Morphological and ecological complexity in early eukaryotic ecosystems

Locked in Structure: Sestrin and GATOR-A Billion-Year Marriage

Sestrins are a conserved family of stress-responsive proteins that play a crucial role in cellular metabolism, stress response, and ageing. Vertebrates have three Sestrin genes (SESN1, SESN2, and SESN3), while invertebrates encode only one. Initially identified as antioxidant proteins that regulate cell viability, Sestrins are now recognised as crucial inhibitors of the mechanistic target of rapamycin complex 1 kinase (mTORC1), a central regulator of anabolism, cell growth, and autophagy. Sestrins suppress mTORC1 through an inhibitory interaction with the GATOR2 protein complex, which, in concert with GATOR1, signals to inhibit the lysosomal docking of mTORC1. A leucine-binding pocket (LBP) is found in most vertebrate Sestrins, and when bound with leucine, Sestrins do not bind GATOR2, prompting mTORC1 activation. This review examines the evolutionary conservation of Sestrins and their functional motifs, focusing on their origins and development. We highlight that the most conserved regions of Sestrins are those involved in GATOR2 binding, and while analogues of Sestrins exist in prokaryotes, the unique feature of eukaryotic Sestrins is their structural presentation of GATOR2-binding motifs.

Proterozoic microfossils continue to provide new insights into the rise of complex eukaryotic life

Eukaryotes have evolved to dominate the biosphere today, accounting for most documented living species and the vast majority of the Earth's biomass. Consequently, understanding how these biologically complex organisms initially diversified in the Proterozoic Eon over 539 million years ago is a foundational question in evolutionary biology. Over the last 70 years, palaeontologists have sought to document the rise of eukaryotes with fossil evidence. However, the delicate and microscopic nature of their sub-cellular features affords early eukaryotes diminished preservation potential. Chemical biomarker signatures of eukaryotes and the genetics of living eukaryotes have emerged as complementary tools for reconstructing eukaryote ancestry. In this review, we argue that exceptionally preserved Proterozoic microfossils are critical to interpreting these complementary tools, providing crucial calibrations to molecular clocks and testing hypotheses of palaeoecology. We highlight recent research on their preservation and biomolecular composition that offers new ways to enhance their utility.

Lateral redox variability in ca. 1.9 Ga marine environments indicated by organic carbon and nitrogen isotope compositions

The stepwise oxygenation of Earth's surficial environment is thought to have shaped the evolutionary history of life. Microfossil records and molecular clocks suggest eukaryotes appeared during the Paleoproterozoic, perhaps shortly after the Great Oxidation Episode at ca. 2.43 Ga. The mildly oxygenated atmosphere and surface oceans likely contributed to the early evolution of eukaryotes. However, the principal trigger for the eukaryote appearance and a potential factor for their delayed expansion (i.e., intermediate ocean redox conditions until the Neoproterozoic) remain poorly understood, largely owing to a lack of constraints on marine and terrestrial nutrient cycling. Here, we analyzed redox-sensitive element contents and organic carbon and nitrogen isotope compositions of relatively low metamorphic-grade (greenschist facies) black shales preserved in the Flin Flon Belt of central Canada to examine open-marine redox conditions and biological activity around the ca. 1.9 Ga Flin Flon oceanic island arc. The black shale samples were collected from the Reed Lake area in the eastern part of the Flin Flon Belt, and the depositional site was likely distal from the Archean cratons. The black shales have low Al/Ti ratios and are slightly depleted in light rare-earth elements relative to the post-Archean average shale, which is consistent with a limited contribution from felsic igneous rocks in Archean upper continental crust. Redox conditions have likely varied between suboxic and euxinic at the depositional site of the studied section, as suggested by variable U/Al and Mo/Al ratios. Organic carbon and nitrogen isotope compositions of the black shales are approximately -23‰ and +13.7‰, respectively, and these values are systematically higher than those of broadly coeval continental margin deposits (approximately -30‰ for δ13Corg and +5‰ for δ15Nbulk). These elevated values are indicative of high productivity that led to enhanced denitrification (i.e., a high denitrification rate relative to nitrogen influx at the depositional site). Similar geochemical patterns have also been observed in the modern Peruvian oxygen minimum zone where dissolved nitrogen compounds are actively lost from the reservoir via denitrification and anammox, but the large nitrate reservoir of the deep ocean prevents exhaustion of the surface nitrate pool. Nitrogen must have been widely bioavailable in the ca. 1.9 Ga oceans, and its supply to upwelling zones must have supported habitable environments for eukaryotes, even in the middle of oceans around island arcs.

The consequences of viral infection on protists

Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.

Frameworks for Interpreting the Early Fossil Record of Eukaryotes

The origin of modern eukaryotes is one of the key transitions in life's history, and also one of the least understood. Although the fossil record provides the most direct view of this process, interpreting the fossils of early eukaryotes and eukaryote-grade organisms is not straightforward. We present two end-member models for the evolution of modern (i.e., crown) eukaryotes-one in which modern eukaryotes evolved early, and another in which they evolved late-and interpret key fossils within these frameworks, including where they might fit in eukaryote phylogeny and what they may tell us about the evolution of eukaryotic cell biology and ecology. Each model has different implications for understanding the rise of complex life on Earth, including different roles of Earth surface oxygenation, and makes different predictions that future paleontological studies can test.

Could the tumor-associated microbiota be the new multi-faceted player in the tumor microenvironment?

Microorganisms have been identified in tumor specimens for over a century. It is only in recent years that tumor-associated microbiota has become a rapidly expanding field. Assessment techniques encompass methods at the frontiers of molecular biology, microbiology, and histology, requiring a transdisciplinary process to carefully decipher this new component of the tumor microenvironment. Due to the low biomass, the study of tumor-associated microbiota poses technical, analytical, biological, and clinical challenges and must be approached as a whole. To date, several studies have begun to shed light on the composition, functions, and clinical relevance of the tumor-associated microbiota. This new piece of the tumor microenvironment puzzle could potentially change the way we think about and treat patients with cancer.

