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

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.

Lipid biomarkers recording marine microbial community structure changes through the Frasnian-Famennian mass extinction event

Studying the response and recovery of marine microbial communities during mass extinction events provides an evolutionary window through which to understand the adaptation and resilience of the marine ecosystem in the face of significant environmental disturbances. The goal of this study is to reconstruct changes in the marine microbial community structure through the Late Devonian Frasnian-Famennian (F-F) transition. We performed a multiproxy investigation on a drill core of the Upper Devonian New Albany Shale from the Illinois Basin (western Kentucky, USA). Aryl isoprenoids show green sulfur bacteria expansion and associated photic zone euxinia (PZE) enhancement during the F-F interval. These changes can be attributed to augmented terrigenous influxes, as recorded collectively by the long-chain/short-chain normal alkane ratio, carbon preference index, C30 moretane/C30 hopane, and diahopane index. Hopane/sterane ratios reveal a more pronounced dominance of eukaryotic over prokaryotic production during the mass extinction interval. Sterane distributions indicate that the microalgal community was primarily composed of green algae clades, and their dominance became more pronounced during the F-F interval and continued to rise in the subsequent periods. The 2α-methylhopane index values do not show an evident shift during the mass extinction interval, whereas the 3β-methylhopane index values record a greater abundance of methanotrophic bacteria during the extinction interval, suggesting enhanced methane cycling due to intensified oxygen depletion. Overall, the Illinois Basin during the F-F extinction experienced heightened algal productivity due to intensified terrigenous influxes, exhibiting similarities to contemporary coastal oceans that are currently undergoing globalized cultural eutrophication. The observed microbial community shifts associated with the F-F environmental disturbances were largely restricted to the extinction interval, which suggests a relatively stable, resilient marine microbial ecosystem during the Late Devonian.

Marine and terrestrial nitrifying bacteria are sources of diverse bacteriohopanepolyols

Hopanoid lipids, bacteriohopanols and bacteriohopanepolyols, are membrane components exclusive to bacteria. Together with their diagenetic derivatives, they are commonly used as biomarkers for specific bacterial groups or biogeochemical processes in the geologic record. However, the sources of hopanoids to marine and freshwater environments remain inadequately constrained. Recent marker gene studies suggest a widespread potential for hopanoid biosynthesis in marine bacterioplankton, including nitrifying (i.e., ammonia- and nitrite-oxidizing) bacteria. To explore their hopanoid biosynthetic capacities, we studied the distribution of hopanoid biosynthetic genes in the genomes of cultivated and uncultivated ammonia-oxidizing (AOB), nitrite-oxidizing (NOB), and complete ammonia-oxidizing (comammox) bacteria, finding that biosynthesis of diverse hopanoids is common among seven of the nine presently cultivated clades of nitrifying bacteria. Hopanoid biosynthesis genes are also conserved among the diverse lineages of bacterial nitrifiers detected in environmental metagenomes. We selected seven representative NOB isolated from marine, freshwater, and engineered environments for phenotypic characterization. All tested NOB produced diverse types of hopanoids, with some NOB producing primarily diploptene and others producing primarily bacteriohopanepolyols. Relative and absolute abundances of hopanoids were distinct among the cultures and dependent on growth conditions, such as oxygen and nitrite limitation. Several novel nitrogen-containing bacteriohopanepolyols were tentatively identified, of which the so called BHP-743.6 was present in all NOB. Distinct carbon isotopic signatures of biomass, hopanoids, and fatty acids in four tested NOB suggest operation of the reverse tricarboxylic acid cycle in Nitrospira spp. and Nitrospina gracilis and of the Calvin-Benson-Bassham cycle for carbon fixation in Nitrobacter vulgaris and Nitrococcus mobilis. We suggest that the contribution of hopanoids by NOB to environmental samples could be estimated by their carbon isotopic compositions. The ubiquity of nitrifying bacteria in the ocean today and the antiquity of this metabolic process suggest the potential for significant contributions to the geologic record of hopanoids.

Lipid biomarkers: molecular tools for illuminating the history of microbial life

Fossilized lipids preserved in sedimentary rocks offer singular insights into the Earth's palaeobiology. These 'biomarkers' encode information pertaining to the oxygenation of the atmosphere and oceans, transitions in ocean plankton, the greening of continents, mass extinctions and climate change. Historically, biomarker interpretations relied on inventories of lipids present in extant microorganisms and counterparts in natural environments. However, progress has been impeded because only a small fraction of the Earth's microorganisms can be cultured, many environmentally significant microorganisms from the past no longer exist and there are gaping holes in knowledge concerning lipid biosynthesis. The revolution in genomics and bioinformatics has provided new tools to expand our understanding of lipid biomarkers, their biosynthetic pathways and distributions in nature. In this Review, we explore how preserved organic molecules provide a unique perspective on the history of the Earth's microbial life. We discuss how advances in molecular biology have helped elucidate biomarker origins and afforded more robust interpretations of fossil lipids and how the rock record provides vital calibration points for molecular clocks. Such studies are open to further exploitation with the expansion of sequenced microbial genomes in accessible databases.

2-Methylhopanoids in geographically distinct, arid biological soil crusts are primarily cyanobacterial in origin

Microbial palaeontology is largely reliant on the interpretation of geologically stable biomarkers or molecular fossils. Biomolecules that are both specific to particular groups of organisms and stable on a geological scale are invaluable for tracing the emergence and diversification of lifeforms, particularly in cases where mineral fossils are lacking. 2-Methylhopanoids and their diagenic product, 2-methylhopanes, are highly abundant bacterial membrane lipids, recoverable from samples in excess of a billion years old. In this work we used degenerate PCR, targeting 2-methylhopanoid biosynthesis genes, and sequencing to show that the ability to produce these molecules in arid biological soil crusts from deserts in diverse geographical locations (Utah, USA, and the Pilbara, Australia) is largely confined to cyanobacteria. These data suggest that 2-methylhopanes can be used as a proxy for cyanobacterial presence within these environments, contributing to our understanding of the emergence of terrestrial life on Earth.

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.

Evidence for enzymatic backbone methylation of the main membrane lipids in the archaeon Methanomassiliicoccus luminyensis

Butanetriol and pentanetriol dibiphytanyl glycerol tetraethers (BDGTs and PDGTs, respectively) are recently identified classes of archaeal membrane lipids that are prominent constituents in anoxic subseafloor sediments. These lipids are intriguing as they possess unusual backbones with four or five carbon atoms instead of the canonical three-carbon glycerol backbone. In this study, we examined the biosynthesis of BDGTs and PDGTs by the methanogen Methanomassiliicoccus luminyensis, the only available isolate known to produce these compounds, via stable isotope labeling with [methyl-¹³C] methionine followed by mass spectrometry analysis. We show that their biosynthesis proceeds from transfer(s) of the terminal methyl group of methionine to the more common archaeal membrane lipids, i.e., glycerol dibiphytanyl glycerol tetraethers (GDGTs). As this methylation targets a methylene group, a radical mechanism involving a radical S-adenosylmethionine (SAM) enzyme is probable. Over the course of the incubation, the abundance of PDGTs relative to BDGTs, expressed as backbone methylation index, increased, implying that backbone methylation may be related to the growth shift to stationary conditions, possibly due to limited energy and/or substrate availability. The increase of the backbone methylation index with increasing sediment age in a sample set from the Mediterranean Sea adds support for such a relationship. Importance Butanetriol and pentanetriol dibiphytanyl glycerol tetraethers are membrane lipids recently discovered in anoxic environments. These lipids differ from typical membrane-spanning tetraether lipids because they possess a non-glycerol backbone. The biosynthetic pathway and physiological role of these unique lipids are currently unknown. Here, we show that in the strain Methanomassiliicoccus luminyensis these lipids are the result of methyl transfer(s) from a S-adenosyl methionine (SAM) intermediate. We observed a relative increase of the doubly methylated compound, pentanetriol dibiphytanyl glycerol tetraether, in the stationary phase of M. luminyensis as well as in the subseafloor of the Mediterranean Sea and thus introduced a backbone methylation index, which could be used to further explore microbial activity in natural settings.

