2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis

Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current

Hopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greater sqhC genetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential "hot spots" of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record.

Carbon isotopes and lipid biomarkers from organic-rich facies of the Shuram Formation, Sultanate of Oman

The largest recorded carbon isotopic excursion in Earth history is observed globally in carbonate rocks of middle Ediacaran age. Known from the Sultanate of Oman as the 'Shuram excursion', this event records a dramatic, systematic shift in δ(13) Ccarbonate values to ca. -12‰. Attempts to explain the nature, magnitude and origin of this excursion include (i) a primary signal resulting from the protracted oxidation of a large dissolved organic carbon reservoir in seawater, release of methane from sediment-hosted clathrates, or water column stratification; and (ii) a secondary signal from diagenetic processes. The compositions and isotope ratios of organic carbon phases during the excursion are critical to evaluating these ideas; however, previous work has focused on localities that are low in organic carbon, hindering straightforward interpretation of the observed time-series trends. We report carbon isotope data from bulk organic carbon, extracted bitumen and kerogen, in addition to lipid biomarker data, from a subsurface well drilled on the eastern flank of the South Oman Salt Basin, Sultanate of Oman. This section captures Nafun Group strata through the Ediacaran-Cambrian boundary in the Ara Group and includes an organic-rich, deeper-water facies of the Shuram Formation. Despite the high organic matter contents, the carbon isotopic compositions of carbonates - which record a negative δ(13) C isotope excursion similar in shape and magnitude to sections elsewhere in Oman - do not covary with those of organic phases (bulk TOC, bitumen and kerogen). Paired inorganic and organic δ(13) C data only display coupled behaviour during the latter part of the excursion's recovery. Furthermore, lipid biomarker data reveal that organic matter composition and source inputs varied stratigraphically, reflecting biological community shifts in non-migrated, syngenetic organic matter deposited during this interval.

Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins

Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding of the evolution of both bacteria and eukaryotes. All phylogenetic dating in the Proterozoic and before is difficult: Significant debates surround potential fossil calibration points based on the interpretation of the Precambrian microbial fossil record, and strict molecular clock methods cannot be expected to yield accurate dates over such vast timescales because of strong heterogeneity in rates. Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating. However, endosymbiosis events and gene duplications provide some additional information that has never been exploited in dating; namely, that certain nodes on a gene tree must represent the same events, and thus must have the same or very similar dates, even if the exact date is uncertain. We devised techniques to exploit this information: cross-calibration, in which node date calibrations are reused across a phylogeny, and cross-bracing, in which node date calibrations are formally linked in a hierarchical Bayesian model. We apply these methods to proteins with ancient duplications that have remained associated and originated from plastid and mitochondrial endosymbionts: the α and β subunits of ATP synthase and its relatives, and the elongation factor thermo unstable. The methods yield reductions in dating uncertainty of 14-26% while only using date calibrations derived from phylogenetically unambiguous Phanerozoic fossils of multicellular plants and animals. Our results suggest that primary plastid endosymbiosis occurred ∼900 Mya and mitochondrial endosymbiosis occurred ∼1,200 Mya.

Oxidation of Fe(II) leads to increased C-2 methylation of pentacyclic triterpenoids in the anoxygenic phototrophic bacterium Rhodopseudomonas palustris strain TIE-1

Hopanoids are among the most widespread biomarkers of bacteria that are used as indicators for past and present bacterial activity. Our understanding of the production, function, and distribution of hopanoids in bacteria has improved greatly, partly due to genetic, culture-independent studies. Culture-based studies are important to determine hopanoid function and the environmental conditions under which these compounds are produced. This study compares the lipid inventory of Rhodopseudomonas palustris strain TIE-1 under anoxic photoautotrophic conditions using either H2 or Fe(II) as electron donor. The high amount to which adenosylhopane is produced irrespective of the used electron donor suggests a specific function of this compound rather than its exclusive role as an intermediate in bacteriohopanepolyol biosynthesis. C-2 methylated hopanoids and tetrahymanol account for as much as 59% of the respective C-2 methylated/non-methylated homologs during growth with Fe(II) as electron donor, as compared with 24% C-2 methylation for growth with H2 . This observation reveals that C-2 methylated hopanoids have a specific function and are preferentially synthesized in response to elevated Fe(II) concentrations. The presence of C-2 methylated pentacyclic triterpenoids has commonly been used as a biosignature for the interpretation of paleoenvironments. These new findings suggest that increased C-2 methylation may indicate anoxic ferrous conditions, in addition to other environmental stressors that have been previously reported.

The general stress response factor EcfG regulates expression of the C-2 hopanoid methylase HpnP in Rhodopseudomonas palustris TIE-1

Lipid molecules preserved in sedimentary rocks facilitate the reconstruction of events that have shaped the evolution of the Earth's biosphere. A key limitation for the interpretation of many of these molecular fossils is that their biological roles are still poorly understood. Here, we use Rhodopseudomonas palustris TIE-1 to identify factors that induce biosynthesis of 2-methyl hopanoids (2-MeBHPs), progenitors of 2-methyl hopanes, one of the most abundant biomarkers in the rock record. This is the first dissection of the regulation of hpnP, the gene encoding the C-2 hopanoid methylase, at the molecular level. We demonstrate that EcfG, the general stress response factor of alphaproteobacteria, regulates expression of hpnP under a variety of challenges, including high temperature, pH stress, and presence of nonionic osmolytes. Although higher hpnP transcription levels did not always result in higher amounts of total methylated hopanoids, the fraction of a particular kind of hopanoid, 2-methyl bacteriohopanetetrol, was consistently higher in the presence of most stressors in the wild type, but not in the ΔecfG mutant, supporting a beneficial role for 2-MeBHPs in stress tolerance. The ΔhpnP mutant, however, did not exhibit a growth defect under the stress conditions tested except in acidic medium. This indicates that the inability to make 2-MeBHPs under most of these conditions can readily be compensated. Although stress is necessary to regulate 2-MeBHP production, the specific conditions under which 2-MeBHP biosynthesis is essential remain to be determined.