A case for an active eukaryotic marine biosphere during the Proterozoic era

The microfossil record demonstrates the presence of eukaryotic organisms in the marine ecosystem by about 1,700 million years ago (Ma). Despite this, steranes, a biomarker indicator of eukaryotic organisms, do not appear in the rock record until about 780 Ma in what is known as the "rise of algae." Before this, it is argued that eukaryotes were minor ecosystem members, with prokaryotes dominating both primary production and ecosystem dynamics. In this view, the rise of algae was possibly sparked by increased nutrient availability supplying the higher nutrient requirements of eukaryotic algae. Here, we challenge this view. We use a size-based ecosystem model to show that the size distribution of preserved eukaryotic microfossils from 1,700 Ma and onward required an active eukaryote ecosystem complete with phototrophy, osmotrophy, phagotrophy, and mixotrophy. Model results suggest that eukaryotes accounted for one-half or more of the living biomass, with eukaryotic algae contributing to about one-half of total marine primary production. These ecosystems lived with deep-water phosphate levels of at least 10% of modern levels. The general lack of steranes in the pre-780-Ma rock record could be a result of poor preservation.

Eukaryogenesis and oxygen in Earth history

The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth's surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and life sciences. While the permanent oxygenation of the atmosphere above trace concentrations is now thought to have occurred 2.2 billion years ago, large parts of the deep ocean remained anoxic until less than 0.5 billion years ago. Neither fossils nor molecular clocks correlate the origin of mitochondria, or eukaryogenesis more broadly, to either of these planetary redox transitions. Instead, mitochondria-bearing eukaryotes are consistently dated to between these two oxygenation events, during an interval of pervasive deep-sea anoxia and variable surface-water oxygenation. The discovery and cultivation of the Asgard archaea has reinforced metabolic evidence that eukaryogenesis was initially mediated by syntrophic H₂ exchange between an archaeal host and an α-proteobacterial symbiont living under anoxia. Together, these results temporally, spatially and metabolically decouple the earliest stages of eukaryogenesis from the oxygen content of the surface ocean and atmosphere. Rather than reflecting the ancestral metabolic state, obligate aerobiosis in eukaryotes is most probably derived, having only become globally widespread over the past 1 billion years as atmospheric oxygen approached modern levels.

Contrasting nutrient availability between marine and brackish waters in the late Mesoproterozoic: Evidence from the Paranoá Group, Brazil

Understanding the delayed rise of eukaryotic life on Earth is one of the most fundamental questions about biological evolution. Numerous studies have presented evidence for oxygen and nutrient limitations in seawater during the Mesoproterozoic era, indicating that open marine settings may not have been able to sustain a eukaryotic biosphere with complex, multicellular organisms. However, many of these data sets represent restricted marine basins, which may bias our view of habitability. Furthermore, it remains untested whether rivers could have supplied significant nutrient fluxes to coastal habitats. To better characterize the sources of the major nutrients nitrogen and phosphorus, we turned to the late Mesoproterozoic Paranoá Group in Brazil (~1.1 Ga), which was deposited on a passive margin of the São Francisco craton. We present carbon, nitrogen and sulphur isotope data from an open shelf setting (Fazenda Funil) and from a brackish-water environment with significant riverine input (São Gabriel). Our results show that waters were well-oxygenated and nitrate was bioavailable in the open ocean setting at Fazenda Funil; the redoxcline appears to have been deeper and further offshore compared to restricted marine basins elsewhere in the Mesoproterozoic. In contrast, the brackish site at São Gabriel received only limited input of marine nitrate and sulphate. Nevertheless, previous reports of acritarchs reveal that this brackish-water setting was habitable to eukaryotic life. Paired with previously published cadmium isotope data, which can be used as a proxy for phosphorus cycling, our results suggest that complex organisms were perhaps not strictly dependent on marine nutrient supplies. Riverine influxes of P and possibly other nutrients likely rendered coastal waters perhaps equally habitable to the Mesoproterozoic open ocean. This conclusion supports the notion that eukaryotic organisms may have thrived in brackish or perhaps even freshwater environments.

Structural and chemical heterogeneity of Proterozoic organic microfossils of the ca. 1 Ga old Angmaat Formation, Baffin Island, Canada

Organic microfossils in Meso- and Neoproterozoic rocks are of key importance to track the emergence and evolution of eukaryotic life. An increasing number of studies combine Raman spectroscopy with synchrotron-based methods to characterize these microfossils. A recurring observation is that Raman spectra of organic microfossils show negligible variation on a sample scale and that variation between different samples can be explained by differences in thermal maturation or in the biologic origin of organic precursor material. There is a paucity of work, however, that explores the extent to which the petrographic framework and diagenetic processes might influence the chemical structure of organic materials. We present a detailed Raman spectroscopy-based study of a complex organic microfossil assemblage in the ca. 1 Ga old Angmaat Formation, Baffin Island, Canada. This formation contains abundant early diagenetic chert that preserves silicified microbial mats with numerous, readily identifiable organic microfossils. Individual chert beds show petrographic differences with discrete episodes of cementation and recrystallization. Raman spectroscopy reveals measurable variation of organic maturity between samples and between neighboring organic microfossils of the same taxonomy and taphonomic state. Scanning transmission X-ray microscopy performed on taphonomically similar coccoidal microfossils from the same thin section shows distinct chemical compositions, with varying ratios of aromatic compounds to ketones and phenols. Such observations imply that geochemical variation of organic matter is not necessarily coupled to thermal alteration or organic precursor material. Variation of the Raman signal across single samples is most likely linked to the diagenetic state of analyzed materials and implies an association between organic preservation and access to diagenetic fluids. Variation in the maturity of individual microfossils may be a natural outcome of local diagenetic processes and potentially exceeds differences derived from precursor organic material. These observations stress the importance of detailed in situ characterization by Raman spectroscopy to identify target specimens for further chemical analysis.

Evidence for a Syncytial Origin of Eukaryotes from Ancestral State Reconstruction

Modern accounts of eukaryogenesis entail an endosymbiotic encounter between an archaeal host and a proteobacterial endosymbiont, with subsequent evolution giving rise to a unicell possessing a single nucleus and mitochondria. The mononucleate state of the last eukaryotic common ancestor (LECA) is seldom, if ever, questioned, even though cells harboring multiple (syncytia, coenocytes, and polykaryons) are surprisingly common across eukaryotic supergroups. Here, we present a survey of multinucleated forms. Ancestral character state reconstruction for representatives of 106 eukaryotic taxa using 16 different possible roots and supergroup sister relationships, indicate that LECA, in addition to being mitochondriate, sexual, and meiotic, was multinucleate. LECA exhibited closed mitosis, which is the rule for modern syncytial forms, shedding light on the mechanics of its chromosome segregation. A simple mathematical model shows that within LECA's multinucleate cytosol, relationships among mitochondria and nuclei were neither one-to-one, nor one-to-many, but many-to-many, placing mitonuclear interactions and cytonuclear compatibility at the evolutionary base of eukaryotic cell origin. Within a syncytium, individual nuclei and individual mitochondria function as the initial lower-level evolutionary units of selection, as opposed to individual cells, during eukaryogenesis. Nuclei within a syncytium rescue each other's lethal mutations, thereby postponing selection for viable nuclei and cytonuclear compatibility to the generation of spores, buffering transitional bottlenecks at eukaryogenesis. The prokaryote-to-eukaryote transition is traditionally thought to have left no intermediates, yet if eukaryogenesis proceeded via a syncytial common ancestor, intermediate forms have persisted to the present throughout the eukaryotic tree as syncytia but have so far gone unrecognized.

