2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis

On Protein Loops, Prior Molecular States and Common Ancestors of Life

The principle of continuity demands the existence of prior molecular states and common ancestors responsible for extant macromolecular structure. Here, we focus on the emergence and evolution of loop prototypes - the elemental architects of protein domain structure. Phylogenomic reconstruction spanning superkingdoms and viruses generated an evolutionary chronology of prototypes with six distinct evolutionary phases defining a most parsimonious evolutionary progression of cellular life. Each phase was marked by strategic prototype accumulation shaping the structures and functions of common ancestors. The last universal common ancestor (LUCA) of cells and viruses and the last universal cellular ancestor (LUCellA) defined stem lines that were structurally and functionally complex. The evolutionary saga highlighted transformative forces. LUCA lacked biosynthetic ribosomal machinery, while the pivotal LUCellA lacked essential DNA biosynthesis and modern transcription. Early proteins therefore relied on RNA for genetic information storage but appeared initially decoupled from it, hinting at transformative shifts of genetic processing. Urancestral loop types suggest advanced folding designs were present at an early evolutionary stage. An exploration of loop geometric properties revealed gradual replacement of prototypes with α-helix and β-strand bracing structures over time, paving the way for the dominance of other loop types. AlphFold2-generated atomic models of prototype accretion described patterns of fold emergence. Our findings favor a ‛processual' model of evolving stem lines aligned with Woese's vision of a communal world. This model prompts discussing the 'problem of ancestors' and the challenges that lie ahead for research in taxonomy, evolution and complexity.

Chapter 8: Searching for Life Beyond Earth

The search for life beyond Earth necessitates a rigorous and comprehensive examination of biosignatures, the types of observable imprints that life produces. These imprints and our ability to detect them with advanced instrumentation hold the key to our understanding of the presence and abundance of life in the universe. Biosignatures are the chemical or physical features associated with past or present life and may include the distribution of elements and molecules, alone or in combination, as well as changes in structural components or physical processes that would be distinct from an abiotic background. The scientific and technical strategies used to search for life on other planets include those that can be conducted in situ to planetary bodies and those that could be observed remotely. This chapter discusses numerous strategies that can be employed to look for biosignatures directly on other planetary bodies using robotic exploration including those that have been deployed to other planetary bodies, are currently being developed for flight, or will become a critical technology on future missions. Search strategies for remote observations using current and planned ground-based and space-based telescopes are also described. Evidence from spectral absorption, emission, or transmission features can be used to search for remote biosignatures and technosignatures. Improving our understanding of biosignatures, their production, transformation, and preservation on Earth can enhance our search efforts to detect life on other planets.

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.

Weathering impacts on petroleum biomarker, aromatic, and polar compounds in the spilled oil at the northeast coast of Brazil over time

After the wide oil spill reached the northeast of Brazil, the resurgence of oil was recorded and to evaluate this oil in detail, two samples collected in the state of Pernambuco in 2019 and 2021 were submitted to multiple analytical techniques. For both, we have found similar saturated biomarkers and triaromatic steroid ratios, implying that they are from the same spilled source. The n-alkanes, isoprenoids, and cycloalkanes were almost completely degraded due to evaporation, photooxidation, and/or biodegradation processes. The preferential loss of less alkylated PAHs than the more alkylated ones suggests that biodegradation was the most active process. This hypothesis is reinforced by the formation of mono and dicarboxylic acids assessed by GC × GC-TOFMS and ESI(-) FT-ICR MS high-resolution techniques. Furthermore, based on the ESI(-) FT-ICR MS results, three new ratios were proposed to evaluate the progress of the biodegradation process over time: O_x>2/O, SO_x/SO, and SO_x/N.

Classification and Multifaceted Potential of Secondary Metabolites Produced by Bacillus subtilis Group: A Comprehensive Review

Despite their remarkable biosynthetic potential, Bacillus subtilis have been widely overlooked. However, their capability to withstand harsh conditions (extreme temperature, Ultraviolet (UV) and γ-radiation, and dehydration) and the promiscuous metabolites they synthesize have created increased commercial interest in them as a therapeutic agent, a food preservative, and a plant-pathogen control agent. Nevertheless, the commercial-scale availability of these metabolites is constrained due to challenges in their accessibility via synthesis and low fermentation yields. In the context of this rising in interest, we comprehensively visualized the antimicrobial peptides produced by B. subtilis and highlighted their prospective applications in various industries. Moreover, we proposed and classified these metabolites produced by the B. subtilis group based on their biosynthetic pathways and chemical structures. The biosynthetic pathway, bioactivity, and chemical structure are discussed in detail for each class. We believe that this review will spark a renewed interest in the often disregarded B. subtilis and its remarkable biosynthetic capabilities.

