Did surface temperatures constrain microbial evolution?

The proposition that glaciation may not have occurred before the Cenozoic--albeit not yet a consensus position--nevertheless raises for reconsideration the surface temperature history of the earth. Glacial episodes, from the Huronian (2.3 billion years ago; BYA) through the late Paleozoic (320 to 250 million years ago; MYA) have been critical constraints on estimation of the upper bounds of temperature (Crowley 1983, Kasting and Toon 1989). Once removed, few if any constraints on the upper temperature limit other than life remain. Walker (1982) recognized that life provides an upper limit to temperature in the Precambrian. We propose a more radical concept: the upper temperature limit for viable growth of a given microbial group corresponds to the actual surface temperature at the time of the group's first appearance. In particular, we propose here that two major evolutionary developments--the emergence of cyanobacteria and aerobic eukaryotes--can be used to determine surface temperature in the Precambrian, and that only subsequent cooling mediated by higher plants and then angiosperms permitted what may possibly be the earth's first glaciation in the late Cenozoic.     

Is something wrong with the tree of life?

A recent study⁽¹⁾ of sequence data from many different proteins has suggested that contemporary prokaryotes and eukaryotes may have shared a common ancestor as recently as 2 billion years ago (the molecular clock). Strong evidence from the geological record, however, indicates that oxygen-producing microorganisms, perhaps similar to modern cyanobacteria, existed 3.5 billion years ago. The fossil evidence, therefore, suggests that any common ancestor of prokaryotes and eukaryotes must have existed at least 1.5 billion years earlier than suggested by the molecular clock evidence. The discrepancy between molecular and geological evidence for the age of modern cells is considered here, as are aspects of gene descent in the tree of life that might help to account for it.     

The history of atmospheric oxygen

A primeval anoxygenic terrestrial atmosphere having been postulated on astronomical grounds, experiments using simulated conditions have shown that the formation of organic molecules by abiogenic processes with proceed freely in such an environment.Atmospheric oxygen will at first be limited to 0.001 PAL through the Urey mechanism which inhibits further dissociation of water above this level. All atmospheric oxygen exceeding this level must be biogenic and produced by photosynthesis. Molecular fossils prove its existence 2.7 billion years ago. Sedimentary ores, notably pyrite sands of gold-uranium reefs and banded iron formations, attest to the existence of an atmosphere with little oxygen up to 1.8 billion years ago. Geochemistry does not, howerver, supply us with data as to the level of oxygen at that time. The Pasteur Point, on the other hand, at which microbes change from fermentation to respiration and vice versa, is a powerful regulating factor situated at 0.01 PAL of free oxygen.It is postulated that the primeval atmosphere of Lower and Middle Precambrian was limited to this level of free oxygen. At this level pre-life — the formation of organic compounds through inorganic processes — still exists. Pre-life and early life therefore were coexistent for two billion years at least, and were able to influence each, other over all this time. The primeval, atmosphere was definitely superseded by an oxygenic one about 1.45 billion years ago, but the level of 0.1 PAL of free oxygen was only reached during the Ordovician, 0.4–0.5 billion years ago.     

Circadian biology: a 2.5 billion year old clock

A recent study suggests that circadian clocks may have evolved at the time of the Great Oxidation Event 2.5 billion years ago in order to drive detoxification of reactive oxygen species.     

Extraterrestrial Flux of Potentially Prebiotic C, N, and P to the Early Earth

With growing evidence for a heavy bombardment period ending 4–3.8 billion years ago, meteorites and comets may have been an important source of prebiotic carbon, nitrogen, and phosphorus on the early Earth. Life may have originated shortly after the late-heavy bombardment, when concentrations of organic compounds and reactive phosphorus were enough to “kick life into gear”. This work quantifies the sources of potentially prebiotic, extraterrestrial C, N, and P and correlates these fluxes with a comparison to total Ir fluxes, and estimates the effect of atmosphere on the survival of material. We find (1) that carbonaceous chondrites were not a good source of organic compounds, but interplanetary dust particles provided a constant, steady flux of organic compounds to the surface of the Earth, (2) extraterrestrial metallic material was much more abundant on the early Earth, and delivered reactive P in the form of phosphide minerals to the Earth’s surface, and (3) large impacts provided substantial local enrichments of potentially prebiotic reagents. These results help elucidate the potential role of extraterrestrial matter in the origin of life.     