Analysis of Bacteriohopanoids from Thermophilic Bacteria by Liquid Chromatography-Mass Spectrometry

Background: Hopanoids modify plasma membrane properties in bacteria and are often compared to sterols that modulate membrane fluidity in eukaryotes. In some microorganisms, they can also allow adaptations to extreme environments. Methods: Hopanoids were identified by liquid chromatography-mass spectrometry in fourteen strains of thermophilic bacteria belonging to five genera, i.e., Alicyclobacillus, Brevibacillus, Geobacillus, Meiothermus, and Thermus. The bacteria were cultivated at temperatures from 42 to 70 °C. Results: Regardless of the source of origin, the strains have the same tendency to adapt the hopanoid content depending on the cultivation temperature. In the case of aminopentol, its content increases; aminotetrol does not show a significant change; and in the case of aminotriol the content decreases by almost a third. The content of bacteriohopanetetrol and bacteriohopanetetrol glycoside decreases with increasing temperature, while in the case of adenosylhopane the opposite trend was found. Conclusions: Changes in hopanoid content can be explained by increased biosynthesis, where adenosylhopane is the first intermediate in the biosynthesis of the hopanoid side chain.

The antimicrobial peptide Polybia-MP1 differentiates membranes with the hopanoid, diplopterol from those with cholesterol

Polybia-MP1 is an antimicrobial peptide that shows a decreased activity in membranes with cholesterol (CHO). Since it is now accepted that hopanoids act as sterol-surrogates in some sterol-lacking bacteria, we here inquire about the impact of Polybia-MP1 on membranes containing the hopanoid diplopterol (DP) in comparison to membranes with CHO. We found that, despite the properties induced on lipid membranes by DP are similar to those induced by CHO, the effect of Polybia-MP1 on membranes with CHO or DP was significantly different. DP did not prevent dye release from LUVs, nor the insertion of Polybia-MP1 into monolayers, and peptide-membrane affinity was higher for those with DP than with CHO. Zeta potentials ( ζ ) for DP-containing LUVs showed a complex behavior at increasing peptide concentration. The effect of the peptide on membrane elasticity, investigated by nanotube retraction experiments, showed that peptide addition softened all membrane compositions, but membranes with DP got stiffer at long times. Considering this, and the ζ results, we propose that peptides accumulate at the interface adopting different arrangements, leading to a non-monotonic behavior. Possible correlations with cell membranes were inquired testing the antimicrobial activity of Polybia-MP1 against hopanoid-lacking bacteria pre-incubated with DP or CHO. The fraction of surviving cells was lower in cultures incubated with DP compared to those incubated with CHO. We propose that the higher activity of Polybia-MP1 against some bacteria compared to mammalian cells is not only related to membrane electrostatics, but also the composition of neutral lipids, particularly the hopanoids, could be important.

Vitamin B12-dependent biosynthesis ties amplified 2-methylhopanoid production during oceanic anoxic events to nitrification

Bacterial hopanoid lipids are ubiquitous in the geologic record and serve as biomarkers for reconstructing Earth's climatic and biogeochemical evolution. Specifically, the abundance of 2-methylhopanoids deposited during Mesozoic ocean anoxic events (OAEs) and other intervals has been interpreted to reflect proliferation of nitrogen-fixing marine cyanobacteria. However, there currently is no conclusive evidence for 2-methylhopanoid production by extant marine cyanobacteria. As an alternative explanation, here we report 2-methylhopanoid production by bacteria of the genus Nitrobacter, cosmopolitan nitrite oxidizers that inhabit nutrient-rich freshwater, brackish, and marine environments. The model organism Nitrobacter vulgaris produced only trace amounts of 2-methylhopanoids when grown in minimal medium or with added methionine, the presumed biosynthetic methyl donor. Supplementation of cultures with cobalamin (vitamin B₁₂) increased nitrite oxidation rates and stimulated a 33-fold increase of 2-methylhopanoid abundance, indicating that the biosynthetic reaction mechanism is cobalamin dependent. Because Nitrobacter spp. cannot synthesize cobalamin, we postulate that they acquire it from organisms inhabiting a shared ecological niche-for example, ammonia-oxidizing archaea. We propose that during nutrient-rich conditions, cobalamin-based mutualism intensifies upper water column nitrification, thus promoting 2-methylhopanoid deposition. In contrast, anoxia underlying oligotrophic surface ocean conditions in restricted basins would prompt shoaling of anaerobic ammonium oxidation, leading to low observed 2-methylhopanoid abundances. The first scenario is consistent with hypotheses of enhanced nutrient loading during OAEs, while the second is consistent with the sedimentary record of Pliocene-Pleistocene Mediterranean sapropel events. We thus hypothesize that nitrogen cycling in the Pliocene-Pleistocene Mediterranean resembled modern, highly stratified basins, whereas no modern analog exists for OAEs.

Understanding the geobiology of the terminal Ediacaran Khatyspyt Lagerstätte (Arctic Siberia, Russia)

The Khatyspyt Lagerstätte (~544 Ma, Russia) provides a valuable window into late Ediacaran Avalon-type ecosystems with rangeomorphs, arboreomorphs, and mega-algae. Here, we tackle the geobiology of this Lagerstätte by the combined analysis of paleontological features, sedimentary facies, and lipid biomarkers. The Khatyspyt Formation was deposited in carbonate ramp environments. Organic matter (0.12-2.22 wt.% TOC) displays characteristic Ediacaran biomarker features (e.g., eukaryotic steranes dominated by the C₂₉ stigmastane). Some samples contain a putative 2-methylgammacerane that was likely sourced by ciliates and/or bacteria. 24-isopropylcholestane and 26-methylstigmastane are consistently scarce (≤0.4% and ≤0.2% of ∑C_27-30 regular steranes, respectively). Thus, Avalon-type organisms occupied different niches than organisms capable of directly synthesizing C₃₀ sterane precursors among their major lipids. Relative abundances of eukaryotic steranes and bacterial hopanes (sterane/hopane ratios = 0.07-0.30) demonstrate oligotrophic and bacterially dominated marine environments, similar to findings from other successions with Ediacara-type fossils. Ediacara-type fossils occur in facies characterized by microbial mats and biomarkers indicative for a stratified marine environment with normal-moderate salinities (moderate-high gammacerane index of 2.3-5.7; low C₃₅ homohopane index of 0.1-0.2). Mega-algae, in contrast, are abundant in facies that almost entirely consist of allochthonous event layers. Biomarkers in these samples indicate a non-stratified marine environment and normal salinities (low gammacerane index of 0.6-0.8; low C₃₅ homohopane index of 0.1). Vertical burrowers occur in similar facies but with biomarker evidence for stratification in the water column or around the seafloor (high gammacerane index of 5.6). Thus, the distribution of macro-organisms and burrowers was controlled by various, dynamically changing environmental factors. It appears likely that dynamic settings like the Khatyspyt Lagerstätte provided metabolic challenges for sustenance and growth which primed eukaryotic organisms to cope with changing environmental habitats, allowing for a later diversification and expansion of complex macroscopic life in the marine realm.

GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean

Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are distinctive archaeal membrane-spanning lipids with up to eight cyclopentane rings and/or one cyclohexane ring. The number of rings added to the GDGT core structure can vary as a function of environmental conditions, such as changes in growth temperature. This physiological response enables cyclic GDGTs preserved in sediments to be employed as proxies for reconstructing past global and regional temperatures and to provide fundamental insights into ancient climate variability. Yet, confidence in GDGT-based paleotemperature proxies is hindered by uncertainty concerning the archaeal communities contributing to GDGT pools in modern environments and ambiguity in the environmental and physiological factors that affect GDGT cyclization in extant archaea. To properly constrain these uncertainties, a comprehensive understanding of GDGT biosynthesis is required. Here, we identify 2 GDGT ring synthases, GrsA and GrsB, essential for GDGT ring formation in Sulfolobus acidocaldarius Both proteins are radical S-adenosylmethionine proteins, indicating that GDGT cyclization occurs through a free radical mechanism. In addition, we demonstrate that GrsA introduces rings specifically at the C-7 position of the core GDGT lipid, while GrsB cyclizes at the C-3 position, suggesting that cyclization patterns are differentially controlled by 2 separate enzymes and potentially influenced by distinct environmental factors. Finally, phylogenetic analyses of the Grs proteins reveal that marine Thaumarchaeota, and not Euryarchaeota, are the dominant source of cyclized GDGTs in open ocean settings, addressing a major source of uncertainty in GDGT-based paleotemperature proxy applications.