Versatile Applications of Cyanobacteria in Biotechnology

Cyanobacteria are blue-green Gram-negative and photosynthetic bacteria which are seen as one of the most morphologically numerous groups of prokaryotes. Because of their ability to fix gaseous nitrogen and carbon dioxide to organic materials, they are known to play important roles in the universal nutrient cycle. Cyanobacteria has emerged as one of the promising resources to combat the issues of global warming, disease outbreaks, nutrition insecurity, energy crises as well as persistent daily human population increases. Cyanobacteria possess significant levels of macro and micronutrient substances which facilitate the versatile popularity to be utilized as human food and protein supplements in many countries such as Asia. Cyanobacteria has been employed as a complementary dietary constituent of feed for poultry and as vitamin and protein supplement in aquatic lives. They are effectively used to deal with numerous tasks in various fields of biotechnology, such as agricultural (including aquaculture), industrial (food and dairy products), environmental (pollution control), biofuel (bioenergy) and pharmaceutical biotechnology (such as antimicrobial, anti-inflammatory, immunosuppressant, anticoagulant and antitumor); recently, the growing interest of applying them as biocatalysts has been observed as well. Cyanobacteria are known to generate a numerous variety of bioactive compounds. However, the versatile potential applications of cyanobacteria in biotechnology could be their significant growth rate and survival in severe environmental conditions due to their distinct and unique metabolic pathways as well as active defensive mechanisms. In this review, we elaborated on the versatile cyanobacteria applications in different areas of biotechnology. We also emphasized the factors that could impede the implementation to cyanobacteria applications in biotechnology and the execution of strategies to enhance their effective applications.

A fungal tolerance trait and selective inhibitors proffer HMG-CoA reductase as a herbicide mode-of-action

Decades of intense herbicide use has led to resistance in weeds. Without innovative weed management practices and new herbicidal modes of action, the unabated rise of herbicide resistance will undoubtedly place further stress upon food security. HMGR (3-hydroxy-3-methylglutaryl-coenzyme A reductase) is the rate limiting enzyme of the eukaryotic mevalonate pathway successfully targeted by statins to treat hypercholesterolemia in humans. As HMGR inhibitors have been shown to be herbicidal, HMGR could represent a mode of action target for the development of herbicides. Here, we present the crystal structure of a HMGR from Arabidopsis thaliana (AtHMG1) which exhibits a wider active site than previously determined structures from different species. This plant conserved feature enables the rational design of specific HMGR inhibitors and we develop a tolerance trait through sequence analysis of fungal gene clusters. These results suggest HMGR to be a viable herbicide target modifiable to provide a tolerance trait.

Managing herbicide resistance problem needs the identification of new herbicidal modes of action. Here, the authors solve the crystal structures of Arabidopsis HMGR and show HMGR as a potential new herbicide target by identifying plant-specific HMGR inhibitors and engineering tolerant trait in Arabidopsis.

Lipid Biomarkers From Microbial Mats on the McMurdo Ice Shelf, Antarctica: Signatures for Life in the Cryosphere

Persistent cold temperatures, a paucity of nutrients, freeze-thaw cycles, and the strongly seasonal light regime make Antarctica one of Earth's least hospitable surface environments for complex life. Cyanobacteria, however, are well-adapted to such conditions and are often the dominant primary producers in Antarctic inland water environments. In particular, the network of meltwater ponds on the 'dirty ice' of the McMurdo Ice Shelf is an ecosystem with extensive cyanobacteria-dominated microbial mat accumulations. This study investigated intact polar lipids (IPLs), heterocyte glycolipids (HGs), and bacteriohopanepolyols (BHPs) in combination with 16S and 18S rRNA gene diversity in microbial mats of twelve ponds in this unique polar ecosystem. To constrain the effects of nutrient availability, temperature and freeze-thaw cycles on the lipid membrane composition, lipids were compared to stromatolite-forming cyanobacterial mats from ice-covered lakes in the McMurdo Dry Valleys as well as from (sub)tropical regions and hot springs. The 16S rRNA gene compositions of the McMurdo Ice Shelf mats confirm the dominance of Cyanobacteria and Proteobacteria while the 18S rRNA gene composition indicates the presence of Ochrophyta, Chlorophyta, Ciliophora, and other microfauna. IPL analyses revealed a predominantly bacterial community in the meltwater ponds, with archaeal lipids being barely detectable. IPLs are dominated by glycolipids and phospholipids, followed by aminolipids. The high abundance of sugar-bound lipids accords with a predominance of cyanobacterial primary producers. The phosphate-limited samples from the (sub)tropical, hot spring, and Lake Vanda sites revealed a higher abundance of aminolipids compared to those of the nitrogen-limited meltwater ponds, affirming the direct affects that N and P availability have on IPL compositions. The high abundance of polyunsaturated IPLs in the Antarctic microbial mats suggests that these lipids provide an important mechanism to maintain membrane fluidity in cold environments. High abundances of HG keto-ols and HG keto-diols, produced by heterocytous cyanobacteria, further support these findings and reveal a unique distribution compared to those from warmer climates.