Spectral characterization of ten cyclic lipids using time-of-flight secondary ion mass spectrometry

RATIONALE

Over the last decade, the high lateral resolution and imaging capabilities of time-of-flight secondary ion mass spectrometry (ToF-SIMS) have increasingly stimulated interest in studying organic molecules in complex environmental materials. However, unlike with the established mass spectrometric techniques, the use of ToF-SIMS in the biogeosciences is still hampered by a lack of reference spectra of the relevant biomarker compounds. Here we present and interpret ToF-SIMS reference spectra of ten different cyclic lipids that are frequently used as biological tracers in ecological, organic geochemical and geobiological studies.

METHODS

Standard compounds of α,β,β-(20R,24S)-24-methylcholestane, (22E)-ergosta-5,7,22-trien-3β-ol, 17α(H),21β-(H)-30-norhopane, hope-17(21)-ene, hop-22(29)-ene, 17β(H),21β(H)-bacteriohopane-32,33,34,35-tetrol, 17β(H),21β(H)-35-aminobacteriohopane-32,33,34-triol, α-tocopherol, β,β-carotene, chlorophyll a, and cryosections of microbial mats and a fungus were analyzed using a ToF-SIMS instrument equipped with a Bi(3)(+) cluster ion source.

RESULTS

The spectra obtained from the standard compounds showed peaks in the molecular weight range (molecular ions, protonated and deprotonated molecules, adduct ions) and diagnostic fragment ion peaks in both, positive and negative ion modes. For the cyclic hydrocarbons, however, the positive ion mode spectra typically showed more and stronger characteristic peaks than the negative ion mode spectra. Using real world samples the capability of ToF-SIMS to detect and image selected compounds in complex organic matrices was tested. 17β(H),21β(H)-35-Aminobacteriohopane-32,33,34-triol, carotene and chlorophyll a were successfully identified in cryosections of microbial mats, and the distribution of ergosterol was mapped at µm resolution in a cryosection of a fungus (Tuber uncinatum).

CONCLUSIONS

This study further highlights the utility of ToF-SIMS for the identification and localization of lipids within environmental samples and as a technique for biomarker-related research in organic geochemistry and geobiology.

Identification and quantification of polyfunctionalized hopanoids by high temperature gas chromatography-mass spectrometry

Hopanoids are triterpenoids produced mainly by bacteria, are ubiquitous in the environment, and have many important applications as biological markers. A wide variety of related hopanoid structures exists, many of which are polyfunctionalized. These modifications render the hopanoids too involatile for conventional gas chromatography (GC) separation, so require either laborious oxidative cleavage of the functional groups or specialized high temperature (HT) columns. Here we describe the systematic evaluation and optimization of a HT-GC method for the analysis of polyfunctionalized hopanoids and their methylated homologs. Total lipid extracts are derivatized with acetic anhydride and no further treatment or workup is required. We show that acid or base hydrolysis to remove di- and triacylglycerides leads to degradation of several BHP structures. DB-XLB type columns can elute hopanoids up to bacteriohopane-tetrol at 350 °C, with baseline separation of all 2-methyl/desmethyl homologs. DB-5HT type columns can additionally elute bacteriohopaneaminotriol and bacteriohopaneaminotetrol, but do not fully separate 2-methyl/desmethyl homologs. The method gave 2- to 7-fold higher recovery of hopanoids than oxidative cleavage and can provide accurate quantification of all analytes including 2-methyl hopanoids. By comparing data from mass spectra with those from a flame ionization detector, we show that the mass spectromet (MS) response factors for different hopanoids using either total ion counts or m/z 191 vary substantially. Similarly, 2-methyl ratios estimated from selected-ion data are lower than those from FID by 10-30% for most hopanoids, but higher by ca. 10% for bacteriohopanetetrol. Mass spectra for a broad suite of hopanoids, including 2-methyl homologs, from Rhodopseudomonas palustris are presented, together with the tentative assignment of several new hopanoid degradation products.

Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event

Cyanobacteria are among the most diverse prokaryotic phyla, with morphotypes ranging from unicellular to multicellular filamentous forms, including those able to terminally (i.e., irreversibly) differentiate in form and function. It has been suggested that cyanobacteria raised oxygen levels in the atmosphere around 2.45-2.32 billion y ago during the Great Oxidation Event (GOE), hence dramatically changing life on the planet. However, little is known about the temporal evolution of cyanobacterial lineages, and possible interplay between the origin of multicellularity, diversification of cyanobacteria, and the rise of atmospheric oxygen. We estimated divergence times of extant cyanobacterial lineages under Bayesian relaxed clocks for a dataset of 16S rRNA sequences representing the entire known diversity of this phylum. We tested whether the evolution of multicellularity overlaps with the GOE, and whether multicellularity is associated with significant shifts in diversification rates in cyanobacteria. Our results indicate an origin of cyanobacteria before the rise of atmospheric oxygen. The evolution of multicellular forms coincides with the onset of the GOE and an increase in diversification rates. These results suggest that multicellularity could have played a key role in triggering cyanobacterial evolution around the GOE.

