The effects of marine eukaryote evolution on phosphorus, carbon and oxygen cycling across the Proterozoic-Phanerozoic transition

Divergence time estimates for the hypoxia-inducible factor-1 alpha (HIF1α) reveal an ancient emergence of animals in low-oxygen environments

Unveiling the tempo and mode of animal evolution is necessary to understand the links between environmental changes and biological innovation. Although the earliest unambiguous metazoan fossils date to the late Ediacaran period, molecular clock estimates agree that the last common ancestor (LCA) of all extant animals emerged ~850 Ma, in the Tonian period, before the oldest evidence for widespread ocean oxygenation at ~635-560 Ma in the Ediacaran period. Metazoans are aerobic organisms, that is, they are dependent on oxygen to survive. In low-oxygen conditions, most animals have an evolutionarily conserved pathway for maintaining oxygen homeostasis that triggers physiological changes in gene expression via the hypoxia-inducible factor (HIFa). However, here we confirm the absence of the characteristic HIFa protein domain responsible for the oxygen sensing of HIFa in sponges and ctenophores, indicating the LCA of metazoans lacked the functional protein domain as well, and so could have maintained their transcription levels unaltered under the very low-oxygen concentrations of their environments. Using Bayesian relaxed molecular clock dating, we inferred that the ancestral gene lineage responsible for HIFa arose in the Mesoproterozoic Era, ~1273 Ma (Credibility Interval 957-1621 Ma), consistent with the idea that important genetic machinery associated with animals evolved much earlier than the LCA of animals. Our data suggest at least two duplication events in the evolutionary history of HIFa, which generated three vertebrate paralogs, products of the two successive whole-genome duplications that occurred in the vertebrate LCA. Overall, our results support the hypothesis of a pre-Tonian emergence of metazoans under low-oxygen conditions, and an increase in oxygen response elements during animal evolution.

Natural ocean iron fertilization and climate variability over geological periods

Marine primary producers are largely dependent on and shape the Earth's climate, although their relationship with climate varies over space and time. The growth of phytoplankton and associated marine primary productivity in most of the modern global ocean is limited by the supply of nutrients, including the micronutrient iron. The addition of iron via episodic and frequent events drives the biological carbon pump and promotes the sequestration of atmospheric carbon dioxide (CO2 ) into the ocean. However, the dependence between iron and marine primary producers adaptively changes over different geological periods due to the variation in global climate and environment. In this review, we examined the role and importance of iron in modulating marine primary production during some specific geological periods, that is, the Great Oxidation Event (GOE) during the Huronian glaciation, the Snowball Earth Event during the Cryogenian, the glacial-interglacial cycles during the Pleistocene, and the period from the last glacial maximum to the late Holocene. Only the change trend of iron bioavailability and climate in the glacial-interglacial cycles is consistent with the Iron Hypothesis. During the GOE and the Snowball Earth periods, although the bioavailability of iron in the ocean and the climate changed dramatically, the changing trend of many factors contradicted the Iron Hypothesis. By detangling the relationship among marine primary productivity, iron availability and oceanic environments in different geological periods, this review can offer some new insights for evaluating the impact of ocean iron fertilization on removing CO2 from the atmosphere and regulating the climate.

The origin and early evolution of plants

Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).

A largely invariant marine dissolved organic carbon reservoir across Earth's history

Marine dissolved organic carbon (DOC), the largest pool of reduced carbon in the oceans, plays an important role in the global carbon cycle and contributes to the regulation of atmospheric oxygen and carbon dioxide abundances. Despite its importance in global biogeochemical cycles, the long-term history of the marine DOC reservoir is poorly constrained. Nonetheless, significant changes to the size of the oceanic DOC reservoir through Earth's history have been commonly invoked to explain changes to ocean chemistry, carbon cycling, and marine ecology. Here, we present a revised view of the evolution of marine DOC concentrations using a mechanistic carbon cycle model that can reproduce DOC concentrations in both oxic and anoxic modern environments. We use this model to demonstrate that the overall size of the marine DOC reservoir has likely undergone very little variation through Earth's history, despite major changes in the redox state of the ocean-atmosphere system and the nature and efficiency of the biological carbon pump. A relatively static marine DOC reservoir across Earth's history renders it unlikely that major changes in marine DOC concentrations have been responsible for driving massive repartitioning of surface carbon or the large carbon isotope excursions observed in Earth's stratigraphic record and casts doubt on previously hypothesized links between marine DOC levels and the emergence and radiation of early animals.