Extended Hopanoid Loss Reduces Bacterial Motility and Surface Attachment and Leads to Heterogeneity in Root Nodule Growth Kinetics in a Bradyrhizobium-Aeschynomene Symbiosis

Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Hopanoid biosynthesis genes are conserved in nitrogen-fixing plant symbionts, and we previously found that the extended (C35) class of hopanoids in Bradyrhizobium diazoefficiens are required for efficient symbiotic nitrogen fixation in the tropical legume host Aeschynomene afraspera. Here, we demonstrate that the nitrogen-fixation defect conferred by extended hopanoid loss can be fully explained by a reduction in root nodule sizes rather than per-bacteroid nitrogen-fixation levels. Using a single-nodule tracking approach to quantify A. afraspera nodule development, we provide a quantitative model of root nodule development in this host, uncovering both the baseline growth parameters for wild-type nodules and a surprising heterogeneity of extended hopanoid mutant developmental phenotypes. These phenotypes include a delay in root nodule initiation and the presence of a subpopulation of nodules with slow growth rates and low final volumes, which are correlated with reduced motility and surface attachment in vitro and lower bacteroid densities in planta, respectively. This work provides a quantitative reference point for understanding the phenotypic diversity of ineffective symbionts in A. afraspera and identifies specific developmental stages affected by extended hopanoid loss for future mechanistic work.

A nematode sterol C4α-methyltransferase catalyzes a new methylation reaction responsible for sterol diversity

Primitive sterol evolution plays an important role in fossil record interpretation and offers potential therapeutic avenues for human disease resulting from nematode infections. Recognizing that C4-methyl stenol products [8(14)-lophenol] can be synthesized in bacteria while C4-methyl stanol products (dinosterol) can be synthesized in dinoflagellates and preserved as sterane biomarkers in ancient sedimentary rock is key to eukaryotic sterol evolution. In this regard, nematodes have been proposed to convert dietary cholesterol to 8(14)-lophenol by a secondary metabolism pathway that could involve sterol C4 methylation analogous to the C2 methylation of hopanoids (radicle-type mechanism) or C24 methylation of sterols (carbocation-type mechanism). Here, we characterized dichotomous cholesterol metabolic pathways in Caenorhabditis elegans that generate 3-oxo sterol intermediates in separate paths to lophanol (4-methyl stanol) and 8(14)-lophenol (4-methyl stenol). We uncovered alternate C3-sterol oxidation and Δ⁷ desaturation steps that regulate sterol flux from which branching metabolite networks arise, while lophanol/8(14)-lophenol formation is shown to be dependent on a sterol C4α-methyltransferse (4-SMT) that requires 3-oxo sterol substrates and catalyzes a newly discovered 3-keto-enol tautomerism mechanism linked to S-adenosyl-l-methionine-dependent methylation. Alignment-specific substrate-binding domains similarly conserved in 4-SMT and 24-SMT enzymes, despite minimal amino acid sequence identity, suggests divergence from a common, primordial ancestor in the evolution of methyl sterols. The combination of these results provides evolutionary leads to sterol diversity and points to cryptic C4-methyl steroidogenic pathways of targeted convergence that mediate lineage-specific adaptations.­­

Environmental controls on bacteriohopanepolyol profiles of benthic microbial mats from Lake Fryxell, Antarctica

Bacteriohopanepolyols (BHPs) are pentacyclic triterpenoid lipids that contribute to the structural integrity and physiology of some bacteria. Because some BHPs originate from specific classes of bacteria, BHPs have potential as taxonomically and environmentally diagnostic biomarkers. For example, a stereoisomer of bacteriohopanetetrol (informally BHT II) has been associated with anaerobic ammonium oxidation (anammox) bacteria and suboxic to anoxic marine environments where anammox is active. As a result, the detection of BHT II in the sedimentary record and fluctuations in the relative abundance of BHT II may inform reconstructions of nitrogen cycling and ocean redox changes through the geological record. However, there are uncertainties concerning the sources of BHT II and whether or not BHT II is produced in abundance in non-marine environments, both of which are pertinent to interpretations of BHT II signatures in sediments. To address these questions, we investigate the BHP composition of benthic microbial mats from Lake Fryxell, Antarctica. Lake Fryxell is a perennially ice-covered lake with a sharp oxycline in a density-stabilized water column. We describe the diversity and abundance of BHPs in benthic microbial mats across a transect from oxic to anoxic conditions. Generally, BHP abundances and diversity vary with the morphologies of microbial mats, which were previously shown to reflect local environmental conditions, such as irradiance and oxygen and sulfide concentrations. BHT II was identified in mats that exist within oxic to anoxic portions of the lake. However, anammox bacteria have yet to be identified in Lake Fryxell. We examine our results in the context of BHPs as biomarkers in modern and ancient environments.

Cobalamin-dependent radical S-adenosyl-l-methionine enzymes in natural product biosynthesis

Covering: 2011 to 2018 This highlight summarizes the investigation of cobalamin (Cbl)- and radical S-adenosyl-l-methionine (SAM)-dependent enzymes found in natural product biosynthesis to date and suggests some possibilities for the future. Though some mechanistic aspects are apparently shared, the overall diversity of this family's functions and abilities is significant and may be tailored to the specific substrate and/or reaction being catalyzed. A little over a year ago, the first crystal structure of a Cbl- and radical SAM-dependent enzyme was solved, providing the first insight into what may be the shared scaffolding of these enzymes.

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.

Bacteriohopanepolyols across environmental gradients in Lake Vanda, Antarctica

Bacteriohopanepolyols (BHPs) are bacterial membrane lipids that may be used as biological or environmental biomarkers. Previous studies have described the diversity, distribution, and abundance of BHPs in a variety of modern environments. However, the regulation of BHP production in polar settings is not well understood. Benthic microbial mats from ice-covered lakes of the McMurdo Dry Valleys, Antarctica provide an opportunity to investigate the sources, physiological roles, and preservation of BHPs in high-latitude environments. Lake Vanda is one of the most stable lakes on Earth, with microbial communities occupying specific niches along environmental gradients. We describe the influence of mat morphology and local environmental conditions on the diversity and distribution of BHPs and their biological sources in benthic microbial mats from Lake Vanda. The abundance and diversity of C-2 methylated hopanoids (2-MeBHP) are of particular interest, given that their stable degradation products, 2-methylhopanes, are among the oldest and most prevalent taxonomically informative biomarkers preserved in sedimentary rocks. Furthermore, the interpretation of sedimentary 2-methylhopanes is of great interest to the geobiology community. We identify cyanobacteria as the sole source of 2-MeBHP in benthic microbial mats from Lake Vanda and assess the hypothesis that 2-MeBHP are regulated in response to a particular environmental variable, namely solar irradiance.

A stable and productive marine microbial community was sustained through the end-Devonian Hangenberg Crisis within the Cleveland Shale of the Appalachian Basin, United States

The end-Devonian Hangenberg Crisis constituted one of the greatest ecological and environmental perturbations of the Paleozoic Era. To date, however, it has been difficult to precisely constrain the occurrence of the Hangenberg Crisis in the Appalachian Basin of the United States and thus to directly assess the effects of this crisis on marine microbial communities and paleoenvironmental conditions. Here, we integrate organic and inorganic chemostratigraphic records compiled from two discrete outcrop locations to characterize the onset and paleoenvironmental transitions associated with the Hangenberg Crisis within the Cleveland Shale member of the Ohio Shale. The upper Cleveland Shale records both positive carbon (δ¹³ C_org ) and nitrogen (δ¹⁵ N_total ) isotopic excursions, and replenished trace metal inventories with links to eustatic rise. These dual but apparently temporally offset isotope excursions may be useful for stratigraphic correlation with other productive end-Devonian epeiric marine locations. Deposition of the black shale succession occurred locally beneath a redox-stratified water column with euxinic zones, with signs of strengthening denitrification during the Hangenberg Crisis interval, but with an otherwise stable and algal-rich marine microbial community structure sustained in the surface mixed layer as ascertained by lipid biomarker assemblages. Discernible trace fossil signals in some horizons suggest, however, that bioturbation and seafloor oxygenation occurred episodically throughout this succession and highlight that geochemical proxies often fail to capture these rapid and sporadic redox fluctuations in ancient black shales. The paleoenvironmental conditions, source biota, and accumulations of black shale are consistent with expressions of the Hangenberg Crisis globally, suggesting this event is likely captured within the uppermost strata of the Cleveland Shale in North America.