Acritarch-like Microorganisms from the 1.9 Ga Gunflint Chert, Canada

Fossil evidence of eukaryotic life older than 1.8 Ga has long been debated because known fossils of that age usually lack cellular micro- and ultra-structures that bear strong affinities to eukaryotes. These include fossils of the ∼1.9 Ga Gunflint Chert microbiota that, despite being exceptionally well preserved, have suffered from cellular degradation, which poses challenges to studying their delicate cellular structures. In this study, we use an extended-focal-depth imaging technique, in combination with scanning electron microscopy, to document multiple types of large (10-35 μm diameter), cyst-like bodies based on distinctive details such as (1) radially arranged internal strands similar to those in some acritarchs and dinoflagellates; (2) regularly spaced long tubular processes, stubby pustules, and/or robust podia on the cell surface; (3) reticulate cell-wall sculpturing such as scale-like tubercles, pits, and ridges; and (4) internal bodies that may represent membrane-bound organelles. These micro- and ultra-structures provide strong morphological evidence for the presence of protists in the late Paleoproterozoic.

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.

Molecular Indicators of Sources and Biodegradation of Organic Matter in Sediments of Fluid Discharge Zones of Lake Baikal

This paper performs a detailed study of a wide set of organic-geochemical proxies in 15 sediment cores collected from the main basins of Lake Baikal (the northern, the central and the southern) where processes of focused fluid discharge were detected. A variety of studied zones includes sites with gas and hydrothermal seepage, mud volcanoes with or without gas-oil fluid discharge, gas hydrates and authigenic carbonates. The composition of the dispersed organic matter and individual hydrocarbon molecular markers (n-alkanes, dimethyl alkanes, isoprenoids, steranes, terpanes and polycyclic aromatic hydrocarbons) testify to the input from predominantly allochthonous terrestrial and autochthonous microbial and algal sources. The studied sources, maturity and biodegradation parameters of organic matter vary significantly for areas with different fluid discharge. The composition of specific biomarkers including isoprenoids and immature hopanoids reflects the lateral and vertical changes of microbial activity in sediments associated with various environmental conditions. The identified types of terpanes distribution (mature, mixed and immature) correlate well with types of fluid discharge and attest to the development of various methanogenic and methanotrophic microbial communities in sediments. Moreover, the revealed specificity of microbial molecular markers distribution allowed us to suggest the fluid discharge processes in zones where they were not previously detected.

Messinian bottom-grown selenitic gypsum: An archive of microbial life

Primary gypsum deposits, which accumulated in the Mediterranean Basin during the so-called Messinian salinity crisis (5.97-5.33 Ma), represent an excellent archive of microbial life. We investigated the molecular fossil inventory and the corresponding compound-specific δ¹³ C values of bottom-grown gypsum formed during the first stage of the crisis in four marginal basins across the Mediterranean (Nijar, Spain; Vena del Gesso, Italy; Heraklion, Crete; and Psematismenos, Cyprus). All studied gypsum samples contain intricate networks of filamentous microfossils, whose phylogenetic affiliation has been debated for a long time. Petrographic analysis, molecular fossil inventories (hydrocarbons, alcohols, and carboxylic acids), and carbon stable isotope patterns suggest that the mazes of filamentous fossils represent benthic microbial assemblages dominated by chemotrophic sulfide-oxidizing bacteria; in some of the samples, the body fossils are accompanied by lipids produced by sulfate-reducing bacteria. Abundant isoprenoid alcohols including diphytanyl glycerol diethers (DGDs) and glycerol dibiphytanyl glycerol tetraethers (GDGTs), typified by highly variable carbon stable isotope composition with δ¹³ C values spanning from -40 to -14‰, reveal the presence of planktic and benthic archaeal communities dwelling in Messinian paleoenvironments. The compound inventory of archaeal lipids indicates the existence of a stratified water column, with a normal marine to diluted upper water column and more saline deeper waters. This study documents the lipid biomarker inventory of microbial life preserved in ancient gypsum deposits, helping to reconstruct the widely debated conditions under which Messinian gypsum formed.

Carbon Materials Advancing Microorganisms in Driving Soil Organic Carbon Regulation

Carbon emission from soil is not only one of the major sources of greenhouse gases but also threatens biological diversity, agricultural productivity, and food security. Regulation and control of the soil carbon pool are political practices in many countries around the globe. Carbon pool management in engineering sense is much bigger and beyond laws and monitoring, as it has to contain proactive elements to restore active carbon. Biogeochemistry teaches us that soil microorganisms are crucial to manage the carbon content effectively. Adding carbon materials to soil is thereby not directly sequestration, as interaction of appropriately designed materials with the soil microbiome can result in both: metabolization and thereby nonsustainable use of the added carbon, or-more favorably-a biological amplification of human efforts and sequestration of extra CO₂ by microbial growth. We review here potential approaches to govern soil carbon, with a special focus set on the emerging practice of adding manufactured carbon materials to control soil carbon and its biological dynamics. Notably, research on so-called "biochar" is already relatively mature, while the role of artificial humic substance (A-HS) in microbial carbon sequestration is still in the developing stage. However, it is shown that the preparation and application of A-HS are large biological levers, as they directly interact with the environment and community building of the biological soil system. We believe that A-HS can play a central role in stabilizing carbon pools in soil.

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.