Thermally-induced structural and chemical alteration of organic-walled microfossils: an experimental approach to understanding fossil preservation in metasediments

The identification and confirmation of bona fide Archean-Paleoproterozoic microfossils can prove to be a challenging task, further compounded by diagenetic and metamorphic histories. While structures of likely biological origin are not uncommon in Precambrian rocks, the search for early fossil life has been disproportionately focused on lesser thermally altered rocks, typically greenschist or lower-grade metamorphism. Recently, however, an increasing number of inferred micro- and macrofossils have been reported from higher-grade metasediments, prompting us to experimentally test and quantify the preservability of organic-walled microfossils over varying durations of controlled heating and under two differing redox conditions. Because of their relatively low-intensity natural thermal alteration, acritarchs from the Mesoproterozoic Ruyang Group were chosen as subjects for experimental heating at approximately 500°C, with durations ranging from 1 to 250 days and in both oxic (normal present day conditions) and anoxic conditions. Upon extraction, the opacity, reflectivity, color, microchemistry, and microstructures of the heated acritarchs were characterized using optic microscopy, scanning electron microscopy, Raman spectroscopy, and X-ray photoelectron spectroscopy. The results differ for acritarchs prepared under oxic vs. anoxic conditions, with the anoxic replicates surviving experimental heating longer and retaining biological morphologies better, despite an increasing degree of carbonization with continuous heating. Conversely, the oxic replicates show aggressive degradation. In conjunction with fossils from high-grade metasediments, our data illustrate the preservational potential of organic-walled microfossils subjected to metamorphism in reducing conditions, offer insights into the search for microfossils in metasediments, and help to elucidate the influence of time on the carbonization/graphitization processes during thermal alteration.

Late Devonian marine anoxia challenged by benthic cyanobacterial mats

Mass occurrence of benthic cyanobacterial mats in a sequence of Late Devonian black shales and bituminous limestones of the Holy Cross Mts. (central Poland), enclosing the famous Kellwasser and Hangenberg extinction horizons, is reported. The microbiota forming the mats is compared with some modern benthic chroococcalean cyanobacteria. Similarly to their extant counterparts, the Devonian cyanobacteria must had been phototrophic and oxygenic aerobes which could, however, tolerate slightly sulfidic conditions characterizing the near-bottom waters of the Late Devonian epicontinental sea. The cyanobacterial mats successfully colonized the oxygen-deficient and H(2)S-enriched seabed otherwise unfavorable for most other benthic biota. The redox state of this sluggish Late Devonian sea, ascribed previously mostly to anoxic or euxinic conditions, is reassessed as probably pulsating between anoxic, dysoxic, and weakly oxic conditions. The redox state was dependent on the rate of oxygen production by the cyanobacterial mats, the intensity of H(2)S emissions from the decaying mat biomass, and the rate of planktonic production.

Hopanoids in marine cyanobacteria: probing their phylogenetic distribution and biological role

Cyanobacteria are key players in the global carbon and nitrogen cycles and are thought to have been responsible for the initial rise of atmospheric oxygen during the Neoarchean. There is evidence that a class of membrane lipids known as hopanoids serve as biomarkers for bacteria, including many cyanobacteria, in the environment and in the geologic record. However, the taxonomic distributions and physiological roles of hopanoids in marine cyanobacteria remain unclear. We examined the distribution of bacteriohopanepolyols (BHPs) in a collection of marine cyanobacterial enrichment and pure cultures and investigated the relationship between the cellular abundance of BHPs and nitrogen limitation in Crocosphaera watsonii, a globally significant nitrogen-fixing cyanobacterium. In pure culture, BHPs were only detected in species capable of nitrogen fixation, implicating hopanoids as potential markers for diazotrophy in the oceans. The enrichment cultures we examined exhibited a higher degree of BHP diversity, demonstrating that there are presently unaccounted for marine bacteria, possibly cyanobacteria, associated with the production of a range of BHP structures. Crocosphaera watsonii exhibited high membrane hopanoid content consistent with the idea that hopanoids have an important effect on the bulk physical properties of the membrane. However, the abundance of BHPs in C. watsonii did not vary considerably when grown under nitrogen-limiting and nitrogen-replete conditions, suggesting that the role of hopanoids in this organism is not directly related to the physiology of nitrogen fixation. Alternatively, we propose that high hopanoid content in C. watsonii may serve to reduce membrane permeability to antimicrobial toxins in the environment.

Diversity of cyanobacterial biomarker genes from the stromatolites of Shark Bay, Western Australia

Families of closely related chemical compounds, which are relatively resistant to degradation, are often used as biomarkers to help trace the evolutionary history of early groups of organisms and the environments in which they lived. Biomarkers derived from hopanoid variations are particularly useful in determining bacterial community compositions. 2-Methylhopananoids have been thought to be diagnostic for cyanobacteria, and 2-methylhopanes in the geological record are taken as evidence for the presence of cyanobacteria-containing communities at the time of sediment deposition. Recently, however, doubt has been cast on the validity of 2-methylhopanes as cyanobacterial biomarkers, since non-cyanobacterial species have been shown to produce significant amounts of 2-methylhopanoids. This study examines the diversity of hpnP, the hopanoid biosynthesis gene coding for the enzyme that methylates hopanoids at the C2 position. Genomic DNA isolated from stromatolite-associated pustular and smooth microbial mat samples from Shark Bay, Western Australia, was analysed for bacterial diversity, and used to construct an hpnP clone library. A total of 117 partial hpnP clones were sequenced, representing 12 operational taxonomic units (OTUs). Phylogenetic analysis showed that 11 of these OTUs, representing 115 sequences, cluster within the cyanobacterial clade. We conclude that the dominant types of microorganisms with the detected capability of producing 2-methylhopanoids within pustular and smooth microbial mats in Shark Bay are cyanobacteria.

The rise of oxygen and aerobic biochemistry

Analysis of conserved protein folding domains across extant genomes by Kim et al. in this issue of Structure provides insights into the timing of some of the earliest aerobic metabolisms to arise on Earth.