Hydrocarbon biomarkers preserved in carbonate veins of potentially Paleoproterozoic age, and implications for the early biosphere

Research on the early rise of oxygenic photosynthesis and eukaryotes has recently encountered a major pitfall, as some hopane and sterane biomarkers reported in Archaean rocks are the results of contamination. Following an extensive petrological framework in the Pilbara Craton, Western Australia, oil-bearing fluid inclusions and solid bitumens were identified in replacement and hydrothermal carbonate veins cross-cutting Archaean metasedimentary rocks. The 2.55-2.63 billion years old metasedimentary rocks were found to be depleted of indigenous biomarkers. Here we show novel biomarker results from the solvent extraction of the carbonate veins. Volcanic rock blanks, outside rinses, and instrumental blanks showed no biomarkers, and the surrounding rocks were metamorphosed to a sufficiently high extent to not yield any biomarkers, but the biomarkers found in the veins are most likely indigenous. Biomarkers detected include C_21-22 ααα- and αββ-steranes (pregnanes), C_27-29 αββ-steranes, C_19-26 tricyclic terpanes, C_29-30,34 αβ-hopanes, C₃₀ 17α-diahopane, and trisnorhopanes, which are in the range 2-180 pg/g. The extracted organic matter is highly mature, based on the biomarker configurations and calculated vitrinite reflectance that ranges from 2.4-3.0 (methylphenanthrene index), 1.4-1.9 (methyladamantane index), and 1.4-2.3 (methyldiamantane index). As the biomarkers are highly mature and the biomarker assemblages have a distinctive pattern to each vein type the likelihood of sample contamination by recent, less mature, biomarkers from a different assemblage is unlikely. The detection of steranes suggests that molecular oxygen was available when the veins were formed, possibly between 2.2 and 1.8 billion years ago, but no evidence for oxygenic photosynthesis in the form of cyanobacterial biomarkers has been found. Carbonate minerals that seem to better preserve biomarkers, such as concretions or veins, show the growing importance of new and exciting opportunities to seek biomarkers in the early Earth rock record, and potentially on other planets. Our results demonstrate for that first time that biomarkers can be found in veins cutting through highly metamorphosed Archaean rocks, and gives an insight into ancient environments.

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

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

Cobalamin-Dependent C-Methyltransferases From Marine Microbes: Accessibility via Rhizobia Expression

Cobalamin-dependent radical S-adenosylmethionine (rSAM) methyltransferases catalyze chemically challenging methylation reactions on diverse natural products at unactivated carbon centers. In vivo reconstitution and biosynthetic studies of natural product gene clusters encoding these enzymes are often severely limited by ineffective heterologous expression hosts, including the otherwise versatile Escherichia coli. In this chapter, we describe the use of rhizobia bacteria as effective expression hosts for cobalamin-dependent rSAM C-methyltransferases. We chose the natural product pathway encoding the heavily modified cytotoxic peptides, the polytheonamides, as our model pathway due to the presence of two methyltransferases responsible for a total of 17 C-methylations. Detailed protocols are given for vector construction, transformation, and heterologous expression in Rhizobium leguminosarum bv. viciae 3841. Additional methods pertaining to analytical separation and mass spectrometric analysis of modified peptides are also entailed. As genomics continues to uncover new enzymes and pathways from unknown and uncultivated microbes, use of metabolically distinct heterologous expression hosts like rhizobia will be a necessary tool to unravel the catalytic and metabolic diversity of marine microbial life.

Hopanoid lipids: from membranes to plant-bacteria interactions

Lipid research represents a frontier for microbiology, as showcased by hopanoid lipids. Hopanoids, which resemble sterols and are found in the membranes of diverse bacteria, have left an extensive molecular fossil record. They were first discovered by petroleum geologists. Today, hopanoid-producing bacteria remain abundant in various ecosystems, such as the rhizosphere. Recently, great progress has been made in our understanding of hopanoid biosynthesis, facilitated in part by technical advances in lipid identification and quantification. A variety of genetically tractable, hopanoid-producing bacteria have been cultured, and tools to manipulate hopanoid biosynthesis and detect hopanoids are improving. However, we still have much to learn regarding how hopanoid production is regulated, how hopanoids act biophysically and biochemically, and how their production affects bacterial interactions with other organisms, such as plants. The study of hopanoids thus offers rich opportunities for discovery.

Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico

Laguna Bacalar is a sulfate-rich freshwater lake on the Yucatan Peninsula that hosts large microbialites. High sulfate concentrations distinguish Laguna Bacalar from other freshwater microbialite sites such as Pavilion Lake and Alchichica, Mexico, as well as from other aqueous features on the Yucatan Peninsula. While cyanobacterial populations have been described here previously, this study offers a more complete characterization of the microbial populations and corresponding biogeochemical cycling using a three-pronged geobiological approach of microscopy, high-throughput DNA sequencing, and lipid biomarker analyses. We identify and compare diverse microbial communities of Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria that vary with location along a bank-to-bank transect across the lake, within microbialites, and within a neighboring mangrove root agglomeration. In particular, sulfate-reducing bacteria are extremely common and diverse, constituting 7%-19% of phylogenetic diversity within the microbialites, and are hypothesized to significantly influence carbonate precipitation. In contrast, Cyanobacteria account for less than 1% of phylogenetic diversity. The distribution of lipid biomarkers reflects these changes in microbial ecology, providing meaningful biosignatures for the microbes in this system. Polysaturated short-chain fatty acids characteristic of cyanobacteria account for <3% of total abundance in Laguna Bacalar microbialites. By contrast, even short-chain and monounsaturated short-chain fatty acids attributable to both Cyanobacteria and many other organisms including types of Alphaproteobacteria and Gammaproteobacteria constitute 43%-69% and 17%-25%, respectively, of total abundance in microbialites. While cyanobacteria are the largest and most visible microbes within these microbialites and dominate the mangrove root agglomeration, it is clear that their smaller, metabolically diverse associates are responsible for significant biogeochemical cycling in this microbialite system.

Cyanobacterial photosynthesis under sulfidic conditions: insights from the isolate Leptolyngbya sp. strain hensonii

We report the isolation of a pinnacle-forming cyanobacterium isolated from a microbial mat covering the sediment surface at Little Salt Spring—a flooded sinkhole in Florida with a perennially microoxic and sulfidic water column. The draft genome of the isolate encodes all of the enzymatic machinery necessary for both oxygenic and anoxygenic photosynthesis, as well as genes for methylating hopanoids at the C-2 position. The physiological response of the isolate to H₂S is complex: (i) no induction time is necessary for anoxygenic photosynthesis; (ii) rates of anoxygenic photosynthesis are regulated by both H₂S and irradiance; (iii) O₂ production is inhibited by H₂S concentrations as low as 1 μM and the recovery rate of oxygenic photosynthesis is dependent on irradiance; (iv) under the optimal light conditions for oxygenic photosynthesis, rates of anoxygenic photosynthesis are nearly double those of oxygenic photosynthesis. We hypothesize that the specific adaptation mechanisms of the isolate to H₂S emerged from a close spatial interaction with sulfate-reducing bacteria. The new isolate, Leptolyngbya sp. strain hensonii, is not closely related to other well-characterized Cyanobacteria that can perform anoxygenic photosynthesis, which further highlights the need to characterize the diversity and biogeography of metabolically versatile Cyanobacteria. The isolate will be an ideal model organism for exploring the adaptation of Cyanobacteria to sulfidic conditions.

Microbial communities and organic biomarkers in a Proterozoic-analog sinkhole

Little Salt Spring (Sarasota County, FL, USA) is a sinkhole with groundwater vents at ~77 m depth. The entire water column experiences sulfidic (~50 μM) conditions seasonally, resulting in a system poised between oxic and sulfidic conditions. Red pinnacle mats occupy the sediment-water interface in the sunlit upper basin of the sinkhole, and yielded 16S rRNA gene clones affiliated with Cyanobacteria, Chlorobi, and sulfate-reducing clades of Deltaproteobacteria. Nine bacteriochlorophyll e homologues and isorenieratene indicate contributions from Chlorobi, and abundant chlorophyll a and pheophytin a are consistent with the presence of Cyanobacteria. The red pinnacle mat contains hopanoids, including 2-methyl structures that have been interpreted as biomarkers for Cyanobacteria. A single sequence of hpnP, the gene required for methylation of hopanoids at the C-2 position, was recovered in both DNA and cDNA libraries from the red pinnacle mat. The hpnP sequence was most closely related to cyanobacterial hpnP sequences, implying that Cyanobacteria are a source of 2-methyl hopanoids present in the mat. The mats are capable of light-dependent primary productivity as evidenced by ¹³ C-bicarbonate photoassimilation. We also observed ¹³ C-bicarbonate photoassimilation in the presence of DCMU, an inhibitor of electron transfer to Photosystem II. Our results indicate that the mats carry out light-driven primary production in the absence of oxygen production-a mechanism that may have delayed the oxygenation of the Earth's oceans and atmosphere during the Proterozoic Eon. Furthermore, our observations of the production of 2-methyl hopanoids by Cyanobacteria under conditions of low oxygen and low light are consistent with the recovery of these structures from ancient black shales as well as their paucity in modern marine environments.