A trophic framework for animal origins

Metazoans emerged in a microbial world and play a unique role in the biosphere as the only complex multicellular eukaryotes capable of phagocytosis. While the bodyplan and feeding mode of the last common metazoan ancestor remain unresolved, the earliest multicellular stem‐metazoans likely subsisted on picoplankton (planktonic microbes 0.2–2 μm in diameter) and dissolved organic matter (DOM), similarly to modern sponges. Once multicellular stem‐metazoans emerged, they conceivably modulated both the local availability of picoplankton, which they preferentially removed from the water column for feeding, and detrital particles 2–100 μm in diameter, which they expelled and deposited into the benthos as waste products. By influencing the availability of these heterotrophic food sources, the earliest multicellular stem‐metazoans would have acted as ecosystem engineers, helping create the ecological conditions under which other metazoans, namely detritivores and non‐sponge suspension feeders incapable of subsisting on picoplankton and DOM, could emerge and diversify. This early style of metazoan feeding, specifically the phagocytosis of small eukaryotic prey, could have also encouraged the evolution of larger, even multicellular, eukaryotic forms less prone to metazoan consumption. Therefore, the first multicellular stem‐metazoans, through their feeding, arguably helped bridge the strictly microbial food webs of the Proterozoic Eon (2.5–0.541 billion years ago) to the more macroscopic, metazoan‐sustaining food webs of the Phanerozoic Eon (0.541–0 billion years ago).     

Proterozoic history and present state of cyanobacteria

The paper delves into the main regularities of the distribution of fossil microorganisms in Precambrian rocks, beginning from the Archean Eon about 3.5 billion years ago and ending in the Cambrian Period about 0.5 billion years ago. The paper analyzes facial peculiarities in the lateral differentiation of microfossils in Proterozoic basins and the main stages of temporal changes in fossil cyanobacterial communities, which are based on the irreversible succession of physicochemical conditions on the Earth and the evolution of eukaryotic microorganisms and their incorporation into prokaryotic ecosystems. To gain insight into Proterozoic fossil records, modern stratified cyanobacterial mats built up from layers of prokaryotes are considered. The analysis of phosphatization, carbonatization, and silification processes in modern algal-bacterial communities suggests that analogous processes took place in Proterozoic microbiotas. A comparison of modern and Precambrian living forms confirms the inference that cyanobacterial communities are very conservative and have changed insignificantly both morphologically and physiologically during the past two billion years.     

The Proterozoic History and Present State of Cyanobacteria

The paper delves into the main regularities of the distribution of fossil microorganisms in Precambrian rocks, beginning from the Archean Eon about 3.5 billion years ago and ending in the Cambrian Period about 0.5 billion years ago. The paper analyzes facial peculiarities in the lateral differentiation of microfossils in Proterozoic basins and the main stages of temporal changes in fossil cyanobacterial communities, which are based on the irreversible succession of physicochemical conditions on the Earth and the evolution of eukaryotic microorganisms and their incorporation into prokaryotic ecosystems. To gain insight into Proterozoic fossil record, modern stratified cyanobacterial mats built up from layers of prokaryotes are considered. The analysis of phosphatization, carbonatization, and silification processes in modern algal–bacterial communities suggests that analogous processes took place in Proterozoic microbiotas. A comparison of modern and Precambrian living forms confirms the inference that cyanobacterial communities are very conservative and have changed insignificantly both morphologically and physiologically during the past two billion years.     

Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision

For almost a decade now, a team of molecular evolutionists has produced a plethora of seemingly precise molecular clock estimates for divergence events ranging from the speciation of cats and dogs to lineage separations that might have occurred approximately 4 billion years ago. Because the appearance of accuracy has an irresistible allure, non-specialists frequently treat these estimates as factual. In this article, we show that all of these divergence-time estimates were generated through improper methodology on the basis of a single calibration point that has been unjustly denuded of error. The illusion of precision was achieved mainly through the conversion of statistical estimates (which by definition possess standard errors, ranges and confidence intervals) into errorless numbers. By employing such techniques successively, the time estimates of even the most ancient divergence events were made to look deceptively precise. For example, on the basis of just 15 genes, the arthropod-nematode divergence event was 'calculated' to have occurred 1167+/-83 million years ago (i.e. within a 95% confidence interval of approximately 350 million years). Were calibration and derivation uncertainties taken into proper consideration, the 95% confidence interval would have turned out to be at least 40 times larger ( approximately 14.2 billion years).     