Origin and Geochemical Implications of Hopanoids in Saline Lacustrine Crude Oils from Huanghekou East Sag and Laizhouwan Northeastern Sag, Bohai Bay Basin

A suite of low-mature crude oils (five high-sulfur oils and six low-sulfur oils) from the Huanghekou and the Laizhouwan Sags, Bohai Bay Basin, are analyzed to investigate the fate of the hopanoids. Abundant hopanes, such as secohopanes, 25-norhopanes, benzohopanes, aromatized secohopanes, and sulfide hopanes, are identified, and their carbon isotope compositions are determined. Varying ¹³C isotope values of C₃₁ hopane (-38.7-34.0‰) and C_29-30 hopanes (-38.5-31.5‰) suggest different bacterial sources of these compounds. The presence of 25-norhopanes with enriched heavy carbon isotopes in severely biodegraded oils suggests that they are microbially mediated products. The detection of the isotopically depleted C₂₉ and C₃₀ D-ring-8,14-secohopanes (-45.6-41.2‰) indicates that secohopanes are from methane-oxidizing bacteria (methanotrophs). The presence of isorenieratane, lower aryl isoprenoid ratios, and a good correlation between the sulfur content and the gammacerane index indicate the presence of green sulfur bacteria (Chlorobiaceae) under photic zone euxinic conditions. Water column stratification results in good preservation of the organic matter, and it is in favor of diversity of aquatic microorganisms. The ratios of C₃₅/C₃₄ sulfide hopane, C₃₅ sulfide hopane-2/C₃₅ sulfide hopane-1, and C₃₅/C₃₄ benzohopane are influenced by the reducing environments in this region. In addition, the D-ring monoaromatized 8,14-secohopanoid/(D-ring monoaromatized 8,14-secohopanoid + benzohopanes) and C₃₁-C₃₅ secomoretanes/secohopanes are affected by the maturity. We hypothesize that the reducing environments and thermal effects are important markers for the hopanoid transformation, including the incorporation of inorganic sulfur in substituting functional groups, cyclizing, aromatizing, and opening ring C of the hopanoids.

Dynamics of cell death across growth stages and the diel cycle in the dinoflagellate Karenia brevis

Recent evidence suggests that programmed cell death (PCD) can play a role in stress-induced decline and termination of harmful algal blooms. However, components of the PCD cascade, i.e. reactive oxygen species (ROS) and caspase-like activity, have also been observed in the absence of exogenous stress, where their activities and functions remain unclear. Here, we characterized the variability of prevalence of cell death, ROS, and caspase-like activity at different growth phases and diel cycles in cultures of dinoflagellate Karenia brevis. Results show that ROS percentages increased with culture age and fluctuated in a phasing diel pattern, while caspase-like activity was observed throughout growth. In actively growing K. brevis cells, PCD components may be involved in key metabolic processes, while in stationary phase they may relate to stress acclimation. The circadian diel pattern of ROS may be explained by the balance between the metabolic generation of ROS and circadian rhythmicity of antioxidant enzymes. Overall, this work highlights not only the involvement of PCD components in the growth of marine phytoplankton, but the importance of understanding mechanisms controlling their accumulation, which would help to better interpret their presence in the field.

Bioactive Metabolites Produced by Cyanobacteria for Growth Adaptation and Their Pharmacological Properties

Cyanobacteria are the most abundant oxygenic photosynthetic organisms inhabiting various ecosystems on earth. As with all other photosynthetic organisms, cyanobacteria release oxygen as a byproduct during photosynthesis. In fact, some cyanobacterial species are involved in the global nitrogen cycles by fixing atmospheric nitrogen. Environmental factors influence the dynamic, physiological characteristics, and metabolic profiles of cyanobacteria, which results in their great adaptation ability to survive in diverse ecosystems. The evolution of these primitive bacteria resulted from the unique settings of photosynthetic machineries and the production of bioactive compounds. Specifically, bioactive compounds play roles as regulators to provide protection against extrinsic factors and act as intracellular signaling molecules to promote colonization. In addition to the roles of bioactive metabolites as indole alkaloids, terpenoids, mycosporine-like amino acids, non-ribosomal peptides, polyketides, ribosomal peptides, phenolic acid, flavonoids, vitamins, and antimetabolites for cyanobacterial survival in numerous habitats, which is the focus of this review, the bioactivities of these compounds for the treatment of various diseases are also discussed.

The characterisation and provenance of crude oils stranded on the South Australian coastline. Part II: Potential parent petroleum systems

In 2014-2016 more than 600 specimens of semi-solid crude oil were recovered from 30 ocean beaches along the coastline of South Australia, as part of the recently completed Great Australian Bight Research Program. All are believed to be products of submarine oil seepage. Their source-specific biomarker signatures provide the basis for their assignment to sixteen oil families, some previously unrecognised. Two of these families (asphaltite and asphaltic tar) likely originated from Cretaceous marine source rocks in the offshore Bight Basin. The others comprise waxy oils of lacustrine, fluvio-deltaic and marine source affinity. Their biomarker characteristics do not match those of any Australian crude oil. However, they are strikingly similar to those of oils found in Cenozoic and Mesozoic basins throughout the Indonesian Archipelago and elsewhere in Southeast Asia.

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.