Cyanobacterial life at low O(2): community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat

Cyanobacteria are renowned as the mediators of Earth's oxygenation. However, little is known about the cyanobacterial communities that flourished under the low-O(2) conditions that characterized most of their evolutionary history. Microbial mats in the submerged Middle Island Sinkhole of Lake Huron provide opportunities to investigate cyanobacteria under such persistent low-O(2) conditions. Here, venting groundwater rich in sulfate and low in O(2) supports a unique benthic ecosystem of purple-colored cyanobacterial mats. Beneath the mat is a layer of carbonate that is enriched in calcite and to a lesser extent dolomite. In situ benthic metabolism chambers revealed that the mats are net sinks for O(2), suggesting primary production mechanisms other than oxygenic photosynthesis. Indeed, (14)C-bicarbonate uptake studies of autotrophic production show variable contributions from oxygenic and anoxygenic photosynthesis and chemosynthesis, presumably because of supply of sulfide. These results suggest the presence of either facultatively anoxygenic cyanobacteria or a mix of oxygenic/anoxygenic types of cyanobacteria. Shotgun metagenomic sequencing revealed a remarkably low-diversity mat community dominated by just one genotype most closely related to the cyanobacterium Phormidium autumnale, for which an essentially complete genome was reconstructed. Also recovered were partial genomes from a second genotype of Phormidium and several Oscillatoria. Despite the taxonomic simplicity, diverse cyanobacterial genes putatively involved in sulfur oxidation were identified, suggesting a diversity of sulfide physiologies. The dominant Phormidium genome reflects versatile metabolism and physiology that is specialized for a communal lifestyle under fluctuating redox conditions and light availability. Overall, this study provides genomic and physiologic insights into low-O(2) cyanobacterial mat ecosystems that played crucial geobiological roles over long stretches of Earth history.

Eco-physiological adaptations that favour freshwater cyanobacteria in a changing climate

Climate change scenarios predict that rivers, lakes, and reservoirs will experience increased temperatures, more intense and longer periods of thermal stratification, modified hydrology, and altered nutrient loading. These environmental drivers will have substantial effects on freshwater phytoplankton species composition and biomass, potentially favouring cyanobacteria over other phytoplankton. In this Review, we examine how several cyanobacterial eco-physiological traits, specifically, the ability to grow in warmer temperatures; buoyancy; high affinity for, and ability to store, phosphorus; nitrogen-fixation; akinete production; and efficient light harvesting, vary amongst cyanobacteria genera and may enable them to dominate in future climate scenarios. We predict that spatial variation in climate change will interact with physiological variation in cyanobacteria to create differences in the dominant cyanobacterial taxa among regions. Finally, we suggest that physiological traits specific to different cyanobacterial taxa may favour certain taxa over others in different regions, but overall, cyanobacteria as a group are likely to increase in most regions in the future.

Dominant eukaryotic export production during ocean anoxic events reflects the importance of recycled NH4+

The Mesozoic is marked by several widespread occurrences of intense organic matter burial. Sediments from the largest of these events, the Cenomanian-Turonian Oceanic Anoxic Event (OAE 2) are characterized by lower nitrogen isotope ratios than are seen in modern marine settings. It has remained a challenge to describe a nitrogen cycle that could achieve such isotopic depletion. Here we use nitrogen-isotope ratios of porphyrins to show that eukaryotes contributed the quantitative majority of export production throughout OAE 2, whereas cyanobacteria contributed on average approximately 20%. Such data require that any explanation for the OAE nitrogen cycle and its isotopic values be consistent with a eukaryote-dominated ecosystem. Our results agree with models that suggest the OAEs were high-productivity events, supported by vigorous upwelling. Upwelling of anoxic deep waters would have supplied reduced N species (i.e., NH(4)(+)) to primary producers. We propose that new production during OAE 2 primarily was driven by direct NH(4)(+)-assimilation supplemented by diazotrophy, whereas chemocline denitrification and anammox quantitatively consumed NO(3)(−) and NO(2)(−). A marine nitrogen reservoir dominated by NH(4)(+), in combination with known kinetic isotope effects, could lead to eukaryotic biomass depleted in (15)N.

Microbial response to limited nutrients in shallow water immediately after the end-Permian mass extinction

Previous work indicates that a variety of microbes bloomed in the oceans after the end-Permian faunal mass extinction, but evidence is sporadically documented. Thus, the nature and geographic distribution of such microbes and their associations are unclear, addressed in this study using a series of biomarker groups. On the basis of microbial biomarker records of the 2-methylhopane index, evidence is presented for cyanobacterial blooms in both the western and eastern Tethys Sea and in both shallow and deep waters, after the mass extinction. The enhanced relative abundance of C(28) (expressed by the C(28) /C(29) ratio of) regular steranes suggests a bloom of prasinophyte algae occurred immediately after the end-Permian faunal extinction, comparable with those observed in some other mass extinctions in Phanerozoic. Significantly, cyanobacteria and prasinophyte algae show a synchronized onset of bloom in the shallow water Bulla section, north Italy, inferring for the first time their coupled response to the biotic crisis and the associated environmental conditions. However, in Meishan of Zhejiang Province in south China, the bloom declined earlier than in Bulla. The association of increased 2-methylhopane index with a negative shift in the nitrogen isotope composition infers a scenario of enhanced nitrogen fixation by cyanobacteria immediately after the faunal mass extinction. N(2) fixation by cyanobacteria is here interpreted to have provided prasinophyte algae with ammonium in nutrient-limited shallow waters, and thus caused their associated blooms.

An astrophysical view of Earth-based metabolic biosignature gases

Microbial life on Earth uses a wide range of chemical and energetic resources from diverse habitats. An outcome of this microbial diversity is an extensive and varied list of metabolic byproducts. We review key points of Earth-based microbial metabolism that are useful to the astrophysical search for biosignature gases on exoplanets, including a list of primary and secondary metabolism gas byproducts. Beyond the canonical, unique-to-life biosignature gases on Earth (O(2), O(3), and N(2)O), the list of metabolic byproducts includes gases that might be associated with biosignature gases in appropriate exoplanetary environments. This review aims to serve as a starting point for future astrophysical biosignature gas research.