Phosphatic scales in vase-shaped microfossil assemblages from Death Valley, Grand Canyon, Tasmania, and Svalbard

Although biomineralized skeletal elements dominate the Phanerozoic fossil record, they did not become common until ~550-520 Ma when independent acquisitions of biomineralization appeared in multiple lineages of animals and a few protists (single-celled eukaryotes). Evidence of biomineralization preceding the late Ediacaran is spotty aside from the apatitic scale microfossils of the ~811 Ma Fifteenmile Group, northwestern Canada. Here, we describe scale-shaped microfossils from four vase-shaped microfossil (VSM)-bearing units of later Tonian age: the Togari Group of Tasmania, Chuar and Pahrump groups of southwestern United States, and the Roaldtoppen Group of Svalbard. These scale-shaped microfossils consist of thin, ~13 micron-long plates typically surrounded by a 1-3 micron-thick colorless envelope; they are found singly and in heterotypic and monotypic clusters of a few to >20 specimens. Raman spectroscopy and confocal laser scanning microscopy indicate these microfossils are composed of apatite and kerogen, just as is seen in the Fifteenmile Group scale microfossils. Despite compositional similarity, however, these scales are probably not homologous, representing instead, an independent acquisition of apatite mineralization. We propose that these apatite-kerogen scale-shaped microfossils are skeletal elements of a protistan cell. In particular, their consistent co-occurrence with VSMs, and similarities with scales of arcellinid testate amoebae, a group to which the VSMs are thought to belong, suggest the possibility that these microfossils may be test-forming scales of ancient arcellinid testate amoebae. The apparent apatite biomineralization in both these microfossils and the Fifteenmile scales is unexpected given its exceedingly rare use in skeletons of modern protists. This modern absence is attributed to the extravagance of using a limiting nutrient in a structural element, but multiple occurrences of apatite biomineralization in the Tonian suggest that phosphorus was not a limiting nutrient for these organisms, a suggestion consistent with the idea that dissolved seawater phosphate concentrations may have been higher at this time.

The origin of phagocytosis in Earth history

Phagocytosis, or 'cell eating', is a eukaryote-specific process where particulate matter is engulfed via invaginations of the plasma membrane. The origin of phagocytosis has been central to discussions on eukaryogenesis for decades-, where it is argued as being either a prerequisite for, or consequence of, the acquisition of the ancestral mitochondrion. Recently, genomic and cytological evidence has increasingly supported the view that the pre-mitochondrial host cell-a bona fide archaeon branching within the 'Asgard' archaea-was incapable of phagocytosis and used alternative mechanisms to incorporate the alphaproteobacterial ancestor of mitochondria. Indeed, the diversity and variability of proteins associated with phagosomes across the eukaryotic tree suggest that phagocytosis, as seen in a variety of extant eukaryotes, may have evolved independently several times within the eukaryotic crown-group. Since phagocytosis is critical to the functioning of modern marine food webs (without it, there would be no microbial loop or animal life), multiple late origins of phagocytosis could help explain why many of the ecological and evolutionary innovations of the Neoproterozoic Era (e.g. the advent of eukaryotic biomineralization, the 'Rise of Algae' and the origin of animals) happened when they did.

On the use of models in understanding the rise of complex life

Recently, several seemingly irreconcilably different models have been proposed for relationships between Earth system processes and the rise of complex life. These models provide very different scenarios of Proterozoic atmospheric oxygen and ocean nutrient levels, whether they constrained complex life, and of how the rise of complex life affected biogeochemical conditions. For non-modellers, it can be hard to evaluate which-if any-of the models and their results have more credence-hence this article. I briefly review relevant hypotheses, how models are being used to incarnate and sometimes test those hypotheses, and key principles of biogeochemical cycling models should embody. Then I critically review the use of biogeochemical models in: inferring key variables from proxies; reconstructing ancient biogeochemical cycling; and examining how complex life affected biogeochemical cycling. Problems are found in published model results purporting to demonstrate long-term stable states of very low Proterozoic atmospheric pO2 and ocean P levels. I explain what they stem from and highlight key empirical uncertainties that need to be resolved. Then I suggest how models and data can be better combined to advance our scientific understanding of the relationship between Earth system processes and the rise of complex life.