The importance of prebiotic chemistry in the RNA world

In vitro selection experiments have clearly demonstrated that RNA can perform many of the functions necessary to support an RNA world. Moreover, it appears that novel functions could have readily evolved from existing functional RNA molecules. Therefore, diverse molecular ecosystems could potentially have arisen from an initial, small population of functional replicators. These findings suggest that the sequences of living systems may have been determined in part by chance occurrences at origins. Any extrapolations linking sequences (as opposed to functions) obtained in the laboratory to what may have occurred ca. 4 billion years ago are tenuous at best. Thus, perhaps the best way to understand origins is not by examining relatively unconstrained sequence information, but by examining the inherent constraints imposed by prebiotic chemistry.     

Evolutionary History of the Enzymes Involved in the Calvin–Benson Cycle in Euglenids

Euglenids are an ancient lineage that may have existed as early as 2 billion years ago. A mere 65 years ago, Melvin Calvin and Andrew A. Benson performed experiments on Euglena gracilis and elucidated the series of reactions by which carbon was fixed and reduced during photosynthesis. However, the evolutionary history of this pathway (Calvin–Benson cycle) in euglenids was more complex than Calvin and Benson could have imagined. The chloroplast present today in euglenophytes arose from a secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga. A long period of evolutionary time existed before this secondary endosymbiotic event took place, which allowed for other endosymbiotic events or gene transfers to occur prior to the establishment of the green chloroplast. This research revealed the evolutionary history of the major enzymes of the Calvin–Benson cycle throughout the euglenid lineage and showed that the majority of genes for Calvin–Benson cycle enzymes shared an ancestry with red algae and/or chromophytes suggesting they may have been transferred to the nucleus prior to the acquisition of the green chloroplast.     

The rise and fall of the RNA world.

It is generally believed that there was a time when life on earth was based on RNA rather than on DNA and protein. Considering the relevant evidence from geophysics, geology, paleobiology, and molecular biology, it is possible to set the time frame for the existence of RNA-based life to a 400 million year interval beginning 4.0 to 4.2 billion years ago and ending 3.6 to 3.8 billion years ago. The minimum level of biochemical complexity that existed during this time consists of those functions necessary for the establishment and maintenance of an RNA-based evolving system, namely, an RNA unwinding activity, an RNA replicase activity, and a primitive biosynthetic apparatus leading to enrichment of the local environment with activated D mononucleotides.     

Clock gene evolution and functional divergence

In considering the impact of the earth's changing geophysical conditions during the history of life, it is surprising to learn that the earth's rotational period may have been as short as 4 h, as recently as 1900 million years ago (or 1.9 billion years ago). The implications of such figures for the origin and evolution of clocks are considerable, and the authors speculate on how this short rotational period might have influenced the development of the "protoclock" in early microorganisms, such as the Cyanobacteria, during the geological periodsin which they arose and flourished. They then discuss the subsequent duplication of clock genes that took place around and after the Cambrian period, 543 million years ago, and its consequences. They compare the relative divergences of the canonical clock genes, which reveal the Per family to be the most rapidly evolving. In addition, the authors use a statistical test to predict which residues within the PER and CRY families may have undergone functional specialization.     

Viruses, masters at downsizing

Viruses are the smallest fruits on the tree of life. Dwarfed by their bacterial and cellular hosts, viruses and their close relatives have long been considered the smallest microbes. The genome of a virus may contain no more than three thousand nucleotides, compared to the three billion base pairs in human genomes. (Lest we feel superior, though, the genomes of some other organisms are much larger than our own.).     

Evolution of the cellular communication syste

We discuss the problem of the evolution of the cellular communication system from the RNA world to progenote to the modern cell. Our method analyses syntactical structure of molecular fossils in the non-coding regions of DNA within the information-processing gene model developed earlier. We concluded that sequence-specific binding is an ancient communication process with its origin in the RNA world. Moreover, we illustrate our viewpoint using four evolution snapshots from the first RNA segments, some 4.1 billion years ago, to the first cell, 3.8 billion years ago.     