Microbialites and global environmental change across the Permian-Triassic boundary: a synthesis

Permian-Triassic boundary microbialites (PTBMs) are thin (0.05-15 m) carbonates formed after the end-Permian mass extinction. They comprise Renalcis-group calcimicrobes, microbially mediated micrite, presumed inorganic micrite, calcite cement (some may be microbially influenced) and shelly faunas. PTBMs are abundant in low-latitude shallow-marine carbonate shelves in central Tethyan continents but are rare in higher latitudes, likely inhibited by clastic supply on Pangaea margins. PTBMs occupied broadly similar environments to Late Permian reefs in Tethys, but extended into deeper waters. Late Permian reefs are also rich in microbes (and cements), so post-extinction seawater carbonate saturation was likely similar to the Late Permian. However, PTBMs lack widespread abundant inorganic carbonate cement fans, so a previous interpretation that anoxic bicarbonate-rich water upwelled to rapidly increase carbonate saturation of shallow seawater, post-extinction, is problematic. Preliminary pyrite framboid evidence shows anoxia in PTBM facies, but interbedded shelly faunas indicate oxygenated water, perhaps there was short-term pulsing of normally saturated anoxic water from the oxygen-minimum zone to surface waters. In Tethys, PTBMs show geographic variations: (i) in south China, PTBMs are mostly thrombolites in open shelf settings, largely recrystallised, with remnant structure of Renalcis-group calcimicrobes; (ii) in south Turkey, in shallow waters, stromatolites and thrombolites, lacking calcimicrobes, are interbedded, likely depth-controlled; and (iii) in the Middle East, especially Iran, stromatolites and thrombolites (calcimicrobes uncommon) occur in different sites on open shelves, where controls are unclear. Thus, PTBMs were under more complex control than previously portrayed, with local facies control playing a significant role in their structure and composition.

A raison d'être for two distinct pathways in the early steps of plant isoprenoid biosynthesis?

When compared to other organisms, plants are atypical with respect to isoprenoid biosynthesis: they utilize two distinct and separately compartmentalized pathways to build up isoprene units. The co-existence of these pathways in the cytosol and in plastids might permit the synthesis of many vital compounds, being essential for a sessile organism. While substrate exchange across membranes has been shown for a variety of plant species, lack of complementation of strong phenotypes, resulting from inactivation of either the cytosolic pathway (growth and development defects) or the plastidial pathway (pigment bleaching), seems to be surprising at first sight. Hundreds of isoprenoids have been analyzed to determine their biosynthetic origins. It can be concluded that in angiosperms, under standard growth conditions, C₂₀-phytyl moieties, C₃₀-triterpenes and C₄₀-carotenoids are made nearly exclusively within compartmentalized pathways, while mixed origins are widespread for other types of isoprenoid-derived molecules. It seems likely that this coexistence is essential for the interaction of plants with their environment. A major purpose of this review is to summarize such observations, especially within an ecological and functional context and with some emphasis on regulation. This latter aspect still requires more work and present conclusions are preliminary, although some general features seem to exist.

Pattern formation in stromatolites: insights from mathematical modelling

To this day, computer models for stromatolite formation have made substantial use of the Kardar-Parisi-Zhang (KPZ) equation. Oddly enough, these studies yielded mutually exclusive conclusions about the biotic or abiotic origin of such structures. We show in this paper that, at our current state of knowledge, a purely biotic origin for stromatolites can neither be proved nor disproved by means of a KPZ-based model. What can be shown, however, is that whatever their (biotic or abiotic) origin might be, some morphologies found in actual stromatolite structures (e.g. overhangs) cannot be formed as a consequence of a process modelled exclusively in terms of the KPZ equation and acting over sufficiently large times. This suggests the need to search for alternative mathematical approaches to model these structures, some of which are discussed in this paper.

Potential fossil endoliths in vesicular pillow basalt, Coral Patch Seamount, eastern North Atlantic Ocean

The chilled rinds of pillow basalt from the Ampère-Coral Patch Seamounts in the eastern North Atlantic were studied as a potential habitat of microbial life. A variety of putative biogenic structures, which include filamentous and spherical microfossil-like structures, were detected in K-phillipsite-filled amygdules within the chilled rinds. The filamentous structures (∼2.5 μm in diameter) occur as K-phillipsite tubules surrounded by an Fe-oxyhydroxide (lepidocrocite) rich membranous structure, whereas the spherical structures (from 4 to 2 μm in diameter) are associated with Ti oxide (anatase) and carbonaceous matter. Several lines of evidence indicate that the microfossil-like structures in the pillow basalt are the fossilized remains of microorganisms. Possible biosignatures include the carbonaceous nature of the spherical structures, their size distributions and morphology, the presence and distribution of native fluorescence, mineralogical and chemical composition, and environmental context. When taken together, the suite of possible biosignatures supports the hypothesis that the fossil-like structures are of biological origin. The vesicular microhabitat of the rock matrix is likely to have hosted a cryptoendolithic microbial community. This study documents a variety of evidence for past microbial life in a hitherto poorly investigated and underestimated microenvironment, as represented by the amygdules in the chilled pillow basalt rinds. This kind of endolithic volcanic habitat would have been common on the early rocky planets in our Solar System, such as Earth and Mars. This study provides a framework for evaluating traces of past life in vesicular pillow basalts, regardless of whether they occur on early Earth or Mars.