Bacteriohopanepolyols along redox gradients in the Humboldt Current System off northern Chile

Marine oxygen minimum zones (OMZs) are characterized by the presence of subsurface suboxic or anoxic waters where diverse microbial processes are responsible for the removal of fixed nitrogen. OMZs have expanded over past decades and are expected to continue expanding in response to the changing climate. The implications for marine biogeochemistry, particularly nitrogen cycling, are uncertain. Cell membrane lipids (biomarkers), such as bacterial bacteriohopanepolyols (BHPs) and their degradation products (hopanoids), have distinctive structural attributes that convey information about their biological sources. Since the discovery of fossil hopanoids in ancient sediments, the study of BHPs has been of great biogeochemical interest due to their potential to serve as proxies for bacteria in the geological record. A stereoisomer of bacteriohopanetetrol (BHT), BHT II, has been previously identified in OMZ waters and has as been unequivocally identified in culture enrichments of anammox bacteria, a key group contributing to nitrogen loss in marine OMZs. We tested BHT II as a proxy for suboxia/anoxia and anammox bacteria in suspended organic matter across OMZ waters of the Humboldt Current System off northern Chile, as well as in surface and deeply buried sediments (125-150 ky). The BHT II ratio (BHT II/total BHT) increases as oxygen content decreases through the water column, consistent with previous results from Perú, the Cariaco Basin and the Arabian Sea, and in line with microbiological evidence indicating intense anammox activity in the Chilean OMZ. Notably, BHT II is transported from the water column to surface sediments, and preserved in deeply buried sediments, where the BHT II ratio correlates with changes in δ¹⁵ N sediment values during glacial-interglacial transitions. This study suggests that BHT II offers a proxy for past changes in the relative importance of anammox, and fluctuations in nitrogen cycling in response to ocean redox changes through the geological record.

Lack of Methylated Hopanoids Renders the Cyanobacterium Nostoc punctiforme Sensitive to Osmotic and pH Stress

To investigate the function of 2-methylhopanoids in modern cyanobacteria, the hpnP gene coding for the radical S-adenosyl methionine (SAM) methylase protein that acts on the C-2 position of hopanoids was deleted from the filamentous cyanobacterium Nostoc punctiforme ATCC 29133S. The resulting ΔhpnP mutant lacked all 2-methylhopanoids but was found to produce much higher levels of two bacteriohopanepentol isomers than the wild type. Growth rates of the ΔhpnP mutant cultures were not significantly different from those of the wild type under standard growth conditions. Akinete formation was also not impeded by the absence of 2-methylhopanoids. The relative abundances of the different hopanoid structures in akinete-dominated cultures of the wild-type and ΔhpnP mutant strains were similar to those of vegetative cell-dominated cultures. However, the ΔhpnP mutant was found to have decreased growth rates under both pH and osmotic stress, confirming a role for 2-methylhopanoids in stress tolerance. Evidence of elevated photosystem II yield and NAD(P)H-dependent oxidoreductase activity in the ΔhpnP mutant under stress conditions, compared to the wild type, suggested that the absence of 2-methylhopanoids increases cellular metabolic rates under stress conditions.IMPORTANCE As the first group of organisms to develop oxygenic photosynthesis, Cyanobacteria are central to the evolutionary history of life on Earth and the subsequent oxygenation of the atmosphere. To investigate the origin of cyanobacteria and the emergence of oxygenic photosynthesis, geobiologists use biomarkers, the remnants of lipids produced by different organisms that are found in geologic sediments. 2-Methylhopanes have been considered indicative of cyanobacteria in some environmental settings, with the parent lipids 2-methylhopanoids being present in many contemporary cyanobacteria. We have created a Nostoc punctiforme ΔhpnP mutant strain that does not produce 2-methylhopanoids to assess the influence of 2-methylhopanoids on stress tolerance. Increased metabolic activity in the mutant under stress indicates compensatory alterations in metabolism in the absence of 2-methylhopanoids.

Pheno- and Genotyping of Hopanoid Production in Acidobacteria

Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium "Ca. Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only "Ca. K. versatilis" contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta-, and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential. Metagenomes of Acidobacteria were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in acidobacterial cultures.

Lipids as paleomarkers to constrain the marine nitrogen cycle

Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction‐oxidation transformations of bio‐available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio‐available nitrogen species. As most microorganisms are soft‐bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically‐important cycle, and provides examples of biomarker applications in the geological past.

Molecular biosignatures reveal common benthic microbial sources of organic matter in ooids and grapestones from Pigeon Cay, The Bahamas

Ooids are sedimentary grains that are distributed widely in the geologic record. Their formation is still actively debated, which limits our understanding of the significance and meaning of these grains in Earth's history. Central questions include the role played by microbes in the formation of ooids and the sources of ubiquitous organic matter within ooid cortices. To address these issues, we investigated the microbial community composition and associated lipids in modern oolitic sands at Pigeon Cay on Cat Island, The Bahamas. Surface samples were taken along a transect from the shallow, turbulent surf zone to calmer, deeper water. Grains transitioned from shiny and abraded ooids in the surf zone, to biofilm-coated ooids at about 3 m water depth. Further offshore, grapestones (cemented aggregates of ooids) dominated. Benthic diatoms and Proteobacteria dominated biofilms. Taxa that may promote carbonate precipitation were abundant, particularly those associated with sulfur cycling. Compared to the lipids associated with surface biofilms, relict lipids bound within carbonate exhibited remarkably similar profiles in all grain types. The enhanced abundance of methyl-branched fatty acids and β-hydroxy fatty acids, 1-O-monoalkyl glycerol ethers and hopanoids bound within ooid and grapestone carbonate confirms a clear association of benthic sedimentary bacteria with these grains. Lipids bound within ooid cortices also contain molecular indicators of microbial heterotrophic degradation of organic matter, possibly in locally reducing conditions. These included the loss of labile unsaturated fatty acids, enhanced long-chain fatty acids/short-chain fatty acids, enriched stable carbon isotopes ratios of fatty acids, and very high stanol/stenol ratios. To what extent some of these molecular signals are derived from later heterotrophic endolithic activity remains to be fully resolved. We speculate that some ooid carbonate forms in microbial biofilms and that early diagenetic degradation of biofilms may also play a role in early stage carbonate precipitation around ooids.

Hopanoids play a role in stress tolerance and nutrient storage in the cyanobacterium Nostoc punctiforme

Hopanes are abundant in ancient sedimentary rocks at discrete intervals in Earth history, yet interpreting their significance in the geologic record is complicated by our incomplete knowledge of what their progenitors, hopanoids, do in modern cells. To date, few studies have addressed the breadth of diversity of physiological functions of these lipids and whether those functions are conserved across the hopanoid-producing bacterial phyla. Here, we generated mutants in the filamentous cyanobacterium, Nostoc punctiforme, that are unable to make all hopanoids (shc) or 2-methylhopanoids (hpnP). While the absence of hopanoids impedes growth of vegetative cells at high temperature, the shc mutant grows faster at low temperature. This finding is consistent with hopanoids acting as membrane rigidifiers, a function shared by other hopanoid-producing phyla. Apart from impacting fitness under temperature stress, hopanoids are dispensable for vegetative cells under other stress conditions. However, hopanoids are required for stress tolerance in akinetes, a resting survival cell type. While 2-methylated hopanoids do not appear to contribute to any stress phenotype, total hopanoids and to a lesser extent 2-methylhopanoids were found to promote the formation of cyanophycin granules in akinetes. Finally, although hopanoids support symbiotic interactions between Alphaproteobacteria and plants, they do not appear to facilitate symbiosis between N. punctiforme and the hornwort Anthoceros punctatus. Collectively, these findings support interpreting hopanes as general environmental stress biomarkers. If hopanoid-mediated enhancement of nitrogen-rich storage products turns out to be a conserved phenomenon in other organisms, a better understanding of this relationship may help us parse the enrichment of 2-methylhopanes in the rock record during episodes of disrupted nutrient cycling.

