting that they provide a reasonably robust record of the δ¹⁵ N of atmospheric N₂ . Application of this proxy to the record of carbonaceous cycad fossils may not only help to constrain changes in atmospheric nitrogen isotope ratios since the late Paleozoic, but also could shed light on the antiquity of the N₂ -fixing symbiosis between cycads and cyanobacteria.

A one-billion-year-old multicellular chlorophyte

Chlorophytes (representing a clade within the Viridiplantae and a sister group of the Streptophyta) probably dominated marine export bioproductivity and played a key role in facilitating ecosystem complexity before the Mesozoic diversification of phototrophic eukaryotes such as diatoms, coccolithophorans and dinoflagellates. Molecular clock and biomarker data indicate that chlorophytes diverged in the Mesoproterozoic or early Neoproterozoic, followed by their subsequent phylogenetic diversification, multicellular evolution and ecological expansion in the late Neoproterozoic and Palaeozoic. This model, however, has not been rigorously tested with palaeontological data because of the scarcity of Proterozoic chlorophyte fossils. Here we report abundant millimetre-sized, multicellular and morphologically differentiated macrofossils from rocks approximately 1,000 million years ago. These fossils are described as Proterocladus antiquus new species and are interpreted as benthic siphonocladalean chlorophytes, suggesting that chlorophytes acquired macroscopic size, multicellularity and cellular differentiation nearly a billion years ago, much earlier than previously thought.

Cyanobacteria evolution: Insight from the fossil record

Cyanobacteria played an important role in the evolution of Early Earth and the biosphere. They are responsible for the oxygenation of the atmosphere and oceans since the Great Oxidation Event around 2.4 Ga, debatably earlier. They are also major primary producers in past and present oceans, and the ancestors of the chloroplast. Nevertheless, the identification of cyanobacteria in the early fossil record remains ambiguous because the morphological criteria commonly used are not always reliable for microfossil interpretation. Recently, new biosignatures specific to cyanobacteria were proposed. Here, we review the classic and new cyanobacterial biosignatures. We also assess the reliability of the previously described cyanobacteria fossil record and the challenges of molecular approaches on modern cyanobacteria. Finally, we suggest possible new calibration points for molecular clocks, and strategies to improve our understanding of the timing and pattern of the evolution of cyanobacteria and oxygenic photosynthesis.

Evolution of cellular metabolism and the rise of a globally productive biosphere

Metabolic processes in cells and chemical processes in the environment are fundamentally intertwined and have evolved in concert for most of Earth's existence. Here I argue that intrinsic properties of cellular metabolism imposed central constraints on the historical trajectories of biopsheric productivity and atmospheric oxygenation. Photosynthesis depends on iron, but iron is highly insoluble under the aerobic conditions produced by oxygenic photosynthesis. These counteracting constraints led to two major stages of Earth oxygenation. After a cyanobacteria-driven biospheric expansion near the Archean-Proterozoic boundary, productivity remained largely restricted to continental boundaries and shallow aquatic environments where weathering inputs made iron more accessible. The anoxic deep open ocean was rich in free iron during the Proterozoic, but this iron was largely inaccessible, partly because an otherwise nutrient-poor ocean was limiting to photosynthesis, but also because a photosynthetic expansion would have quenched its own iron supply. Near the Proterozoic-Phanerozoic boundary, bioenergetics innovations allowed eukaryotic photosynthesis to overcome these interconnected negative feedbacks and begin expanding into the deep open oceans and onto the continents, where nutrients are inherently harder to come by. Key insights into what drove the ecological rise of eukaryotic photosynthesis emerge from analyses of marine Synechococcus and Prochlorococcus, abundant marine picocyanobacteria whose ancestors colonized the oceans in the Neoproterozoic. The reconstructed evolution of this group reveals a sequence of innovations that ultimately produced a form of photosynthesis in Prochlorococcus that is more like that of green plant cells than other cyanobacteria. Innovations increased the energy flux of cells, thereby enhancing their ability to acquire sparse nutrients, and as by-product also increased the production of organic carbon waste. Some of these organic waste products had the ability to chelate iron and make it bioavailable, thereby indirectly pushing the oceans through a transition from an anoxic state rich in free iron to an oxygenated state with organic carbon-bound iron. Resulting conditions (and parallel processes on the continents) in turn led to a series of positive feedbacks that increased the availability of other nutrients, thereby promoting the rise of a globally productive biosphere. In addition to the occurrence of major biospheric expansions, the several hundred million-year periods around the Archean-Proterozoic and Proterozoic-Phanerozoic boundaries share a number of other parallels. Both epochs have also been linked to major carbon cycle perturbations and global glaciations, as well as changes in the nature of plate tectonics and increases in continental exposure and weathering. This suggests the dynamics of life and Earth are intimately intertwined across many levels and that general principles governed transitions in these coupled dynamics at both times in Earth history.