The RND-family transporter, HpnN, is required for hopanoid localization to the outer membrane of Rhodopseudomonas palustris TIE-1

Rhodopseudomonas palustris TIE-1 is a gram-negative bacterium that produces structurally diverse hopanoid lipids that are similar to eukaryotic steroids. Its genome encodes several homologues to proteins involved in eukaryotic steroid trafficking. In this study, we explored the possibility that two of these proteins are involved in intracellular hopanoid transport. R. palustris has a sophisticated membrane system comprising outer, cytoplasmic, and inner cytoplasmic membranes. It also divides asymmetrically, producing a mother and swarmer cell. We deleted genes encoding two putative hopanoid transporters that belong to the resistance-nodulation-cell division superfamily. Phenotypic analyses revealed that one of these putative transporters (HpnN) is essential for the movement of hopanoids from the cytoplasmic to the outer membrane, whereas the other (Rpal_4267) plays a minor role. C(30) hopanoids, such as diploptene, are evenly distributed between mother and swarmer cells, whereas hpnN is required for the C(35) hopanoid, bacteriohopanetetrol, to remain localized to the mother cell type. Mutant cells lacking HpnN grow like the WT at 30 °C but slower at 38 °C. Following cell division at 38 °C, the ΔhpnN cells remain connected by their cell wall, forming long filaments. This phenotype may be attributed to hopanoid mislocalization because a double mutant deficient in both hopanoid biosynthesis and transport does not form filaments. However, the lack of hopanoids severely compromises cell growth at higher temperatures more generally. Because hopanoid mutants only manifest a strong phenotype under certain conditions, R. palustris is an attractive model organism in which to study their transport and function.

Amorphous manganese-calcium oxides as a possible evolutionary origin for the CaMn₄ cluster in photosystem II

In this paper a few calcium-manganese oxides and calcium-manganese minerals are studied as catalysts for water oxidation. The natural mineral marokite is also studied as a catalyst for water oxidation for the first time. Marokite is made up of edge-sharing Mn(3+) in a distorted octahedral environment and eight-coordinate Ca(2+) centered polyhedral layers. The structure is similar to recent models of the oxygen evolving complex in photosystem II. Thus, the oxygen evolving complex in photosystem II does not have an unusual structure and could be synthesized hydrothermally. Also in this paper, oxygen evolution is studied with marokite (CaMn₂O₄), pyrolusite (MnO₂) and compared with hollandite (Ba(0.2)Ca(0.15)K(0.3)Mn(6.9)Al(0.2)Si(0.3)O(16)), hausmannite (Mn₃O₄), Mn₂O₃.H₂O, Ca Mn₃O₆.H₂O, CaMn₄O₈.H₂O, CaMn₂O₄.H₂O and synthetic marokite (CaMn₂O₄). I propose that the origin of the oxygen evolving complex in photosystem II resulted from absorption of calcium and manganese ions that were precipitated together in the archean oceans by protocyanobacteria because of changing pH from ~5 to ~8-10. As reported in this paper, amorphous calcium-manganese oxides with different ratios of manganese and calcium are effective catalysts for water oxidation. The bond types and lengths of the calcium and manganese ions in the calcium-manganese oxides are directly comparable to those in the OEC. This primitive structure of these amorphous calcium-manganese compounds could be changed and modified by environmental groups (amino acids) to form the oxygen evolving complex in photosystem II.

A late methanogen origin for molybdenum-dependent nitrogenase

Mounting evidence indicates the presence of a near complete biological nitrogen cycle in redox-stratified oceans during the late Archean to early Proterozoic (c. 2.5-2.0 Ga). It has been suggested that the iron (Fe)- or vanadium (V)-dependent nitrogenase rather than molybdenum (Mo)-dependent form was responsible for dinitrogen fixation during this time because oceans were depleted in Mo and rich in Fe. We evaluated this hypothesis by examining the phylogenetic relationships of proteins that are required for the biosynthesis of the active site cofactor of Mo-nitrogenase in relation to structural proteins required for Fe-, V- and Mo-nitrogenase. The results are highly suggestive that among extant nitrogen-fixing organisms for which genomic information exists, Mo-nitrogenase is unlikely to have been associated with the Last Universal Common Ancestor. Rather, the origin of Mo-nitrogenase can be traced to an ancestor of the anaerobic and hydrogenotrophic methanogens with acquisition in the bacterial domain via lateral gene transfer involving an anaerobic member of the Firmicutes. A comparison of substitution rates estimated for proteins required for the biosynthesis of the nitrogenase active site cofactor and for a set of paralogous proteins required for the biosynthesis of bacteriochlorophyll suggests that Nif emerged from a nitrogenase-like ancestor approximately 1.5-2.2 Ga. An origin and ensuing proliferation of Mo-nitrogenase under anoxic conditions would likely have occurred in an environment where anaerobic methanogens and Firmicutes coexisted and where Mo was at least episodically available, such as in a redox-stratified Proterozoic ocean basin.

Insights into chemotaxonomic composition and carbon cycling of phototrophic communities in an artesian sulfur-rich spring (Zodletone, Oklahoma, USA), a possible analog for ancient microbial mat systems

Zodletone spring in Oklahoma is a unique environment with high concentrations of dissolved-sulfide (10 mm) and short-chain gaseous alkanes, exhibiting characteristics that are reminiscent of conditions that are thought to have existed in Earth's history, in particular the late Archean and early-to-mid Proterozoic. Here, we present a process-oriented investigation of the microbial community in two distinct mat formations at the spring source, (1) the top of the sediment in the source pool and (2) the purple streamers attached to the side walls. We applied a combination of pigment and lipid biomarker analyses, while functional activities were investigated in terms of oxygen production (microsensor analysis) and carbon utilization ((13)C incorporation experiments). Pigment analysis showed cyanobacterial pigments, in addition to pigments from purple sulfur bacteria (PSB), green sulfur bacteria (GSB) and Chloroflexus-like bacteria (CLB). Analysis of intact polar lipids (IPLs) in the source sediment confirmed the presence of phototrophic organisms via diacylglycerol phospholipids and betaine lipids, whereas glyceroldialkylglyceroltetraether additionally indicated the presence of archaea. No archaeal IPLs were found in the purple streamers, which were strongly dominated by betaine lipids. (13)C-bicarbonate- and -acetate-labeling experiments indicated cyanobacteria as predominant phototrophs in the source sediment, carbon was actively fixed by PSB/CLB/GSB in purple streamers by using near infrared light. Despite the presence of cyanobacteria, no oxygen could be detected in the presence of light, suggesting anoxygenic photosynthesis as the major metabolic process at this site. Our investigations furthermore indicated photoheterotrophy as an important process in both habitats. We obtained insights into a syntrophically operating phototrophic community in an ecosystem that bears resemblance to early Earth conditions, where cyanobacteria constitute an important contributor to carbon fixation despite the presence of high sulfide concentrations.