Xeropreservation of functionalized lipid biomarkers in hyperarid soils in the Atacama Desert

Our understanding of long-term organic matter preservation comes mostly from studies in aquatic systems. In contrast, taphonomic processes in extremely dry environments are relatively understudied and are poorly understood. We investigated the accumulation and preservation of lipid biomarkers in hyperarid soils in the Yungay region of the Atacama Desert. Lipids from seven soil horizons in a 2.5 m vertical profile were extracted and analyzed using GC-MS and LC-MS. Diagnostic functionalized lipids and geolipids were detected and increased in abundance and diversity with depth. Deeper clay units contain fossil organic matter (radiocarbon dead) that has been protected from rainwater since the onset of hyperaridity. We show that these clay units contain lipids in an excellent state of structural preservation with functional groups and unsaturated bonds in carbon chains. This indicates that minimal degradation of lipids has occurred in these soils since the time of their deposition between >40,000 and 2 million years ago. The exceptional structural preservation of biomarkers is likely due to the long-term hyperaridity that has minimized microbial and enzymatic activity, a taphonomic process we term xeropreservation (i.e. preservation by drying). The degree of biomarker preservation allowed us to reconstruct major changes in ecology in the Yungay region that reflect a shift in hydrological regime from wet to dry since the early Quaternary. Our results suggest that hyperarid environments, which comprise 7.5% of the continental landmass, could represent a rich and relatively unexplored source of paleobiological information on Earth.

Mechanistic insights into class B radical-S-adenosylmethionine methylases: ubiquitous tailoring enzymes in natural product biosynthesis

Class B radical S-adenosylmethionine (SAM) methylases are notable for their ability to catalyse methylation reactions in the biosynthesis of a wide variety of natural products, including polyketides, ribosomally biosynthesised and post-translationally modified peptides (RiPPs), nonribosomal peptides (NRPs), aminoglycosides, β-lactams, phosphonates, enediynes, aminocoumarins and terpenes. Here, we discuss the diversity of substrates and catalytic mechanism utilised by such enzymes, highlighting the stereochemical course of methylation reactions at un-activated carbon centres and the ability of some members of the family to catalyse multiple methylations.

Timescales of Oxygenation Following the Evolution of Oxygenic Photosynthesis

Among the most important bioenergetic innovations in the history of life was the invention of oxygenic photosynthesis-autotrophic growth by splitting water with sunlight-by Cyanobacteria. It is widely accepted that the invention of oxygenic photosynthesis ultimately resulted in the rise of oxygen by ca. 2.35 Gya, but it is debated whether this occurred more or less immediately as a proximal result of the evolution of oxygenic Cyanobacteria or whether they originated several hundred million to more than one billion years earlier in Earth history. The latter hypothesis involves a prolonged period during which oxygen production rates were insufficient to oxidize the atmosphere, potentially due to redox buffering by reduced species such as higher concentrations of ferrous iron in seawater. To examine the characteristic timescales for environmental oxygenation following the evolution of oxygenic photosynthesis, we applied a simple mathematical approach that captures many of the salient features of the major biogeochemical fluxes and reservoirs present in Archean and early Paleoproterozoic surface environments. Calculations illustrate that oxygenation would have overwhelmed redox buffers within ~100 kyr following the emergence of oxygenic photosynthesis, a geologically short amount of time unless rates of primary production were far lower than commonly expected. Fundamentally, this result arises because of the multiscale nature of the carbon and oxygen cycles: rates of gross primary production are orders of magnitude too fast for oxygen to be masked by Earth's geological buffers, and can only be effectively matched by respiration at non-negligible O2 concentrations. These results suggest that oxygenic photosynthesis arose shortly before the rise of oxygen, not hundreds of millions of years before it.

The role of biology in planetary evolution: cyanobacterial primary production in low-oxygen Proterozoic oceans

Understanding the role of biology in planetary evolution remains an outstanding challenge to geobiologists. Progress towards unravelling this puzzle for Earth is hindered by the scarcity of well-preserved rocks from the Archean (4.0 to 2.5 Gyr ago) and Proterozoic (2.5 to 0.5 Gyr ago) Eons. In addition, the microscopic life that dominated Earth's biota for most of its history left a poor fossil record, consisting primarily of lithified microbial mats, rare microbial body fossils and membrane-derived hydrocarbon molecules that are still challenging to interpret. However, it is clear from the sulfur isotope record and other geochemical proxies that the production of oxygen or oxidizing power radically changed Earth's surface and atmosphere during the Proterozoic Eon, pushing it away from the more reducing conditions prevalent during the Archean. In addition to ancient rocks, our reconstruction of Earth's redox evolution is informed by our knowledge of biogeochemical cycles catalysed by extant biota. The emergence of oxygenic photosynthesis in ancient cyanobacteria represents one of the most impressive microbial innovations in Earth's history, and oxygenic photosynthesis is the largest source of O2 in the atmosphere today. Thus the study of microbial metabolisms and evolution provides an important link between extant biota and the clues from the geologic record. Here, we consider the physiology of cyanobacteria (the only microorganisms capable of oxygenic photosynthesis), their co-occurrence with anoxygenic phototrophs in a variety of environments and their persistence in low-oxygen environments, including in water columns as well as mats, throughout much of Earth's history. We examine insights gained from both the rock record and cyanobacteria presently living in early Earth analogue ecosystems and synthesize current knowledge of these ancient microbial mediators in planetary redox evolution. Our analysis supports the hypothesis that anoxygenic photosynthesis, including the activity of metabolically versatile cyanobacteria, played an important role in delaying the oxygenation of Earth's surface ocean during the Proterozoic Eon.

Specific hopanoid classes differentially affect free-living and symbiotic states of Bradyrhizobium diazoefficiens

A better understanding of how bacteria resist stresses encountered during the progression of plant-microbe symbioses will advance our ability to stimulate plant growth. Here, we show that the symbiotic system comprising the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens and the legume Aeschynomene afraspera requires hopanoid production for optimal fitness. While methylated (2Me) hopanoids contribute to growth under plant-cell-like microaerobic and acidic conditions in the free-living state, they are dispensable during symbiosis. In contrast, synthesis of extended (C35) hopanoids is required for growth microaerobically and under various stress conditions (high temperature, low pH, high osmolarity, bile salts, oxidative stress, and antimicrobial peptides) in the free-living state and also during symbiosis. These defects might be due to a less rigid membrane resulting from the absence of free or lipidA-bound C35 hopanoids or the accumulation of the C30 hopanoid diploptene. Our results also show that C35 hopanoids are necessary for symbiosis only with the host Aeschynomene afraspera but not with soybean. This difference is likely related to the presence of cysteine-rich antimicrobial peptides in Aeschynomene nodules that induce drastic modification in bacterial morphology and physiology. The study of hopanoid mutants in plant symbionts thus provides an opportunity to gain insight into host-microbe interactions during later stages of symbiotic progression, as well as the microenvironmental conditions for which hopanoids provide a fitness advantage.

IMPORTANCE

Because bradyrhizobia provide fixed nitrogen to plants, this work has potential agronomical implications. An understanding of how hopanoids facilitate bacterial survival in soils and plant hosts may aid the engineering of more robust agronomic strains, especially relevant in regions that are becoming warmer and saline due to climate change. Moreover, this work has geobiological relevance: hopanes, molecular fossils of hopanoids, are enriched in ancient sedimentary rocks at discrete intervals in Earth history. This is the first study to uncover roles for 2Me- and C35 hopanoids in the context of an ecological niche that captures many of the stressful environmental conditions thought to be important during (2Me)-hopane deposition. Though much remains to be done to determine whether the conditions present within the plant host are shared with niches of relevance to the rock record, our findings represent an important step toward identifying conserved mechanisms whereby hopanoids contribute to fitness.