Anaerobic 3-methylhopanoid production by an acidophilic photosynthetic purple bacterium

Bacterial lipids are well-preserved in ancient rocks and certain ones have been used as indicators of specific bacterial metabolisms or environmental conditions existing at the time of rock deposition. Here we show that an anaerobic bacterium produces 3-methylhopanoids, pentacyclic lipids previously detected only in aerobic bacteria and widely used as biomarkers for methane-oxidizing bacteria. Both Rhodopila globiformis, a phototrophic purple nonsulfur bacterium isolated from an acidic warm spring in Yellowstone, and a newly isolated Rhodopila species from a geochemically similar spring in Lassen Volcanic National Park (USA), synthesized 3-methylhopanoids and a suite of related hopanoids and contained the genes encoding the necessary biosynthetic enzymes. Our results show that 3-methylhopanoids can be produced under anoxic conditions and challenges the use of 3-methylhopanoids as biomarkers of oxic conditions in ancient rocks and as prima facie evidence that methanotrophic bacteria were active when the rocks were deposited.

A Proposed Geobiology-Driven Nomenclature for Astrobiological In Situ Observations and Sample Analyses

As the exploration of Mars and other worlds for signs of life has increased, the need for a common nomenclature and consensus has become significantly important for proper identification of nonterrestrial/non-Earth biology, biogenic structures, and chemical processes generated from biological processes. The fact that Earth is our single data point for all life, diversity, and evolution means that there is an inherent bias toward life as we know it through our own planet's history. The search for life "as we don't know it" then brings this bias forward to decision-making regarding mission instruments and payloads. Understandably, this leads to several top-level scientific, theoretical, and philosophical questions regarding the definition of life and what it means for future life detection missions. How can we decide on how and where to detect known and unknown signs of life with a single biased data point? What features could act as universal biosignatures that support Darwinian evolution in the geological context of nonterrestrial time lines? The purpose of this article is to generate an improved nomenclature for terrestrial features that have mineral/microbial interactions within structures and to confirm which features can only exist from life (biotic), features that are modified by biological processes (biogenic), features that life does not affect (abiotic), and properties that can exist or not regardless of the presence of biology (abiogenic). These four categories are critical in understanding and deciphering future returned samples from Mars, signs of potential extinct/ancient and extant life on Mars, and in situ analyses from ocean worlds to distinguish and separate what physical structures and chemical patterns are due to life and which are not. Moreover, we discuss hypothetical detection and preservation environments for extant and extinct life, respectively. These proposed environments will take into account independent active and ancient in situ detection prospects by using previous planetary exploration studies and discuss the geobiological implications within an astrobiological context.

Cell Death and Metabolic Stress in Gymnodinium catenatum Induced by Allelopathy

Allelopathy between phytoplankton species can promote cellular stress and programmed cell death (PCD). The raphidophyte Chattonella marina var. marina, and the dinoflagellates Margalefidinium polykrikoides and Gymnodinium impudicum have allelopathic effects on Gymnodinium catenatum; however, the physiological mechanisms are unknown. We evaluated whether the allelopathic effect promotes cellular stress and activates PCD in G. catenatum. Cultures of G. catenatum were exposed to cell-free media of C. marina var. marina, M. polykrikoides and G. impudicum. The mortality, superoxide radical (O₂^●-) production, thiobarbituric acid reactive substances (TBARS) levels, superoxide dismutase (SOD) activity, protein content, and caspase-3 activity were quantified. Mortality (between 57 and 79%) was registered in G. catenatum after exposure to cell-free media of the three species. The maximal O₂^●- production occurred with C. marina var. marina cell-free media. The highest TBARS levels and SOD activity in G. catenatum were recorded with cell-free media from G. impudicum. The highest protein content was recorded with cell-free media from M. polykrikoides. All cell-free media caused an increase in the activity of caspase-3. These results indicate that the allelopathic effect in G. catenatum promotes cell stress and caspase-3 activation, as a signal for the induction of programmed cell death.

Principles of Membrane Adaptation Revealed through Environmentally Induced Bacterial Lipidome Remodeling

Cells, from microbes to mammals, adapt their membrane lipid composition in response to environmental changes to maintain optimal properties. Global patterns of lipidome remodeling are poorly understood, particularly in organisms with simple lipid compositions that can provide insight into fundamental principles of membrane adaptation. Using shotgun lipidomics, we examine the simple yet, as we show here, adaptive lipidome of the plant-associated Gram-negative bacterium Methylobacterium extorquens. We observe that minimally 11 lipids account for 90% of total variability, thus constraining the upper limit of variable lipids required for an adaptive living membrane. Through lipid features analysis, we reveal that acyl chain remodeling is not evenly distributed across lipid classes, resulting in headgroup-specific effects of acyl chain variability on membrane properties. Results herein implicate headgroup-specific acyl chain remodeling as a mechanism for fine-tuning the membrane's physical state and provide a resource for using M. extorquens to explore the design principles of living membranes.

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.