Evolution of photosynthesis

Energy conversion of sunlight by photosynthetic organisms has changed Earth and life on it. Photosynthesis arose early in Earth's history, and the earliest forms of photosynthetic life were almost certainly anoxygenic (non-oxygen evolving). The invention of oxygenic photosynthesis and the subsequent rise of atmospheric oxygen approximately 2.4 billion years ago revolutionized the energetic and enzymatic fundamentals of life. The repercussions of this revolution are manifested in novel biosynthetic pathways of photosynthetic cofactors and the modification of electron carriers, pigments, and existing and alternative modes of photosynthetic carbon fixation. The evolutionary history of photosynthetic organisms is further complicated by lateral gene transfer that involved photosynthetic components as well as by endosymbiotic events. An expanding wealth of genetic information, together with biochemical, biophysical, and physiological data, reveals a mosaic of photosynthetic features. In combination, these data provide an increasingly robust framework to formulate and evaluate hypotheses concerning the origin and evolution of photosynthesis.

Raman spectra of biomarkers of relevance to analytical astrobiological exploration: hopanoids, sterols and steranes

The aim of this work is to investigate the viability and potential of three groups of organic compounds as biomarkers in a future robotic analytical exploration of Mars. The three compounds have been identified as suitable candidates for potential biomarkers for extant or extinct life from the terrestrial fossil record. The three groups of compound were all similar in structure, being either tetra- or penta-cyclic compounds. The limits of detection for a sample were also tested to estimate what concentrations it would still be amenable to Raman spectroscopic investigation. This was investigated using both solid mixtures and liquid solutions. The spectra of these compounds are characterised so that they can be added to the Raman database for future Mars missions. This involved identifying functional group characteristics, assigning peaks for each individual sample and characteristic features which would categorise the samples.

Intracellular assembly of cyanophage Syn5 proceeds through a scaffold-containing procapsid

Syn5 is a marine cyanophage that is propagated on the marine photosynthetic cyanobacterial strain Synechococcus sp. WH8109 under laboratory conditions. Cryoelectron images of this double-stranded DNA (dsDNA) phage reveal an icosahedral capsid with short tail appendages and a single novel hornlike structure at the vertex opposite the tail. Despite the major impact of cyanophages on life in the oceans, there is limited information on cyanophage intracellular assembly processes within their photosynthetic hosts. The one-step growth curve of Syn5 demonstrated a short cycle with an eclipse period of ∼45 min, a latent phase of ∼60 min, and a burst size of 20 to 30 particles per cell at 28°C. SDS-PAGE and Western blot analysis of cell lysates at different times after infection showed the synthesis of major virion proteins and their increase as the infection progressed. The scaffolding protein of Syn5, absent from virions, was identified in the lysates and expressed from the cloned gene. It migrated anomalously on SDS-PAGE, similar to the phage T7 scaffolding protein. Particles lacking DNA but containing the coat and scaffolding proteins were purified from Syn5-infected cells using CsCl centrifugation followed by sucrose gradient centrifugation. Electron microscopic images of the purified particles showed shells lacking condensed DNA but filled with protein density, presumably scaffolding protein. These findings suggest that the cyanophages form infectious virions through the initial assembly of scaffolding-containing procapsids, similar to the assembly pathways for the enteric dsDNA bacteriophages. Since cyanobacteria predate the enteric bacteria, this procapsid-mediated assembly pathway may have originated with the cyanophages.

NMR spectral assignment of 2α- and 3β-methylhopanes and evidence for boat conformation in D ring of 17α(H),21α(H)-hopanes

The full (1)H and (13)C NMR chemical shift assignment of 2α-methyl-17α(H),21β(H)-hopane is presented. This compound is formed in mature sediments from biogenic sources of 2β-methyl-17β(H),21β(H)-hopanoids, which include several cyanobacteria. In addition, full (1)H and (13)C NMR chemical shift data of all four 17,21 isomers of 3β-methylhopane have been assigned. The thermodynamically most stable 3β-configuration corresponds to that found in bacterial sources. The data presented here suggest minor corrections to the (13)C chemical assignments reported earlier for 17α(H)-hopanes. Moreover, spectral evidence indicates an unexpected ring-D boat conformation of 17α(H),21α(H)-hopanes, which may serve to explain the steric strain reported for this isomer.

Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation

Neutrophilic Fe-oxidizing bacteria (FeOB) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by Gallionella ferruginea or Mariprofundus ferrooxydans. Similar filaments preserved in silica are often identified as FeOB fossils in rocks. Although it is assumed that twisted iron stalks are indicative of FeOB, the stalk's metabolic role has not been established. To this end, we studied the marine FeOB M. ferrooxydans by light, X-ray and electron microscopy. Using time-lapse light microscopy, we observed cells excreting stalks during growth (averaging 2.2  μm  h(-1)). Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy show that stalks are Fe(III)-rich, whereas cells are low in Fe. Transmission electron microscopy reveals that stalks are composed of several fibrils, which contain few-nanometer-sized iron oxyhydroxide crystals. Lepidocrocite crystals that nucleated on the fibril surface are much larger (∼100  nm), suggesting that mineral growth within fibrils is retarded, relative to sites surrounding fibrils. C and N 1s NEXAFS spectroscopy and fluorescence probing show that stalks primarily contain carboxyl-rich polysaccharides. On the basis of these results, we suggest a physiological model for Fe oxidation in which cells excrete oxidized Fe bound to organic polymers. These organic molecules retard mineral growth, preventing cell encrustation. This model describes an essential role for stalk formation in FeOB growth. We suggest that stalk-like morphologies observed in modern and ancient samples may be correlated confidently with the Fe-oxidizing metabolism as a robust biosignature.