Specific hopanoid classes differentially affect free-living and symbiotic states of Bradyrhizobium diazoefficiens

A better understanding of how bacteria resist stresses encountered during the progression of plant-microbe symbioses will advance our ability to stimulate plant growth. Here, we show that the symbiotic system comprising the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens and the legume Aeschynomene afraspera requires hopanoid production for optimal fitness. While methylated (2Me) hopanoids contribute to growth under plant-cell-like microaerobic and acidic conditions in the free-living state, they are dispensable during symbiosis. In contrast, synthesis of extended (C35) hopanoids is required for growth microaerobically and under various stress conditions (high temperature, low pH, high osmolarity, bile salts, oxidative stress, and antimicrobial peptides) in the free-living state and also during symbiosis. These defects might be due to a less rigid membrane resulting from the absence of free or lipidA-bound C35 hopanoids or the accumulation of the C30 hopanoid diploptene. Our results also show that C35 hopanoids are necessary for symbiosis only with the host Aeschynomene afraspera but not with soybean. This difference is likely related to the presence of cysteine-rich antimicrobial peptides in Aeschynomene nodules that induce drastic modification in bacterial morphology and physiology. The study of hopanoid mutants in plant symbionts thus provides an opportunity to gain insight into host-microbe interactions during later stages of symbiotic progression, as well as the microenvironmental conditions for which hopanoids provide a fitness advantage.

IMPORTANCE

Because bradyrhizobia provide fixed nitrogen to plants, this work has potential agronomical implications. An understanding of how hopanoids facilitate bacterial survival in soils and plant hosts may aid the engineering of more robust agronomic strains, especially relevant in regions that are becoming warmer and saline due to climate change. Moreover, this work has geobiological relevance: hopanes, molecular fossils of hopanoids, are enriched in ancient sedimentary rocks at discrete intervals in Earth history. This is the first study to uncover roles for 2Me- and C35 hopanoids in the context of an ecological niche that captures many of the stressful environmental conditions thought to be important during (2Me)-hopane deposition. Though much remains to be done to determine whether the conditions present within the plant host are shared with niches of relevance to the rock record, our findings represent an important step toward identifying conserved mechanisms whereby hopanoids contribute to fitness.

Lipid remodeling in Rhodopseudomonas palustris TIE-1 upon loss of hopanoids and hopanoid methylation

The sedimentary record of molecular fossils (biomarkers) can potentially provide important insights into the composition of ancient organisms; however, it only captures a small portion of their original lipid content. To interpret what remains, it is important to consider the potential for functional overlap between different lipids in living cells, and how the presence of one type might impact the abundance of another. Hopanoids are a diverse class of steroid analogs made by bacteria and found in soils, sediments, and sedimentary rocks. Here, we examine the trade-off between hopanoid production and that of other membrane lipids. We compare lipidomes of the metabolically versatile α-proteobacterium Rhodopseudomonas palustris TIE-1 and two hopanoid mutants, detecting native hopanoids simultaneously with other types of polar lipids by electrospray ionization mass spectrometry. In all strains, the phospholipids contain high levels of unsaturated fatty acids (often >80%). The degree to which unsaturated fatty acids are modified to cyclopropyl fatty acids varies by phospholipid class. Deletion of the capacity for hopanoid production is accompanied by substantive changes to the lipidome, including a several-fold rise of cardiolipins. Deletion of the ability to make methylated hopanoids has a more subtle effect; however, under photoautotrophic growth conditions, tetrahymanols are upregulated twofold. Together, these results illustrate that the 'lipid fingerprint' produced by a micro-organism can vary depending on the growth condition or loss of single genes, reminding us that the absence of a biomarker does not necessarily imply the absence of a particular source organism.

Cyanobacterial Inhabitation on Archean Rock Surfaces in the Pilbara Craton, Western Australia

High abundances of 7- and 6-monomethylalkanes as well as C17 n-alkane, indicative of cyanobacteria, have been discovered near the surfaces of Archean carbonate rocks of the Fortescue Group in the Pilbara region, Western Australia. The presence of cyanobacterial biomarkers is mostly limited to the surface layer (<1 cm thickness) of the rocks, indicating that the cyanobacteria are an endolithic species. Biomarkers are found in bitumen I (solvent-extracted rock) and also in bitumen II (solvent-extracted decarbonated rock). The abundance of biomarkers is generally the same between both bitumen fractions in the surface layer, which suggests that the cyanobacteria penetrated into the carbonate minerals. Trace amounts of the biomarkers have also diffused into a deeper part of the rocks, but this influence is only seen in bitumen I. This implies that hydrocarbons moved toward the inside of the rock through pores and fissures in the rock fabric. In contrast, hydrocarbons in bitumen II, which mainly come from within the carbonate minerals, are isolated from the hydrocarbon migration from the outside of the rock and may be ancient indigenous organic matter. To the best of our knowledge, this is the first report of the past or modern inhabitation of cyanobacteria on Archean rocks in the Pilbara region for which hydrocarbon biomarker analyses was used.

Paleobiological Perspectives on Early Microbial Evolution

Microfossils, stromatolites, and chemical biosignatures indicate that Earth became a biological planet more than 3.5 billion years ago, making most of life's history microbial. Proterozoic rocks preserve a rich record of cyanobacteria, including derived forms that differentiate multiple cell types. Stromatolites, in turn, show that microbial communities covered the seafloor from tidal flats to the base of the photic zone. The Archean record is more challenging to interpret, particularly on the question of cyanobacterial antiquity, which remains to be resolved. In the late Neoproterozoic Era, increasing oxygen and radiating eukaryotes altered the biosphere, with planktonic algae gaining ecological prominence in the water column, whereas seaweeds and, eventually, animals spread across shallow seafloors. From a microbial perspective, however, animals, algae, and, later, plants simply provided new opportunities for diversification, and, to this day, microbial metabolisms remain the only essential components of biogeochemical cycles.

Quantitative hopanoid analysis enables robust pattern detection and comparison between laboratories

Hopanoids are steroid-like lipids from the isoprenoid family that are produced primarily by bacteria. Hopanes, molecular fossils of hopanoids, offer the potential to provide insight into environmental transitions on the early Earth, if their sources and biological functions can be constrained. Semiquantitative methods for mass spectrometric analysis of hopanoids from cultures and environmental samples have been developed in the last two decades. However, the structural diversity of hopanoids, and possible variability in their ionization efficiencies on different instruments, have thus far precluded robust quantification and hindered comparison of results between laboratories. These ionization inconsistencies give rise to the need to calibrate individual instruments with purified hopanoids to reliably quantify hopanoids. Here, we present new approaches to obtain both purified and synthetic quantification standards. We optimized 2-methylhopanoid production in Rhodopseudomonas palustris TIE-1 and purified 2Me-diplopterol, 2Me-bacteriohopanetetrol (2Me-BHT), and their unmethylated species (diplopterol and BHT). We found that 2-methylation decreases the signal intensity of diplopterol between 2 and 34% depending on the instrument used to detect it, but decreases the BHT signal less than 5%. In addition, 2Me-diplopterol produces 10× higher ion counts than equivalent quantities of 2Me-BHT. Similar deviations were also observed using a flame ionization detector for signal quantification in GC. In LC-MS, however, 2Me-BHT produces 11× higher ion counts than 2Me-diplopterol but only 1.2× higher ion counts than the sterol standard pregnane acetate. To further improve quantification, we synthesized tetradeuterated (D4) diplopterol, a precursor for a variety of hopanoids. LC-MS analysis on a mixture of (D4)-diplopterol and phospholipids showed that under the influence of co-eluted phospholipids, the D4-diplopterol internal standard quantifies diplopterol more accurately than external diplopterol standards. These new quantitative approaches permit meaningful comparisons between studies, allowing more accurate hopanoid pattern detection in both laboratory and environmental samples.