Elucidating the Geometric Substitution of Petroporphyrins by Spectroscopic Analysis and Atomic Force Microscopy Molecular Imaging

Determination of the molecular structures of petroporphyrins has been crucial to understand the diagenetic pathways and maturation of petroleum. However, these studies have been hampered by their structural complexity and the challenges associated with their isolation. In comparison to the skeletal macrocyclic structures, much less is known about the substitutions, which are more sensitive to the maturation and diagenesis pathways. While these isolated vanadyl petroporphyrins largely consist of etioporphyrin and deoxophylloerythroetioporphyrin as expected, surprisingly, we find evidence that one or a few β hydrogens are present in petroporphyrins of low carbon numbers using a combination of ultraviolet-visible spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry, and non-contact atomic force microscopy. Petroporphyrins with β hydrogens were not anticipated on the basis of their biological precursors. The data support dealkylation under catagenesis but not transalkylation or random alkylation of the β and meso positions, despite the fact that more complex porphyrin structures are formed.

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.

Digging deeper: why we need more Proterozoic algal fossils and how to get them

Known Proterozoic algal fossils raise compelling questions about the origin and diversification of cyanobacteria and eukaryotic algae, and their ecological influence in deep time. This Perspectives article describes particular examples of persistent evolutionary and biogeochemical issues whose resolution would be aided by additional algal fossil evidence from Proterozoic deposits, which have been the subjects of recent intensive study. New Proterozoic geosciences literature relevant to the early diversification of algae is surveyed. Previously underappreciated algal traits that might improve taxonomic attributions of fossil remains are highlighted. Processes that phycologists could use to improve detection of algal fossils are recommended. Potential geological sources of new Proterozoic fossils are suggested.

Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter

We report a novel technical approach for subcritical fluid extraction (SFE) for organic matter characterization in complex matrices such as soil.

Day and Night: Metabolic Profiles and Evolutionary Relationships of Six Axenic Non-Marine Cyanobacteria

Cyanobacteria are dominant primary producers of various ecosystems and they colonize marine as well as freshwater and terrestrial habitats. On the basis of their oxygenic photosynthesis they are known to synthesize a high number of secondary metabolites, which makes them promising for biotechnological applications. State-of-the-art sequencing and analytical techniques and the availability of several axenic strains offer new opportunities for the understanding of the hidden metabolic potential of cyanobacteria beyond those of single model organisms. Here, we report comprehensive genomic and metabolic analyses of five non-marine cyanobacteria, that is, Nostoc sp. DSM 107007, Anabaena variabilis DSM 107003, Calothrix desertica DSM 106972, Chroococcidiopsis cubana DSM 107010, Chlorogloeopsis sp. PCC 6912, and the reference strain Synechocystis sp. PCC 6803. Five strains that are prevalently belonging to the order Nostocales represent the phylogenetic depth of clade B1, a morphologically highly diverse sister lineage of clade B2 that includes strain PCC 6803. Genome sequencing, light and scanning electron microscopy revealed the characteristics and axenicity of the analyzed strains. Phylogenetic comparisons showed the limits of the 16S rRNA gene for the classification of cyanobacteria, but documented the applicability of a multilocus sequence alignment analysis based on 43 conserved protein markers. The analysis of metabolites of the core carbon metabolism showed parts of highly conserved metabolic pathways as well as lineage specific pathways such as the glyoxylate shunt, which was acquired by cyanobacteria at least twice via horizontal gene transfer. Major metabolic changes were observed when we compared alterations between day and night samples. Furthermore, our results showed metabolic potential of cyanobacteria beyond Synechocystis sp. PCC 6803 as model organism and may encourage the cyanobacterial community to broaden their research to related organisms with higher metabolic activity in the desired pathways.

Oxygenated Mesoproterozoic lake revealed through magnetic mineralogy

Terrestrial environments have been suggested as an oxic haven for eukaryotic life and diversification during portions of the Proterozoic Eon when the ocean was dominantly anoxic. However, iron speciation and Fe/Al data from the ca. 1.1-billion-year-old Nonesuch Formation, deposited in a large lake and bearing a diverse assemblage of early eukaryotes, are interpreted to indicate persistently anoxic conditions. To shed light on these distinct hypotheses, we analyzed two drill cores spanning the transgression into the lake and its subsequent shallowing. While the proportion of highly reactive to total iron (FeHR/FeT) is consistent through the sediments and typically in the range taken to be equivocal between anoxic and oxic conditions, magnetic experiments and petrographic data reveal that iron exists in three distinct mineral assemblages resulting from an oxycline. In the deepest waters, reductive dissolution of iron oxides records an anoxic environment. However, the remainder of the sedimentary succession has iron oxide assemblages indicative of an oxygenated environment. At intermediate water depths, a mixed-phase facies with hematite and magnetite indicates low oxygen conditions. In the shallowest waters of the lake, nearly every iron oxide has been oxidized to its most oxidized form, hematite. Combining magnetics and textural analyses results in a more nuanced understanding of ambiguous geochemical signals and indicates that for much of its temporal duration, and throughout much of its water column, there was oxygen in the waters of Paleolake Nonesuch.