The influence of elevated SiO2 (aq) on intracellular silica uptake and microbial metabolism

Microbes are known to accumulate intracellular SiO₂ (aq) up to 100s of mmol/l from modern seawater (SiO₂ (aq) <100 µmol/l), despite having no known nutrient requirement for Si. Before the evolution of siliceous skeletons, marine silica concentrations were likely an order of magnitude higher than the modern ocean, raising the possibility that intracellular SiO₂ (aq) accumulation interfered with normal cellular function in non-silicifying algae. Yet, because few culturing studies have isolated the effects of SiO₂ (aq) at high concentration, the potential impact of elevated marine silica on early microbial evolution is unknown. Here, we test the influence of elevated SiO₂ (aq) on eukaryotic algae, as well as a prokaryote species. Our results demonstrate that under SiO₂ (aq) concentrations relevant to ancient seawater, intracellular Si accumulates to concentrations comparable to those found in siliceous algae such as diatoms. In addition, all eukaryotic algae showed a statistically significant response to the high-Si treatment, including reduced average cell sizes and/or a reduction in the maximum growth rate. In contrast, there was no consistent response to the high-Si treatment by the prokaryote species. Our results highlight the possibility that elevated marine SiO₂ (aq) may have been an environmental stressor during early eukaryotic evolution.

RNA Viruses in Aquatic Unicellular Eukaryotes

Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.

Insights into eukaryogenesis from the fossil record

Eukaryogenesis-the process by which the eukaryotic cell emerged-has long puzzled scientists. It has been assumed that the fossil record has little to say about this process, in part because important characters such as the nucleus and mitochondria are rarely preserved, and in part because the prevailing model of early eukaryotes implies that eukaryogenesis occurred before the appearance of the first eukaryotes recognized in the fossil record. Here, I propose a different scenario for early eukaryote evolution than is widely assumed. Rather than crown group eukaryotes originating in the late Paleoproterozoic and remaining ecologically minor components for more than half a billion years in a prokaryote-dominated world, I argue for a late Mesoproterozoic origin of the eukaryotic crown group, implying that eukaryogenesis can be studied using the fossil record. I review the proxy records of four crown group characters: the capacity to form cysts as evidenced by the presence of excystment structures; a complex cytoskeleton as evidenced by spines or pylomes; sterol synthesis as evidenced by steranes; and aerobic respiration-and therefore mitochondria-as evidenced by eukaryotes living in oxic environments, and argue that it might be possible to use these proxy records to infer the order in which these characters evolved. The records indicate that both cyst formation and a complex cytoskeleton appeared by late Paleoproterozoic time, and sterol synthesis appeared in the late Mesoproterozioc or early Neoproterozoic. The origin of aerobic respiration cannot as easily be pinned down, but current evidence permits the possibility that it evolved sometime in the Mesoproterozoic.

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

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

The impact of marine nutrient abundance on early eukaryotic ecosystems

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

Antagonistic co-limitation through ion promiscuity - On the metal sensitivity of Thalassiosira oceanica under phosphorus stress

Nutrient limitation of primary producers is a fundamental principle in biogeochemical oceanography and has been used with great success in prescribing understanding to patterns of marine primary productivity. In recent years the paradigm of nutrient limitation has expanded from single nutrient limitation towards concepts of co-limitation by multiple resources. Interactive effects between multiple limiting resources are now thought commonplace in marine microbial communities. Here we investigate the response exhibited by phosphate-limited Thalassiosira oceanica to elevated concentrations of the phosphate analogs vanadate, arsenate and molybdate. Enrichments in external arsenate and vanadate to phosphate-limited cultures act to suppress growth rates entirely, an effect not seen in phosphate replete conditions. Retardation of growth rates is attributed to mistaken uptake through ion promiscuity as evidenced by observations of significant intracellular accumulation of both arsenic and vanadium under phosphate limited conditions. We describe this novel co-limitation scenario as dependent antagonistic co-limitation (DAC), and suggest that this phenomenon of non-deliberate intracellular accumulation could be used as both a proxy of phosphate stress in the modern ocean and a possible marker of phosphate depletion limiting the duration of oceanic anoxic events.

Evaluating Biogenicity on the Geological Record With Synchrotron-Based Techniques

The biogenicity problem of geological materials is one of the most challenging ones in the field of paleo and astrobiology. As one goes deeper in time, the traces of life become feeble and ambiguous, blending with the surrounding geology. Well-preserved metasedimentary rocks from the Archaean are relatively rare, and in very few cases contain structures resembling biological traces or fossils. These putative biosignatures have been studied for decades and many biogenicity criteria have been developed, but there is still no consensus for many of the proposed structures. Synchrotron-based techniques, especially on new generation sources, have the potential for contributing to this field of research, providing high sensitivity and resolution that can be advantageous for different scientific problems. Exploring the X-ray and matter interactions on a range of geological materials can provide insights on morphology, elemental composition, oxidation states, crystalline structure, magnetic properties, and others, which can measurably contribute to the investigation of biogenicity of putative biosignatures. Here, we provide an overview of selected synchrotron-based techniques that have the potential to be applied in different types of questions on the study of biosignatures preserved in the geological record. The development of 3rd and recently 4th generation synchrotron sources will favor a deeper understanding of the earliest records of life on Earth and also bring up potential analytical approaches to be applied for the search of biosignatures in meteorites and samples returned from Mars in the near future.

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.

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.