Biomarker stratigraphy in the Athel Trough of the South Oman Salt Basin at the Ediacaran-Cambrian Boundary

The South Oman Salt Basin (SOSB) has been studied extensively for knowledge concerning the habitat of the enigmatic Ediacaran-Cambrian oils that are produced from that region. Geological, geochemical, geophysical, and geochronological investigations have all contributed to improved understanding of the range of late Neoproterozoic depositional environments recorded there. Of particular interest has been the deep Athel depocenter within the SOSB that features a silica-rich interval known as the Al Shomou Member or Athel Silicilyte and the co-eval A4 carbonate-evaporite sequence that straddles the Ediacaran-Cambrian boundary. The deep basin has been suggested to be anoxic and euxinic based on studies of sulfur isotopes, trace metal distributions and other proxies. Organic geochemistry has provided some clues concerning aspects of the depositional environments and microbial communities prevailing during this interval. However, ambiguities remain including a paucity of convincing molecular evidence for euxinia in the photic zone of the basin. Here, we present a comprehensive study of biomarker hydrocarbons, including steroids, triterpenoids, and carotenoids. Among the compounds detected is a distinctive array of aromatic carotenoids. Relatively low abundances of monoaromatic carotenoids, such as chlorobactane, okenane, and β-isorenieratane, suggest the possibility of transient photic zone euxinia with a shallow chemocline or, perhaps, exogenous inputs from microbial mats. However, it is the dominance of renieratane and renierapurpurane over isorenieratane in diaromatic carotenoids and their association with abundant C₃₈ and C₃₉ carotenoids that identifies cyanobacteria as major contributors to the inventory of carotenoids. Our results, based on multiple lines of molecular evidence and statistical analysis, also suggest that the Athel Silicilyte was biogeochemically distinct from the other units of the Ara Group. Overall, our study has important implications for understanding other late Neoproterozoic depositional environments.

The Chemistry, Biochemistry and Pharmacology of Marine Natural Products from Leptolyngbya, a Chemically Endowed Genus of Cyanobacteria

Leptolyngbya, a well-known genus of cyanobacteria, is found in various ecological habitats including marine, fresh water, swamps, and rice fields. Species of this genus are associated with many ecological phenomena such as nitrogen fixation, primary productivity through photosynthesis and algal blooms. As a result, there have been a number of investigations of the ecology, natural product chemistry, and biological characteristics of members of this genus. In general, the secondary metabolites of cyanobacteria are considered to be rich sources for drug discovery and development. In this review, the secondary metabolites reported in marine Leptolyngbya with their associated biological activities or interesting biosynthetic pathways are reviewed, and new insights and perspectives on their metabolic capacities are gained.

Carbon Oxidation State in Microbial Polar Lipids Suggests Adaptation to Hot Spring Temperature and Redox Gradients

The influence of oxidation-reduction (redox) potential on the expression of biomolecules is a topic of ongoing exploration in geobiology. In this study, we investigate the novel possibility that structures and compositions of lipids produced by microbial communities are sensitive to environmental redox conditions. We extracted lipids from microbial biomass collected along the thermal and redox gradients of four alkaline hot springs in Yellowstone National Park (YNP) and investigated patterns in the average oxidation state of carbon (Z_C), a metric calculated from the chemical formulae of lipid structures. Carbon in intact polar lipids (IPLs) and their alkyl chains becomes more oxidized (higher Z_C) with increasing distance from each of the four hot spring sources. This coincides with decreased water temperature and increased concentrations of oxidized inorganic solutes, such as dissolved oxygen, sulfate, and nitrate. Carbon in IPLs is most reduced (lowest Z_C) in the hot, reduced conditions upstream, with abundance-weighted Z_C values between −1.68 and −1.56. These values increase gradually downstream to around −1.36 to −1.33 in microbial communities living between 29.0 and 38.1°C. This near-linear increase in Z_C can be attributed to a shift from ether-linked to ester-linked alkyl chains, a decrease in average aliphatic carbons per chain (nC), an increase in average degree of unsaturation per chain (nUnsat), and increased cyclization in tetraether lipids. The Z_C of lipid headgroups and backbones did not change significantly downstream. Expression of lipids with relatively reduced carbon under reduced conditions and oxidized lipids under oxidized conditions may indicate microbial adaptation across environmental gradients in temperature and electron donor/acceptor supply.

Recent magmatism drives hydrocarbon generation in north-east Java, Indonesia

Conventional studies of petroleum basins associate oil generation with the gradual burial of organic-rich sediments. These classical models rely on the interplay between pressure, temperature, and the time required for organic matter transformation to oil and gas. These processes usually occur over geological timescales, but may be accelerated by rapid reactions when carbon-rich sediments are exposed to migrating magmatic fluids. The spectacular Lusi eruption (north-east Java, Indonesia) is the surface expression of the present-day deep interaction between volcanic and sedimentary domains. Here we report the ongoing generation of large amounts of hydrocarbons induced by a recent magmatic intrusion from the neighbouring Arjuno-Welirang volcanic complex. We have investigated a unique suite of oil and clast samples, and developed a detailed conceptual model for the complex hydrocarbon migration history in this part of the basin by integrating multidisciplinary techniques. Our results show that palynology, organic petrology, and chlorite microthermometry are the most sensitive geothermometers for basins affected by recent magmatic activity. These findings further our understanding of the driving mechanisms fueling the world’s largest active mud eruption and provide a unique dataset to investigate modern hydrocarbon generation processes.