Crown group Oxyphotobacteria postdate the rise of oxygen

The rise of oxygen ca. 2.3 billion years ago (Ga) is the most distinct environmental transition in Earth history. This event was enabled by the evolution of oxygenic photosynthesis in the ancestors of Cyanobacteria. However, long‐standing questions concern the evolutionary timing of this metabolism, with conflicting answers spanning more than one billion years. Recently, knowledge of the Cyanobacteria phylum has expanded with the discovery of non‐photosynthetic members, including a closely related sister group termed Melainabacteria, with the known oxygenic phototrophs restricted to a clade recently designated Oxyphotobacteria. By integrating genomic data from the Melainabacteria, cross‐calibrated Bayesian relaxed molecular clock analyses show that crown group Oxyphotobacteria evolved ca. 2.0 billion years ago (Ga), well after the rise of atmospheric dioxygen. We further estimate the divergence between Oxyphotobacteria and Melainabacteria ca. 2.5–2.6 Ga, which—if oxygenic photosynthesis is an evolutionary synapomorphy of the Oxyphotobacteria—marks an upper limit for the origin of oxygenic photosynthesis. Together, these results are consistent with the hypothesis that oxygenic photosynthesis evolved relatively close in time to the rise of oxygen.     

Increased frequency of cysteine,tyrosine, and phenylalanine residues since the last universal ancestor

Analysis of extant proteomes has the potential of revealing how amino acid frequencies within proteins have evolved over biological time. Evidence is presented here that cysteine, tyrosine, and phenylalanine residues have substantially increased in frequency since the three primary lineages diverged more than three billion years ago. This inference was derived from a comparison of amino acid frequencies within conserved and non-conserved residues of a set of proteins dating to the last universal ancestor in the face of empirical knowledge of the relative mutability of these amino acids. The under-representation of these amino acids within last universal ancestor proteins relative to their modern descendants suggests their late introduction into the genetic code. Thus, it appears that extant ancient proteins contain evidence pertaining to early events in the formation of biological systems.     

Molecular cloning of the beta-subunit of the Na,K-ATPase in the brine shrimp, Artemia. The cDNA-derived amino acid sequence shows low homology with the beta-subunits of vertebrates except in the single transmembrane and the carboxy-terminal domains

A cDNA encoding the beta-subunit of the Na,K-ATPase of brine shrimp (Artemia) has been cloned. Its nucleotide sequence and predicted amino acid sequence have been determined. The amino acid sequence shows considerable divergence from that of chicken, dog, human, pig, rat, sheep, Torpedo, and Xenopus. This is not entirely unexpected since brine shrimp is a 'fast clock' organism which diverged from the precursor of the vertebrates 0.5-1.0 billion years ago. However, a highly hydrophobic putative transmembrane domain and the carboxy-terminal domain show considerable conservation. The relatively small degree of conservation in the beta-subunit of Artemia should provide information about the functional significance of this protein.     

Estimation of downwind viable airborne microbes from a wet cooling tower—Including settling

In recent years, reuse of municipal waste water as the coolant in drift-producing cooling towers at electrical generating plants has become increasingly common. A hueristic model is presented that can be used to estimate the concentrations of viable airborne microbes in the drift from a wet cooling tower given the concentration of microbes in the cooling tower. The purpose of this presentation is to allow the nonmeteorologist to understand the factors affecting airborne concentration and to make crude estimates of ground-level concentrations of airborne microorganisms. Concentrations are calculated using a standard meterological method, the Gaussian dispersion model, in which terms have been included for droplet settling and microbial death rate.On assignment from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce.     

Archaea--timeline of the third domain

The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature about 130 years ago. Moreover, the Archaea were formally proposed as the third domain of life only 20 years ago. Over this very short period of investigative history, the scientific community has learned many remarkable things about the Archaea--their unique cellular components and pathways, their abundance and critical function in diverse natural environments, and their quintessential role in shaping the evolutionary path of life on Earth. This Review charts the 'archaea movement', from its genesis through to key findings that, when viewed together, illustrate just how strongly the field has built on new knowledge to advance our understanding not only of the Archaea, but of biology as a whole.