Absence of biomarker evidence for early eukaryotic life from the Mesoproterozoic Roper Group: Searching across a marine redox gradient in mid-Proterozoic habitability

By about 2.0 billion years ago (Ga), there is evidence for a period best known for its extended, apparent geochemical stability expressed famously in the carbonate-carbon isotope data. Despite the first appearance and early innovation among eukaryotic organisms, this period is also known for a rarity of eukaryotic fossils and an absence of organic biomarker fingerprints for those organisms, suggesting low diversity and relatively small populations compared to the Neoproterozoic era. Nevertheless, the search for diagnostic biomarkers has not been performed with guidance from paleoenvironmental redox constrains from inorganic geochemistry that should reveal the facies that were most likely hospitable to these organisms. Siltstones and shales obtained from drill core of the ca. 1.3-1.4 Ga Roper Group from the McArthur Basin of northern Australia provide one of our best windows into the mid-Proterozoic redox landscape. The group is well dated and minimally metamorphosed (of oil window maturity), and previous geochemical data suggest a relatively strong connection to the open ocean compared to other mid-Proterozoic records. Here, we present one of the first integrated investigations of Mesoproterozoic biomarker records performed in parallel with established inorganic redox proxy indicators. Results reveal a temporally variable paleoredox structure through the Velkerri Formation as gauged from iron mineral speciation and trace-metal geochemistry, vacillating between oxic and anoxic. Our combined lipid biomarker and inorganic geochemical records indicate at least episodic euxinic conditions sustained predominantly below the photic zone during the deposition of organic-rich shales found in the middle Velkerri Formation. The most striking result is an absence of eukaryotic steranes (4-desmethylsteranes) and only traces of gammacerane in some samples-despite our search across oxic, as well as anoxic, facies that should favor eukaryotic habitability and in low maturity rocks that allow the preservation of biomarker alkanes. The dearth of Mesoproterozoic eukaryotic sterane biomarkers, even within the more oxic facies, is somewhat surprising but suggests that controls such as the long-term nutrient balance and other environmental factors may have throttled the abundances and diversity of early eukaryotic life relative to bacteria within marine microbial communities. Given that molecular clocks predict that sterol synthesis evolved early in eukaryotic history, and (bacterial) fossil steroids have been found previously in 1.64 Ga rocks, then a very low environmental abundance of eukaryotes relative to bacteria is our preferred explanation for the lack of regular steranes and only traces of gammacerane in a few samples. It is also possible that early eukaryotes adapted to Mesoproterozoic marine environments did not make abundant steroid lipids or tetrahymanol in their cell membranes.

Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments

Oxygen reducing terminal oxidases differ with respect to their subunit composition, heme groups, operon structure, and affinity for O₂. Six families of terminal oxidases are currently recognized, all of which occur in alphaproteobacterial genomes, two of which are also present in mitochondria. Many alphaproteobacteria encode several different terminal oxidases, likely reflecting ecological versatility with respect to oxygen levels. Terminal oxidase evolution likely started with the advent of O₂ roughly 2.4 billion years ago and terminal oxidases diversified in the Proterozoic, during which oxygen levels remained low, around the Pasteur point (ca. 2 μM O₂). Among the alphaproteobacterial genomes surveyed, those from members of the Rhodospirillaceae reveal the greatest diversity in oxygen reductases. Some harbor all six terminal oxidase types, in addition to many soluble enzymes typical of anaerobic fermentations in mitochondria and hydrogenosomes of eukaryotes. Recent data have it that O₂ levels increased to current values (21% v/v or ca. 250 μM) only about 430 million years ago. Ecological adaptation brought forth different lineages of alphaproteobacteria and different lineages of eukaryotes that have undergone evolutionary specialization to high oxygen, low oxygen, and anaerobic habitats. Some have remained facultative anaerobes that are able to generate ATP with or without the help of oxygen and represent physiological links to the ancient proteobacterial lineage at the origin of mitochondria and eukaryotes. Our analysis reveals that the genomes of alphaproteobacteria appear to retain signatures of ancient transitions in aerobic metabolism, findings that are relevant to mitochondrial evolution in eukaryotes as well.

A small marine biosphere in the Proterozoic

The riverine supply of the globally limiting nutrient, phosphorus, to the ocean accounts for only a few percent of nutrient supply to photosynthetic organisms in surface waters. Recycling of marine organic matter by heterotrophic organisms provides almost all of the phosphorus that drives net primary production in the modern ocean. In the low-oxygen environments of the Proterozoic, the lack of free oxygen would have limited rates of oxic respiration, slowing the recycling of nutrients and thus limiting global rates of photosynthesis. A series of steady-state mass balance calculations suggest that the rate of net primary production in the ocean was no more than 10% of its modern value during the Proterozoic eon, and possibly less than 1%. The supply of nutrients in such a world would be dominated by river input, rather than recycling within the water column, leading to a small marine biosphere found primarily within estuarine environments.

Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes

Elucidating the diversity of the Archaea has many important ecological and evolutionary implications. The Asgard superphylum of the archaea, described recently from metagenomic data, has reignited the decades-old debate surrounding the topology of the tree of life. This review synthesizes recent findings through publicly available genomes and literature to describe the current ecological and evolutionary significance of the Asgard superphylum. Asgard archaea have been found in a diverse range of microbiomes across the globe, primarily from sedimentary environments. Within these environments, positive correlations between specific members of the Asgard archaea and Candidate Division TA06 bacteria have been observed, opening up the possibility of symbiotic interactions between the groupings. Asgard archaeal genomes encode functionally diverse metabolic pathways, including the Wood-Ljungdahl pathway as a carbon-fixation strategy, putative nucleotide salvaging pathways, and novel mechanisms of phototrophy including new rhodopsins. Asgard archaea also appear to be active in nitrogen cycling. Asgard archaea encode genes involved in both dissimilatory nitrate reduction and denitrification, and for the potential to use atmospheric nitrogen or nitrite as nitrogen sources. Asgard archaea also may be involved in the transformation of sulfur compounds, indicating a putative role in sulfur cycling. To date, all Asgard archaeal genomes identified were described as obligately anaerobic. The Asgard archaea also appear to have important evolutionary implications. The presence of eukaryotic signature proteins and the affiliation of Asgard archaea in phylogenetic analyses appears to support two-domain topologies of the tree of life with eukaryotes emerging from within the domain of archaea, as opposed to the eukaryotes being a separate domain of life. Thus far, Heimdallarchaeota appears as the closest archaeal relative of eukaryotes.