Cell membrane fatty acid and pigment composition of the psychrotolerant cyanobacterium Nodularia spumigena CHS1 isolated from Hopar glacier, Pakistan

In the present study, cyanobacterium isolate CHS1 isolated from Hopar glacier, Pakistan, was analyzed for the first time for cell membrane fatty acids and production of pigments. Sequencing of the 16-23S intergenetic region confirmed identification of the isolate CHS1 as Nodularia spumigena. All chlorophyll and carotenoid pigments were quantified using high-performance liquid chromatography and experiments to test tolerance against a range of physico-chemical conditions were conducted. Likewise, the fatty acid profile of the cell membrane CHS1 was analyzed using gas chromatography and mass spectroscopy. The cyanobacterium isolate CHS1 demonstrated tolerance to 8 g/L% NaCl, 35°C and pH 5-9. The characteristic polyunsaturated fatty acid (PUFA) of isolate CHS1, C18:4, was observed in fatty acid methyl esters (FAMEs) extracted from the cell membrane. CHS1 was capable of producing saturated fatty acids (SFA) (e.g., C16:0), monounsaturated fatty acids (MUFA) (e.g., C18:1) and polyunsaturated fatty acids (e.g., C20:5) in the cell membrane. In this study, we hypothesize that one mechanism of cold adaptation displayed by isolate CHS1 is the accumulation of high amounts of PUFA in the cell membrane.

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.

Cyanobacteria evolution: Insight from the fossil record

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

Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation

Eukaryotes arose about 1.6 billion years ago, at a time when oxygen levels were still very low on Earth, both in the atmosphere and in the ocean. According to newer geochemical data, oxygen rose to approximately its present atmospheric levels very late in evolution, perhaps as late as the origin of land plants (only about 450 million years ago). It is therefore natural that many lineages of eukaryotes harbor, and use, enzymes for oxygen-independent energy metabolism. This paper provides a concise overview of anaerobic energy metabolism in eukaryotes with a focus on anaerobic energy metabolism in mitochondria. We also address the widespread assumption that oxygen improves the overall energetic state of a cell. While it is true that ATP yield from glucose or amino acids is increased in the presence of oxygen, it is also true that the synthesis of biomass costs thirteen times more energy per cell in the presence of oxygen than in anoxic conditions. This is because in the reaction of cellular biomass with O2, the equilibrium lies very far on the side of CO2. The absence of oxygen offers energetic benefits of the same magnitude as the presence of oxygen. Anaerobic and low oxygen environments are ancient. During evolution, some eukaryotes have specialized to life in permanently oxic environments (life on land), other eukaryotes have remained specialized to low oxygen habitats. We suggest that the Km of mitochondrial cytochrome c oxidase of 0.1-10 μM for O2, which corresponds to about 0.04%-4% (avg. 0.4%) of present atmospheric O2 levels, reflects environmental O2 concentrations that existed at the time that the eukaryotes arose.

Enhanced weathering as a trigger for the rise of atmospheric O2 level from the late Ediacaran to the early Cambrian

A shift toward a higher oxygen level in both ocean and atmosphere systems during the late Ediacaran to the early Cambrian has been suggested from multiple indirect proxies. However, the mechanism and magnitude of this oxidation remain unclear. To solve this issue, we measured carbon isotopes in both carbonate and organic matter as well as their trace element compositions for an Ediacaran-Cambrian sequence in the Lower Yangtze basin, South China. The δ13Corg and δ13Ccarb excursions of this sequence are coupled and can be compared with contemporaneous global carbon isotope curves. A 2‰ rise in Δ13Ccarb-org occurred from the late Ediacaran to the early Cambrian, suggesting a substantial increase in atmospheric oxygen level from 16% to 30% of the present atmospheric level (PAL). Furthermore, the distribution pattern of rare earth elements and the concentrations of water-insoluble elements in the carbonates indicate a sudden enhancement in chemical weathering of the continental crust during the early Cambrian, which may be a trigger for the rise of atmospheric O2 level. Both the supply of a large amount of nutrients due to the enhanced continental weathering and the contemporary increase of atmospheric oxygen concentrations may have promoted the appearance of large metazoans in the early Cambrian.

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.

ROS changes are responsible for tributyl phosphate (TBP)-induced toxicity in the alga Phaeodactylum tricornutum

As a newly emerging environmental contaminant, tributyl phosphate (TBP) is an additive flame retardant of high production volume that is frequently detected in biota and the environment. Despite evidence that TBP is a potential threat to marine organisms, ecotoxicology data for TBP in marine organisms at low trophic levels are scarce. In this study, the acute toxicological effect of TBP on the marine phytoplankton Phaeodactylum tricornutum was thoroughly investigated, and the possible mechanism was explored. The results showed that TBP at concentrations ≥0.2 mg L^-1 significantly inhibited P. tricornutum growth in a clear dose-response manner, with 72-h EC₁₀, EC₂₀, EC₅₀ and EC₉₀ values of 0.067, 0.101, 0.219 and 0.716 mg L^-1, respectively. Algal cells treated with TBP exhibited distorted shapes, ruptured cell membranes and damaged organelles, especially mitochondria. Additionally, apoptosis was triggered, followed by a decrease in mitochondrial membrane potential, indicating that cellular damage occurred during exposure. Although the activities of two antioxidant enzymes, superoxide peroxidase and catalase, were upregulated by TBP at 1.2 mg L^-1, excess reactive oxygen species (ROS) and malondialdehyde still accumulated in algal cells after exposure, suggesting that the cells experienced oxidative stress. Moreover, both growth inhibition and apoptosis were positively correlated with ROS levels and were ameliorated by pretreatment with the ROS scavenger N-acetyl-l-cysteine. Taken together, the results indicate that TBP exposure leads to growth inhibition and cellular damage in P. tricornutum, and a ROS-mediated pathway might contribute to these observed toxicological effects.