Fossilized glycolipids reveal past oceanic N2 fixation by heterocystous cyanobacteria

N(2)-fixing cyanobacteria play an essential role in sustaining primary productivity in contemporary oceans and freshwater systems. However, the significance of N(2)-fixing cyanobacteria in past nitrogen cycling is difficult to establish as their preservation potential is relatively poor and specific biological markers are presently lacking. Heterocystous N(2)-fixing cyanobacteria synthesize unique long-chain glycolipids in the cell envelope covering the heterocyst cell to protect the oxygen-sensitive nitrogenase enzyme. We found that these heterocyst glycolipids are remarkably well preserved in (ancient) lacustrine and marine sediments, unambiguously indicating the (past) presence of N(2)-fixing heterocystous cyanobacteria. Analysis of Pleistocene sediments of the eastern Mediterranean Sea showed that heterocystous cyanobacteria, likely as epiphytes in symbiosis with planktonic diatoms, were particularly abundant during deposition of sapropels. Eocene Arctic Ocean sediments deposited at a time of large Azolla blooms contained glycolipids typical for heterocystous cyanobacteria presently living in symbiosis with the freshwater fern Azolla, indicating that this symbiosis already existed in that time. Our study thus suggests that heterocystous cyanobacteria played a major role in adding "new" fixed nitrogen to surface waters in past stratified oceans.

Evolutionary inheritance of elemental stoichiometry in phytoplankton

The elemental composition of phytoplankton is a fusion of the evolutionary history of the host and plastid, resulting in differences in genetic constraints and selection pressures associated with environmental conditions. The evolutionary inheritance hypothesis predicts similarities in elemental composition within related taxonomic lineages of phytoplankton. To test this hypothesis, we measured the elemental composition (C, N, P, S, K, Mg, Ca, Sr, Fe, Mn, Zn, Cu, Co, Cd and Mo) of 14 phytoplankton species and combined these with published data from 15 more species from both marine and freshwater environments grown under nutrient-replete conditions. The largest differences in the elemental profiles of the species distinguish between the prokaryotic Cyanophyta and primary endosymbiotic events that resulted in the green and red plastid lineages. Smaller differences in trace element stoichiometry within the red and green plastid lineages are consistent with changes in trace elemental stoichiometry owing to the processes associated with secondary endosymbioses and inheritance by descent with modification.

Circadian input kinases and their homologs in cyanobacteria: evolutionary constraints versus architectural diversification

The circadian input kinase A (cikA) gene encodes a protein relaying environmental signal to the central circadian oscillator in cyanobacteria. The CikA protein has a variable architecture and usually consists of four tandemly arrayed domains: GAF, histidine kinase (HisKA), histidine kinase-like ATPase (HATPase_c), and a pseudo-receiver (REC). Among them, HisKA and HATPase_c are the least polymorphic, and REC is not present in heterocystic filamentous cyanobacteria. CikA contains several conserved motifs that are likely important for circadian function. There are at least three types of circadian systems, each of which possesses a different set of circadian genes. The originally described circadian system (kaiABC system) possesses both cikA and kaiA, while the others lack either only cikA (kaiABC (Delta)) or both (kaiBC). The results we obtained allowed us to approximate the time of the cikA origin to be about 2600-2200 MYA and the time of its loss in the species with the kaiABC (Delta) or kaiBC system between 1100 and 600 MYA. Circadian specialization of CikA, as opposed to its non-circadian homologs, is a result of several factors, including the unique conserved domain architecture and high evolutionary constraints of some domains and regions, which were previously identified as critical for the circadian function of the gene.

Identification of a methylase required for 2-methylhopanoid production and implications for the interpretation of sedimentary hopanes

The rise of atmospheric oxygen has driven environmental change and biological evolution throughout much of Earth's history and was enabled by the evolution of oxygenic photosynthesis in the cyanobacteria. Dating this metabolic innovation using inorganic proxies from sedimentary rocks has been difficult and one important approach has been to study the distributions of fossil lipids, such as steranes and 2-methylhopanes, as biomarkers for this process. 2-methylhopanes arise from degradation of 2-methylbacteriohopanepolyols (2-MeBHPs), lipids thought to be synthesized primarily by cyanobacteria. The discovery that 2-MeBHPs are produced by an anoxygenic phototroph, however, challenged both their taxonomic link with cyanobacteria and their functional link with oxygenic photosynthesis. Here, we identify a radical SAM methylase encoded by the hpnP gene that is required for methylation at the C-2 position in hopanoids. This gene is found in several, but not all, cyanobacteria and also in alpha -proteobacteria and acidobacteria. Thus, one cannot extrapolate from the presence of 2-methylhopanes alone, in modern environments or ancient sedimentary rocks, to a particular taxonomic group or metabolism. To understand the origin of this gene, we reconstructed the evolutionary history of HpnP. HpnP proteins from cyanobacteria, Methylobacterium species, and other alpha-proteobacteria form distinct phylogenetic clusters, but the branching order of these clades could not be confidently resolved. Hence,it is unclear whether HpnP, and 2-methylhopanoids, originated first in the cyanobacteria. In summary, existing evidence does not support the use of 2-methylhopanes as biomarkers for oxygenic photosynthesis.