Engineering yeast endosymbionts as a step toward the evolution of mitochondria

It has been hypothesized that mitochondria evolved from a bacterial ancestor that initially became established in an archaeal host cell as an endosymbiont. Here we model this first stage of mitochondrial evolution by engineering endosymbiosis between Escherichia coli and Saccharomyces cerevisiae An ADP/ATP translocase-expressing E. coli provided ATP to a respiration-deficient cox2 yeast mutant and enabled growth of a yeast-E. coli chimera on a nonfermentable carbon source. In a reciprocal fashion, yeast provided thiamin to an endosymbiotic E. coli thiamin auxotroph. Expression of several SNARE-like proteins in E. coli was also required, likely to block lysosomal degradation of intracellular bacteria. This chimeric system was stable for more than 40 doublings, and GFP-expressing E. coli endosymbionts could be observed in the yeast by fluorescence microscopy and X-ray tomography. This readily manipulated system should allow experimental delineation of host-endosymbiont adaptations that occurred during evolution of the current, highly reduced mitochondrial genome.

It's a protist-eat-protist world: recalcitrance, predation, and evolution in the Tonian–Cryogenian ocean

Predation, and how organisms respond to it, is an important ecological interaction across the tree of life. Much of our understanding of predation focuses on modern metazoa. However, predation is equally important in single-celled eukaryotes (commonly referred to as protists). In the fossil record, we see evidence of protists preying on other protists beginning in the Tonian Period (1000–720 Ma). In addition, the first evidence of eukaryotic biomineralization and the appearance of multiple unmineralized but recalcitrant forms are also seen in the Tonian and Cryogenian (720–635 Ma), potentially indirect evidence of predation. This fossil evidence, coupled with molecular clock analyses, is coincident with multiple metrics that show an increase in the diversity of eukaryotic clades and fossil assemblages. Predation, thus, may have played a critical role in the diversification of eukaryotes and the evolution of protistan armor in the Neoproterozoic Era. Here, we review the current understanding of predation in the Tonian and Cryogenian oceans as viewed through the fossil record, and discuss how the rise of eukaryotic predation upon other eukaryotes (eukaryovory) may have played a role in major evolutionary transitions including the origins of biomineralization.

Implications of selective predation on the macroevolution of eukaryotes: evidence from Arctic Canada

Existing paleontological data indicate marked eukaryote diversification in the Neoproterozoic, ca. 800 Ma, driven by predation pressure and various other biotic and abiotic factors. Although the eukaryotic record remains less diverse before that time, molecular clock estimates and earliest crown-group affiliated microfossils suggest that the diversification may have originated during the Mesoproterozoic. Within new assemblages of organic-walled microfossils from the ca. 1150 to 900 Ma lower Shaler Supergroup of Arctic Canada, numerous specimens from various taxa display circular and ovoid perforations on their walls, interpreted as probable traces of selective protist predation, 150-400 million years before their first reported incidence in the Neoproterozoic. Selective predation is a more complex behavior than phagotrophy, because it requires sensing and selection of prey followed by controlled lysis of the prey wall. The ca. 800 Ma eukaryotic diversification may have been more gradual than previously thought, beginning in the late Mesoproterozoic, as indicated by recently described microfossil assemblages, in parallel with the evolution of selective eukaryovory and the spreading of eukaryotic photosynthesis in marine environments.

High pCO2-induced exopolysaccharide-rich ballasted aggregates of planktonic cyanobacteria could explain Paleoproterozoic carbon burial

The contribution of planktonic cyanobacteria to burial of organic carbon in deep-sea sediments before the emergence of eukaryotic predators ~1.5 Ga has been considered negligible owing to the slow sinking speed of their small cells. However, global, highly positive excursion in carbon isotope values of inorganic carbonates ~2.22-2.06 Ga implies massive organic matter burial that had to be linked to oceanic cyanobacteria. Here to elucidate that link, we experiment with unicellular planktonic cyanobacteria acclimated to high partial CO2 pressure (pCO2) representative of the early Paleoproterozoic. We find that high pCO2 boosts generation of acidic extracellular polysaccharides (EPS) that adsorb Ca and Mg cations, support mineralization, and aggregate cells to form ballasted particles. The down flux of such self-assembled cyanobacterial aggregates would decouple the oxygenic photosynthesis from oxidative respiration at the ocean scale, drive export of organic matter from surface to deep ocean and sustain oxygenation of the planetary surface.

The Boring Billion, a slingshot for Complex Life on Earth

The period 1800 to 800 Ma (“Boring Billion”) is believed to mark a delay in the evolution of complex life, primarily due to low levels of oxygen in the atmosphere. Earlier studies highlight the remarkably flat C, Cr isotopes and low trace element trends during the so-called stasis, caused by prolonged nutrient, climatic, atmospheric and tectonic stability. In contrast, we suggest a first-order variability of bio-essential trace element availability in the oceans by combining systematic sampling of the Proterozoic rock record with sensitive geochemical analyses of marine pyrite by LA-ICP-MS technique. We also recall that several critical biological evolutionary events, such as the appearance of eukaryotes, origin of multicellularity & sexual reproduction, and the first major diversification of eukaryotes (crown group) occurred during this period. Therefore, it appears possible that the period of low nutrient trace elements (1800–1400 Ma) caused evolutionary pressures which became an essential trigger for promoting biological innovations in the eukaryotic domain. Later periods of stress-free conditions, with relatively high nutrient trace element concentration, facilitated diversification. We propose that the “Boring Billion” was a period of sequential stepwise evolution and diversification of complex eukaryotes, triggering evolutionary pathways that made possible the later rise of micro-metazoans and their macroscopic counterparts.