Hopanoid inventory of Rhodoplanes spp

Hopanoids are pentacyclic triterpenoid lipids and are important for bacterial membrane stability and functioning. These pentacyclic triterpenoids of hopane series are biomarkers for eubacteria and can be used as chemotaxonomic markers. Anoxygenic phototrophic bacteria are good producers of hopanoids, and their inventory to date is restricted to a few members. Rhodoplanes spp. are phototrophic prokaryotes which grow and thrive in subsurface and sediment environments. A study on the diversity of hopanoids of several species of Rhodoplanes revealed a rich diversity of hopanoids with carbon length of C30/C31 and C35. Hop-22(29)-ene (II), diplopterol (V), tetrahymanol (VII), 2-methyldiplopterol (VI), 2-methyltetrahymanol (VIII), bacteriohopanetetrol (IX), bacteriohopaneaminotriol (X) and bacteriohopanepolyols [BHP-492 (XIII), BHP-550 (XIV), BHP-508 (XII)] are the major hopanoids of the genus Rhodoplanes. Tetrahymanol (VII) content is high (38-60 %) among all the members, except for Rhodoplanes elegans. Hopanoid fingerprints allowed differentiation of species of the genus Rhodoplanes. Statistical analyses also indicate hopanoids as good chemotaxonomic markers to distinguish species of the genus Rhodoplanes.

Phylogenetic analysis of HpnP reveals the origin of 2-methylhopanoid production in Alphaproteobacteria

Hopanoids are bacterial steroid-like lipids that can be preserved in the rock record on billion-year timescales. 2-Methylhopanoids are of particular interest to geobiologists because methylation is one of the few chemical modifications that remain after diagenesis and catagenesis. 2-Methylhopanes, the molecular fossils of 2-methylhopanoids, are episodically enriched in the rock record, but we do not have a robust interpretation for their abundance patterns. Here, we exploit the evolutionary record found in molecular sequences from extant organisms to reconstruct the biosynthetic history of 2-methylhopanoids using the C-2 hopanoid methylase, HpnP. Based on HpnP phylogenetic analysis, we find that 2-methylhopanoids originated in a subset of the Alphaproteobacteria. This conclusion is statistically robust and reproducible in multiple trials varying the outgroup, trimming stringency, and ingroup dataset used to infer the evolution of this protein family. The capacity for 2-methylhopanoid production was likely horizontally transferred from the Alphaproteobacteria into the Cyanobacteria after the Cyanobacteria's major divergences. Together, these results suggest that the ancestral function of 2-methylhopanoids was not related to oxygenic photosynthesis but instead to a trait already present in the Alphaproteobacteria. Moreover, given that early 2-methylhopane deposits could have been made solely by Alphaproteobacteria before the acquisition of hpnP by Cyanobacteria, and that the Alphaproteobacteria are thought to be ancestrally aerobic, we infer that 2-methylhopanoids likely arose after the oxygenation of the atmosphere. This finding is consistent with the geologic record-the oldest syngenetic 2-methylhopanes occur after the rise of oxygen, in middle Proterozoic strata of the Barney Creek Formation.

Hydrocarbons preserved in a ~2.7 Ga outcrop sample from the Fortescue Group, Pilbara Craton, Western Australia

The hydrocarbons preserved in an Archean rock were extracted, and their composition and distribution in consecutive slices from the outside to the inside of the rock were examined. The 2.7 Ga rock was collected from the Fortescue Group in the Pilbara region, Western Australia. The bitumen I (solvent-extracted rock) and bitumen II (solvent-extracted hydrochloric acid-treated rock) fractions have different hydrocarbon compositions. Bitumen I contains only trace amounts of aliphatic hydrocarbons and virtually no aromatic hydrocarbons. In contrast, bitumen II contains abundant aliphatic and aromatic hydrocarbons. The difference seems to reflect the weathering history and preservational environment of the investigated rock. Aliphatic hydrocarbons in bitumen I are considered to be mainly from later hydrocarbon inputs, after initial deposition and burial, and are therefore not indigenous. The lack of aromatic hydrocarbons in bitumen I suggests a severe weathering environment since uplift and exposure of the rock at the Earth's surface in the Cenozoic. On the other hand, the high abundance of aromatic hydrocarbons in bitumen II suggests that bitumen II hydrocarbons have been physically isolated from removal by their encapsulation within carbonate minerals. The richness of aromatic hydrocarbons and the relative scarcity of aliphatic hydrocarbons may reflect the original compositions of organic materials biosynthesised in ancient organisms in the Archean era, or the high thermal maturity of the rock. Cyanobacterial biomarkers were observed in the surficial slices of the rock, which may indicate that endolithic cyanobacteria inhabited the surface outcrop. The distribution of aliphatic and aromatic hydrocarbons implies a high thermal maturity, which is consistent with the lack of any specific biomarkers, such as hopanes and steranes, and the prehnite-pumpellyite facies metamorphic grade.

Methylation at the C-2 position of hopanoids increases rigidity in native bacterial membranes

Sedimentary rocks host a vast reservoir of organic carbon, such as 2-methylhopane biomarkers, whose evolutionary significance we poorly understand. Our ability to interpret this molecular fossil record is constrained by ignorance of the function of their molecular antecedents. To gain insight into the meaning of 2-methylhopanes, we quantified the dominant (des)methylated hopanoid species in the membranes of the model hopanoid-producing bacterium Rhodopseudomonas palustris TIE-1. Fluorescence polarization studies of small unilamellar vesicles revealed that hopanoid 2-methylation specifically renders native bacterial membranes more rigid at concentrations that are relevant in vivo. That hopanoids differentially modify native membrane rigidity as a function of their methylation state indicates that methylation itself promotes fitness under stress. Moreover, knowing the in vivo (2Me)-hopanoid concentration range in different cell membranes, and appreciating that (2Me)-hopanoids' biophysical effects are tuned by the lipid environment, permits the design of more relevant in vitro experiments to study their physiological functions.

DOI:http://dx.doi.org/10.7554/eLife.05663.001

The cell membrane that separates the inside of a cell from its outside environment is not a fixed structure. A cell can change the amount and type of different molecules in its membrane, which can alter the rigidity and permeability of the membrane and allow the cell to adapt to changing conditions.

The cell membranes of many bacteria contain molecules called hopanoids. Hopanes are the fossilized forms of these molecules and many hopanes are found extensively in sedimentary rocks. For example, 2-methylated hopanes—the fossilized forms of hopanoids that have a methyl group added to a particular carbon atom—have been found in ancient rocks that formed up to 1.6 billion years ago.

Many researchers have suggested that 2-methylated hopanes (and other molecular fossils) in sedimentary rocks could act as ‘biomarkers’ and be used to deduce what primitive life and ancient living conditions were like. Millions of years ago, several periods occurred where the Earth's oceans lost almost all of their oxygen; this likely placed all life on Earth under great stress. A greater proportion of the hopanes found in rocks formed during those periods are methylated than those seen in rocks from other time periods. However, it was difficult to interpret this observation about the fossil record, as the role of 2-methylated hopanoids in living bacterial cells was unknown.

Wu et al. have now investigated the role of 2-methylated hopanoids by performing experiments on bacterial membranes and found that 2-methylated hopanoids help the other molecules that make up the membrane to pack more tightly together. This makes the membrane more rigid, and the extent of this stiffening depends on the length of the 2-methylated hopanoid and on the other molecules that are present in the membrane. A more rigid membrane would protect the bacteria more in times of stress; therefore, rock layers containing an increased amount of 2-methylhopane are likely to indicate times when the bacteria living at that time were under a great deal of stress.

DOI:http://dx.doi.org/10.7554/eLife.05663.002

Draft genome sequence of Rhodomicrobium udaipurense JA643T with special reference to hopanoid biosynthesis

Hopanoids are present in vast amounts as integral components of bacteria and plants with their primary function to strengthen rigidity of the plasma membrane. To establish their roles more precisely, we conducted sequencing of the whole genome of Rhodomicrobium udaipurense JA643(T) isolated from a fresh water stream of Udaipur in Himachal Pradesh, India, by using the Illumina HiSeq pair end chemistry of 2 × 100 bp platform. Determined genome showed a high degree of similarity to the genome of R. vannielii ATCC17100(T) and the 13.7 million reads generated a sequence of 3,649,277 bp possessing 3,611 putative genes. The genomic data were subsequently investigated with respect to genes involved in various features. The machinery required for the degradation of aromatic compounds and resistance to solvents as well as all that required for photosynthesis are present in this organism. Also, through extensive functional annotation, 18 genes involved in the biosynthesis of hopanoids are predicted, namely those responsible for the synthesis of diploptene, diplopterol, adenosylhopane, ribosylhopane, aminobacteriohopanetriol, glycosyl group containing hopanoids and unsaturated hopanoids. The hopanoid biosynthetic pathway was then inferred based on the genes identified and through experimental validation of individual hopanoid molecules. The genome data of R. udaipurense JA643(T) will be useful in understanding the functional features of hopanoids in this bacterium.