The influence of environmental setting on the community ecology of Ediacaran organisms

The broad-scale environment plays a substantial role in shaping modern marine ecosystems, but the degree to which palaeocommunities were influenced by their environment is unclear. To investigate how broad-scale environment influenced the community ecology of early animal ecosystems, we employed spatial point process analyses (SPPA) to examine the community structure of seven late Ediacaran (558-550 Ma) bedding-plane assemblages drawn from a range of environmental settings and global localities. The studied palaeocommunities exhibit marked differences in the response of their component taxa to sub-metre-scale habitat heterogeneities on the seafloor. Shallow-marine (nearshore) palaeocommunities were heavily influenced by local habitat heterogeneities, in contrast to their deeper-water counterparts. The local patchiness within shallow-water communities may have been further accentuated by the presence of grazers and detritivores, whose behaviours potentially initiated a propagation of increasing habitat heterogeneity of benthic communities from shallow to deep-marine depositional environments. Higher species richness in shallow-water Ediacaran assemblages compared to deep-water counterparts across the studied time-interval could have been driven by this environmental patchiness, because habitat heterogeneities increase species richness in modern marine environments. Our results provide quantitative support for the 'Savannah' hypothesis for early animal diversification-whereby Ediacaran diversification was driven by patchiness in the local benthic environment.

Food sources for the Ediacara biota communities

The Ediacara biota represents the first complex macroscopic organisms in the geological record, foreshadowing the radiation of eumetazoan animals in the Cambrian explosion. However, little is known about the contingencies that lead to their emergence, including the possible roles of nutrient availability and the quality of food sources. Here we present information on primary producers in the Ediacaran based on biomarker molecules that were extracted from sediments hosting Ediacaran macrofossils. High relative abundances of algal steranes over bacterial hopanes suggest that the Ediacara biota inhabited nutrient replete environments with an abundance of algal food sources comparable to Phanerozoic ecosystems. Thus, organisms of the Ediacara biota inhabited nutrient-rich environments akin to those that later fuelled the Cambrian explosion.

Stepwise Earth oxygenation is an inherent property of global biogeochemical cycling

Oxygenation of Earth's atmosphere and oceans occurred across three major steps during the Paleoproterozoic, Neoproterozoic, and Paleozoic eras, with each increase having profound consequences for the biosphere. Biological or tectonic revolutions have been proposed to explain each of these stepwise increases in oxygen, but the principal driver of each event remains unclear. Here we show, using a theoretical model, that the observed oxygenation steps are a simple consequence of internal feedbacks in the long-term biogeochemical cycles of carbon, oxygen, and phosphorus, and that there is no requirement for a specific stepwise external forcing to explain the course of Earth surface oxygenation. We conclude that Earth's oxygenation events are entirely consistent with gradual oxygenation of the planetary surface after the evolution of oxygenic photosynthesis.

Bisnorgammacerane traces predatory pressure and the persistent rise of algal ecosystems after Snowball Earth

Eukaryotic algae rose to ecological relevance after the Neoproterozoic Snowball Earth glaciations, but the causes for this consequential evolutionary transition remain enigmatic. Cap carbonates were globally deposited directly after these glaciations, but they are usually organic barren or thermally overprinted. Here we show that uniquely-preserved cap dolostones of the Araras Group contain exceptional abundances of a newly identified biomarker: 25,28-bisnorgammacerane. Its secular occurrence, carbon isotope systematics and co-occurrence with other demethylated terpenoids suggest a mechanistic connection to extensive microbial degradation of ciliate-derived biomass in bacterially dominated ecosystems. Declining 25,28-bisnorgammacerane concentrations, and a parallel rise of steranes over hopanes, indicate the transition from a bacterial to eukaryotic dominated ecosystem after the Marinoan deglaciation. Nutrient levels already increased during the Cryogenian and were a prerequisite, but not the ultimate driver for the algal rise. Intense predatory pressure by bacterivorous protists may have irrevocably cleared self-sustaining cyanobacterial ecosystems, thereby creating the ecological opportunity that allowed for the persistent rise of eukaryotic algae to global importance.

Early Earth and the rise of complex life

The history of life on Earth progressed in parallel with the evolving oxygen state of the atmosphere and oceans, but the details of that relationship remain poorly known and debated. There is, however, general agreement that the first appreciable and persistent accumulation of oxygen in the oceans and atmosphere occurred around 2.3 to 2.4 billion years ago. Following this Great Oxidation Event, biospheric oxygen remained at relatively stable intermediate levels for more than a billion years. Much current research focuses on the transition from the intermediate conditions of this middle chapter in Earth history to the more oxygenated periods that followed - often emphasizing whether increasing and perhaps episodic oxygenation drove fundamental steps in the evolution of complex life and, if so, when. These relationships among early organisms and their environments are the thematic threads that stitch together the papers in this collection. Expert authors bring a mix of methods and opinions to their leading-edge reviews of the earliest proliferation and ecological impacts of eukaryotic life, the subsequent emergence and ecological divergence of animals, and the corresponding causes and consequences of environmental change.