Dating phototrophic microbial lineages with reticulate gene histories

Phototrophic bacteria are among the most biogeochemically significant organisms on Earth and are physiologically related through the use of reaction centers to collect photons for energy metabolism. However, the major phototrophic lineages are not closely related to one another in bacterial phylogeny, and the origins of their respective photosynthetic machinery remain obscured by time and low sequence similarity. To better understand the co-evolution of Cyanobacteria and other ancient anoxygenic phototrophic lineages with respect to geologic time, we designed and implemented a variety of molecular clocks that use horizontal gene transfer (HGT) as additional, relative constraints. These HGT constraints improve the precision of phototroph divergence date estimates and indicate that stem green non-sulfur bacteria are likely the oldest phototrophic lineage. Concurrently, crown Cyanobacteria age estimates ranged from 2.2 Ga to 2.7 Ga, with stem Cyanobacteria diverging ~2.8 Ga. These estimates provide a several hundred Ma window for oxygenic photosynthesis to evolve prior to the Great Oxidation Event (GOE) ~2.3 Ga. In all models, crown green sulfur bacteria diversify after the loss of the banded iron formations from the sedimentary record (~1.8 Ga) and may indicate the expansion of the lineage into a new ecological niche following the GOE. Our date estimates also provide a timeline to investigate the temporal feasibility of different photosystem HGT events between phototrophic lineages. Using this approach, we infer that stem Cyanobacteria are unlikely to be the recipient of an HGT of photosystem I proteins from green sulfur bacteria but could still have been either the HGT donor or the recipient of photosystem II proteins with green non-sulfur bacteria, prior to the GOE. Together, these results indicate that HGT-constrained molecular clocks are useful tools for the evaluation of various geological and evolutionary hypotheses, using the evolutionary histories of both genes and organismal lineages.

Life: the first two billion years

Microfossils, stromatolites, preserved lipids and biologically informative isotopic ratios provide a substantial record of bacterial diversity and biogeochemical cycles in Proterozoic (2500-541 Ma) oceans that can be interpreted, at least broadly, in terms of present-day organisms and metabolic processes. Archean (more than 2500 Ma) sedimentary rocks add at least a billion years to the recorded history of life, with sedimentological and biogeochemical evidence for life at 3500 Ma, and possibly earlier; phylogenetic and functional details, however, are limited. Geochemistry provides a major constraint on early evolution, indicating that the first bacteria were shaped by anoxic environments, with distinct patterns of major and micronutrient availability. Archean rocks appear to record the Earth's first iron age, with reduced Fe as the principal electron donor for photosynthesis, oxidized Fe the most abundant terminal electron acceptor for respiration, and Fe a key cofactor in proteins. With the permanent oxygenation of the atmosphere and surface ocean ca 2400 Ma, photic zone O2 limited the access of photosynthetic bacteria to electron donors other than water, while expanding the inventory of oxidants available for respiration and chemoautotrophy. Thus, halfway through Earth history, the microbial underpinnings of modern marine ecosystems began to take shape.This article is part of the themed issue 'The new bacteriology'.

The Physiology of Phagocytosis in the Context of Mitochondrial Origin

How mitochondria came to reside within the cytosol of their host has been debated for 50 years. Though current data indicate that the last eukaryote common ancestor possessed mitochondria and was a complex cell, whether mitochondria or complexity came first in eukaryotic evolution is still discussed. In autogenous models (complexity first), the origin of phagocytosis poses the limiting step at eukaryote origin, with mitochondria coming late as an undigested growth substrate. In symbiosis-based models (mitochondria first), the host was an archaeon, and the origin of mitochondria was the limiting step at eukaryote origin, with mitochondria providing bacterial genes, ATP synthesis on internalized bioenergetic membranes, and mitochondrion-derived vesicles as the seed of the eukaryote endomembrane system. Metagenomic studies are uncovering new host-related archaeal lineages that are reported as complex or phagocytosing, although images of such cells are lacking. Here we review the physiology and components of phagocytosis in eukaryotes, critically inspecting the concept of a phagotrophic host. From ATP supply and demand, a mitochondrion-lacking phagotrophic archaeal fermenter would have to ingest about 34 times its body weight in prokaryotic prey to obtain enough ATP to support one cell division. It would lack chemiosmotic ATP synthesis at the plasma membrane, because phagocytosis and chemiosmosis in the same membrane are incompatible. It would have lived from amino acid fermentations, because prokaryotes are mainly protein. Its ATP yield would have been impaired relative to typical archaeal amino acid fermentations, which involve chemiosmosis. In contrast, phagocytosis would have had great physiological benefit for a mitochondrion-bearing cell.

The Trophic Role of Marine Microorganisms Through Time

Microorganisms (prokaryotes and protists) seldom fossilize, but they form much of the trophic structure in marine pelagic and benthic environments, chiefly as primary producers and secondary consumers. The fossil record of unskeletonized groups is meager or non-existent. Skeletonized groups have excellent records but represent a small portion of the total microbial diversity.

The evolution of trophic structures and roles of microorganisms can be reconstructed broadly for most of geologic history. When life first evolved, it had a trophic structure. The first microbial fossils appear to be benthic mats; these are abundant in the Precambrian but sparse later; body fossils are very rare. The Archean saw pelagic and benthic prokaryotes and possibly protists later on. Proterozoic trophic structures became increasingly complex as protists entered pelagic environments. Benthic assemblages likewise became complex, as prokaryotes and protists formed mats and stromatolites in many environments. At the end of the eon, animals appeared; microbial primary producers and predation on microorganisms and among animals fueled these assemblages. The fundamental trophic structures that developed then persisted with modification into modern times. Phanerozoic ecosystems became very complex as skeletonized animals and protists evolved. Among the important trophic developments in the Phanerozoic history of microorganisms were the early diversification of phytoplankton and siliceous micro-zooplankton (Cambrian), algal endosymbiosis with benthic metazoans (Cambrian to Recent) and rock-forming foraminifera (late Paleozoic to Recent), the radiation of pelagic skeletal primary producers and micro-zooplankton (mid-Mesozoic), and radiations in the deep sea, reefs, and shallow areas (Mesozoic and Cenozoic). Each evolutionary change increased trophic complexity by adding more species at each level, while episodic mass extinctions decreased species diversity and trophic complexity.

Marine trophic structures evolved over immense intervals of geologic time, growing complex and then suffering destruction at major extinction events. The effects of human impact on these structures should be examined, for without them, Earth may change dramatically.

The fossil record of early eukaryotic diversification

The Cambrian explosion can be thought of as the culmination of a diversification of eukaryotes that had begun several hundred million years before. Eukaryotes - one of the three domains of life — originated by late Archean time, and probably underwent a long period of stem group evolution during the Paleoproterozoic Era. A suite of taxonomically resolved body fossils and biomarkers, together with estimates of acritarch and compression fossil diversity, suggest that while divergences among major eukaryotic clades or 'super-groups' may have occurred as early as latest Paleoproterozoic through Mesoproterozoic time, the main phase of eukaryotic diversification took place several hundred million years later, during the middle Neoproterozoic Era. Hypotheses for Neoproterozoic diversification must therefore explain why eukaryotic diversification is delayed several hundred million years after the origin of the eukaryotic crown group, and why diversification appears to have occurred independently within several eukaryotic super-groups at the same time. Evolutionary explanations for eukaryotic diversification (the evolution of sex; the acquisition of plastids) fail to account for these patterns, but ecological explanations (the advent of microbial predators) and environmental explanations (changes in ocean chemistry) are both consistent with them. Both ecology and environment may have played a role in triggering or at least fueling Neoproterozoic eukaryotic diversification.