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.

The Ladder of Life Detection

We describe the history and features of the Ladder of Life Detection, a tool intended to guide the design of investigations to detect microbial life within the practical constraints of robotic space missions. To build the Ladder, we have drawn from lessons learned from previous attempts at detecting life and derived criteria for a measurement (or suite of measurements) to constitute convincing evidence for indigenous life. We summarize features of life as we know it, how specific they are to life, and how they can be measured, and sort these features in a general sense based on their likelihood of indicating life. Because indigenous life is the hypothesis of last resort in interpreting life-detection measurements, we propose a small but expandable set of decision rules determining whether the abiotic hypothesis is disproved. In light of these rules, we evaluate past and upcoming attempts at life detection. The Ladder of Life Detection is not intended to endorse specific biosignatures or instruments for life-detection measurements, and is by no means a definitive, final product. It is intended as a starting point to stimulate discussion, debate, and further research on the characteristics of life, what constitutes a biosignature, and the means to measure them.

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.

Evolving paradigms in biological carbon cycling in the ocean

Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO2, CaCO3, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO2. The concepts of the biological carbon pump (BCP) and the microbial loop (ML) shaped our understanding of the marine carbon cycle. The more recent concept of the microbial carbon pump (MCP), which is closely connected to those of the BCP and the ML, explicitly considers the significance of the ocean's RDOC reservoir and provides a mechanistic framework for the exploration of its formation and persistence. Understanding of the MCP has benefited from advanced ‘omics’ and novel research in biological oceanography and microbial biogeochemistry. The need to predict the ocean's response to climate change makes an integrative understanding of the BCP, ML and MCP a high priority. In this review, we summarize and discuss progress since the proposal of the MCP in 2010 and formulate research questions for the future.

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.

Ancient Biomolecules and Evolutionary Inference

Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.

Constraining the Time Interval for the Origin of Life on Earth

Estimates of the time at which life arose on Earth make use of two types of evidence. First, astrophysical and geophysical studies provide a timescale for the formation of Earth and the Moon, for large impact events on early Earth, and for the cooling of the early magma ocean. From this evidence, we can deduce a habitability boundary, which is the earliest point at which Earth became habitable. Second, biosignatures in geological samples, including microfossils, stromatolites, and chemical isotope ratios, provide evidence for when life was actually present. From these observations we can deduce a biosignature boundary, which is the earliest point at which there is clear evidence that life existed. Studies with molecular phylogenetics and records of the changing level of oxygen in the atmosphere give additional information that helps to determine the biosignature boundary. Here, we review the data from a wide range of disciplines to summarize current information on the timings of these two boundaries. The habitability boundary could be as early as 4.5 Ga, the earliest possible estimate of the time at which Earth had a stable crust and hydrosphere, or as late as 3.9 Ga, the end of the period of heavy meteorite bombardment. The lack of consensus on whether there was a late heavy meteorite bombardment that was significant enough to prevent life is the largest uncertainty in estimating the time of the habitability boundary. The biosignature boundary is more closely constrained. Evidence from carbon isotope ratios and stromatolite fossils both point to a time close to 3.7 Ga. Life must have emerged in the interval between these two boundaries. The time taken for life to appear could, therefore, be within 200 Myr or as long as 800 Myr. Key Words: Origin of life-Astrobiology-Habitability-Biosignatures-Geochemistry-Early Earth. Astrobiology 18, 343-364.

Reactive Oxygen Species: Radical Factors in the Evolution of Animal Life: A molecular timescale from Earth's earliest history to the rise of complex life

Introduction of O₂ to Earth's early biosphere stimulated remarkable evolutionary adaptations, and a wide range of electron acceptors allowed diverse, energy-yielding metabolic pathways. Enzymatic reduction of O₂ yielded a several-fold increase in energy production, enabling evolution of multi-cellular animal life. However, utilization of O₂ also presented major challenges as O₂ and many of its derived reactive oxygen species (ROS) are highly toxic, possibly impeding multicellular evolution after the Great Oxidation Event. Remarkably, ROS, and especially hydrogen peroxide, seem to play a major part in early diversification and further development of cellular respiration and other oxygenic pathways, thus becoming an intricate part of evolution of complex life. Hence, although harnessing of chemical and thermo-dynamic properties of O₂ for aerobic metabolism is generally considered to be an evolutionary milestone, the ability to use ROS for cell signaling and regulation may have been the first true breakthrough in development of complex life.

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.