Origins and Early Evolution of Predation

Predation, in the broad sense of an organism killing another organism for nutritional purposes, is probably as old as life itself and has originated many times during the history of life. Although little of the beginnings is caught in the fossil record, observations in the rock record and theoretical considerations suggest that predation played a crucial role in some of the major transitions in evolution. The origin of eukaryotic cells, poorly constrained to about 2.7 Ga by geochemical evidence, was most likely the ultimate result of predation among prokaryotes. Multicellularity (or syncytiality), as a means of acquiring larger size, is visible in the fossil record soon after 2 Ga and is likely to have been mainly a response to selective pressure from predation among protists. The appearance of mobile predators on bacteria and protists may date back as far as 2 Ga or it may be not much older than the Cambrian explosion, or about 600 Ma. The combined indications from the decline of stromatolites and the diversification of acritarchs, however, suggest that such predation may have begun around 1 Ga. The Cambrian explosion, culminating around 550 Ma, represents the transition from simple, mostly microbial, ecosystems to ones with complex food webs and second- and higher-order consumers. Macrophagous predators were involved from the beginning, but it is not clear whether they originated in the plankton or in the benthos. Although predation was a decisive selective force in the Cambrian explosion, it was a shaper rather than a trigger of this evolutionary event.

Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae

The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n. gen, n. sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs. Another filamentous form, Denaricion mendax n. gen., n. sp., has coin-like cells reminiscent of those in large sulfur-oxidizing bacteria but much more recalcitrant than the liquid-vacuole-filled cells of the latter. There are also resemblances with oscillatoriacean cyanobacteria, although cell volumes in the latter are much smaller. The wider affinities of Denaricion are uncertain. Ramathallus lobatus n. gen., n. sp. is a lobate sessile alga with pseudoparenchymatous thallus, “cell fountains,” and apical growth, suggesting florideophycean affinity. If these inferences are correct, Rafatazmia and Ramathallus represent crown-group multicellular rhodophytes, antedating the oldest previously accepted red alga in the fossil record by about 400 million years.

The last common ancestor of modern eukaryotes is generally believed to have lived during the Mesoproterozoic era, about 1.6 to 1 billion years ago, or possibly somewhat earlier. We studied exquisitely preserved fossil communities from ~1.6 billion-year-old sedimentary rocks in central India representing a shallow-water marine environment characterized by photosynthetic biomats. We discovered amidst extensive cyanobacterial mats a biota of filamentous and lobate organisms that share significant features with modern eukaryotic algae, more specifically red algae. The rocks mainly consist of calcium and magnesium carbonates, but the microbial mats and the fossils are preserved in calcium phosphate, letting us view the cellular and subcellular structures in three dimensions with the use of synchrotron-radiation X-ray tomographic microscopy. The most conspicuous internal objects in the cells of the filamentous forms are rhomboidal platelets that we interpret to be part of the photosynthetic machinery of red algae. The lobate forms grew as radiating globular or finger-like protrusions from a common centre. These fossils predate the previously earliest accepted red algae by about 400 million years, suggesting that eukaryotes may have a longer history than commonly assumed.

Origin of a major infectious disease in vertebrates: The timing of Cryptosporidium evolution and its hosts

Protozoan parasites of the genus Cryptosporidium infect all vertebrate groups and display some host specificity in their infections. It is therefore possible to assume that Cryptosporidium parasites evolved intimately aside with vertebrate lineages. Here we propose a scenario of Cryptosporidium–Vertebrata coevolution testing the hypothesis that the origin of Cryptosporidium parasites follows that of the origin of modern vertebrates. We use calibrated molecular clocks and cophylogeny analyses to provide and compare age estimates and patterns of association between these clades. Our study provides strong support for the evolution of parasitism of Cryptosporidium with the rise of the vertebrates about 600 million years ago (Mya). Interestingly, periods of increased diversification in Cryptosporidium coincides with diversification of crown mammalian and avian orders after the Cretaceous-Palaeogene (K-Pg) boundary, suggesting that adaptive radiation to new mammalian and avian hosts triggered the diversification of this parasite lineage. Despite evidence for ongoing host shifts we also found significant correlation between protozoan parasites and vertebrate hosts trees in the cophylogenetic analysis. These results help us to understand the underlying macroevolutionary mechanisms driving evolution in Cryptosporidium and may have important implications for the ecology, dynamics and epidemiology of cryptosporidiosis disease in humans and other animals.

ER fatalities-The role of ER-mitochondrial contact sites in yeast life and death decisions

Following extracellular stress signals, all eukaryotic cells choose whether to elicit a pro-survival or pro-death response. The decision over which path to take is governed by the severity and duration of the damage. In response to mild stress, pro-survival programs are initiated (unfolded protein response, autophagy, mitophagy) whereas severe or chronic stress forces the cell to abandon these adaptive programs and shift towards regulated cell death to remove irreversibly damaged cells. Both pro-survival and pro-death programs involve regulated communication between the endoplasmic reticulum (ER) and mitochondria. In yeast, recent data suggest this inter-organelle contact is facilitated by the endoplasmic reticulum mitochondria encounter structure (ERMES). These membrane contacts are not only important for the exchange of cellular signals, but also play a role in mitochondrial tethering during mitophagy, mitochondrial fission and mitochondrial inheritance. This review focuses on recent findings in yeast that shed light on how ER-mitochondrial communication mediates critical cell fate decisions.

Gene expression analysis at the onset of sex differentiation in turbot (Scophthalmus maximus)

BACKGROUND

Controlling sex ratios is essential for the aquaculture industry, especially in those species with sex dimorphism for relevant productive traits, hence the importance of knowing how the sexual phenotype is established in fish. Turbot, a very important fish for the aquaculture industry in Europe, shows one of the largest sexual growth dimorphisms amongst marine cultured species, being all-female stocks a desirable goal for the industry. Although important knowledge has been achieved on the genetic basis of sex determination (SD) in this species, the master SD gene remains unknown and precise information on gene expression at the critical stage of sex differentiation is lacking. In the present work, we examined the expression profiles of 29 relevant genes related to sex differentiation, from 60 up to 135 days post fertilization (dpf), when gonads are differentiating. We also considered the influence of three temperature regimes on sex differentiation.

RESULTS

The first sex-related differences in molecular markers could be observed at 90 days post fertilization (dpf) and so we have called that time the onset of sex differentiation. Three genes were the first to show differential expression between males and females and also allowed us to sex turbot accurately at the onset of sex differentiation (90 dpf): cyp19a1a, amh and vasa. The expression of genes related to primordial germ cells (vasa, gsdf, tdrd1) started to increase between 75-90 dpf and vasa and tdrd1 later presented higher expression in females (90-105 dpf). Two genes placed on the SD region of turbot (sox2, fxr1) did not show any expression pattern suggestive of a sex determining function. We also detected changes in the expression levels of several genes (ctnnb1, cyp11a, dmrt2 or sox6) depending on culture temperature.

CONCLUSION

Our results enabled us to identify the first sex-associated genetic cues (cyp19a1a, vasa and amh) at the initial stages of gonad development in turbot (90 dpf) and to accurately sex turbot at this age, establishing the correspondence between gene expression profiles and histological sex. Furthermore, we profiled several genes involved in sex differentiation and found specific temperature effects on their expression.

Biosignatures on Mars: What, Where, and How? Implications for the Search for Martian Life

The search for traces of life is one of the principal objectives of Mars exploration. Central to this objective is the concept of habitability, the set of conditions that allows the appearance of life and successful establishment of microorganisms in any one location. While environmental conditions may have been conducive to the appearance of life early in martian history, habitable conditions were always heterogeneous on a spatial scale and in a geological time frame. This "punctuated" scenario of habitability would have had important consequences for the evolution of martian life, as well as for the presence and preservation of traces of life at a specific landing site. We hypothesize that, given the lack of long-term, continuous habitability, if martian life developed, it was (and may still be) chemotrophic and anaerobic. Obtaining nutrition from the same kinds of sources as early terrestrial chemotrophic life and living in the same kinds of environments, the fossilized traces of the latter serve as useful proxies for understanding the potential distribution of martian chemotrophs and their fossilized traces. Thus, comparison with analog, anaerobic, volcanic terrestrial environments (Early Archean >3.5-3.33 Ga) shows that the fossil remains of chemotrophs in such environments were common, although sparsely distributed, except in the vicinity of hydrothermal activity where nutrients were readily available. Moreover, the traces of these kinds of microorganisms can be well preserved, provided that they are rapidly mineralized and that the sediments in which they occur are rapidly cemented. We evaluate the biogenicity of these signatures by comparing them to possible abiotic features. Finally, we discuss the implications of different scenarios for life on Mars for detection by in situ exploration, ranging from its non-appearance, through preserved traces of life, to the presence of living microorganisms.

KEY WORDS

Mars-Early Earth-Anaerobic chemotrophs-Biosignatures-Astrobiology missions to Mars.

The neomuran revolution and phagotrophic origin of eukaryotes and cilia in the light of intracellular coevolution and a revised tree of life

Three kinds of cells exist with increasingly complex membrane-protein targeting: Unibacteria (Archaebacteria, Posibacteria) with one cytoplasmic membrane (CM); Negibacteria with a two-membrane envelope (inner CM; outer membrane [OM]); eukaryotes with a plasma membrane and topologically distinct endomembranes and peroxisomes. I combine evidence from multigene trees, palaeontology, and cell biology to show that eukaryotes and archaebacteria are sisters, forming the clade neomura that evolved ~1.2 Gy ago from a posibacterium, whose DNA segregation and cell division were destabilized by murein wall loss and rescued by the evolving novel neomuran endoskeleton, histones, cytokinesis, and glycoproteins. Phagotrophy then induced coevolving serial major changes making eukaryote cells, culminating in two dissimilar cilia via a novel gliding-fishing-swimming scenario. I transfer Chloroflexi to Posibacteria, root the universal tree between them and Heliobacteria, and argue that Negibacteria are a clade whose OM, evolving in a green posibacterium, was never lost.

Redox heterogeneity of subsurface waters in the Mesoproterozoic ocean

A substantial body of evidence suggests that subsurface water masses in mid-Proterozoic marine basins were commonly anoxic, either euxinic (sulfidic) or ferruginous (free ferrous iron). To further document redox variations during this interval, a multiproxy geochemical and paleobiological investigation was conducted on the approximately 1000-m-thick Mesoproterozoic (Lower Riphean) Arlan Member of the Kaltasy Formation, central Russia. Iron speciation geochemistry, supported by organic geochemistry, redox-sensitive trace element abundances, and pyrite sulfur isotope values, indicates that basinal calcareous shales of the Arlan Member were deposited beneath an oxygenated water column, and consistent with this interpretation, eukaryotic microfossils are abundant in basinal facies. The Rhenium-Osmium (Re-Os) systematics of the Arlan shales yield depositional ages of 1414±40 and 1427±43 Ma for two horizons near the base of the succession, consistent with previously proposed correlations. The presence of free oxygen in a basinal environment adds an important end member to Proterozoic redox heterogeneity, requiring an explanation in light of previous data from time-equivalent basins. Very low total organic carbon contents in the Arlan Member are perhaps the key--oxic deep waters are more likely (under any level of atmospheric O2) in oligotrophic systems with low export production. Documentation of a full range of redox heterogeneity in subsurface waters and the existence of local redox controls indicate that no single stratigraphic section or basin can adequately capture both the mean redox profile of Proterozoic oceans and its variance at any given point in time.

Of early animals, anaerobic mitochondria, and a modern sponge

The origin and early evolution of animals marks an important event in life's history. This event is historically associated with an important variable in Earth history - oxygen. One view has it that an increase in oceanic oxygen levels at the end of the Neoproterozoic Era (roughly 600 million years ago) allowed animals to become large and leave fossils. How important was oxygen for the process of early animal evolution? New data show that some modern sponges can survive for several weeks at low oxygen levels. Many groups of animals have mechanisms to cope with low oxygen or anoxia, and very often, mitochondria - organelles usually associated with oxygen - are involved in anaerobic energy metabolism in animals. It is a good time to refresh our memory about the anaerobic capacities of mitochondria in modern animals and how that might relate to the ecology of early metazoans.