Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic

Leptochelins A-C, Cytotoxic Metallophores Produced by Geographically Dispersed Leptothoe Strains of Marine Cyanobacteria

Metals are important cofactors in the metabolic processes of cyanobacteria, including photosynthesis, cellular respiration, DNA replication, and the biosynthesis of primary and secondary metabolites. In adaptation to the marine environment, cyanobacteria use metallophores to acquire trace metals when necessary as well as to reduce potential toxicity from excessive metal concentrations. Leptochelins A-C were identified as structurally novel metallophores from three geographically dispersed cyanobacteria of the genus Leptothoe. Determination of the complex structures of these metabolites presented numerous challenges, but they were ultimately solved using integrated data from NMR, mass spectrometry and deductions from the biosynthetic gene cluster. The leptochelins are comprised of halogenated linear NRPS-PKS hybrid products with multiple heterocycles that have potential for hexadentate and tetradentate coordination with metal ions. The genomes of the three leptochelin producers were sequenced, and retrobiosynthetic analysis revealed one candidate biosynthetic gene cluster (BGC) consistent with the structure of leptochelin. The putative BGC is highly homologous in all three Leptothoe strains, and all possess genetic signatures associated with metallophores. Postcolumn infusion of metals using an LC-MS metabolomics workflow performed with leptochelins A and B revealed promiscuous binding of iron, copper, cobalt, and zinc, with greatest preference for copper. Iron depletion and copper toxicity experiments support the hypothesis that leptochelin metallophores may play key ecological roles in iron acquisition and in copper detoxification. In addition, the leptochelins possess significant cytotoxicity against several cancer cell lines.

Gut Microbiome-Brain Alliance: A Landscape View into Mental and Gastrointestinal Health and Disorders

Gut microbiota includes a vast collection of microorganisms residing within the gastrointestinal tract. It is broadly recognized that the gut and brain are in constant bidirectional communication, of which gut microbiota and its metabolic production are a major component, and form the so-called gut microbiome-brain axis. Disturbances of microbiota homeostasis caused by imbalance in their functional composition and metabolic activities, known as dysbiosis, cause dysregulation of these pathways and trigger changes in the blood-brain barrier permeability, thereby causing pathological malfunctions, including neurological and functional gastrointestinal disorders. In turn, the brain can affect the structure and function of gut microbiota through the autonomic nervous system by regulating gut motility, intestinal transit and secretion, and gut permeability. Here, we examine data from the CAS Content Collection, the largest collection of published scientific information, and analyze the publication landscape of recent research. We review the advances in knowledge related to the human gut microbiome, its complexity and functionality, its communication with the central nervous system, and the effect of the gut microbiome-brain axis on mental and gut health. We discuss correlations between gut microbiota composition and various diseases, specifically gastrointestinal and mental disorders. We also explore gut microbiota metabolites with regard to their impact on the brain and gut function and associated diseases. Finally, we assess clinical applications of gut-microbiota-related substances and metabolites with their development pipelines. We hope this review can serve as a useful resource in understanding the current knowledge on this emerging field in an effort to further solving of the remaining challenges and fulfilling its potential.

Generation and Physiology of Hydrogen Sulfide and Reactive Sulfur Species in Bacteria

Sulfur is not only one of the most abundant elements on the Earth, but it is also essential to all living organisms. As life likely began and evolved in a hydrogen sulfide (H₂S)-rich environment, sulfur metabolism represents an early form of energy generation via various reactions in prokaryotes and has driven the sulfur biogeochemical cycle since. It has long been known that H₂S is toxic to cells at high concentrations, but now this gaseous molecule, at the physiological level, is recognized as a signaling molecule and a regulator of critical biological processes. Recently, many metabolites of H₂S, collectively called reactive sulfur species (RSS), have been gradually appreciated as having similar or divergent regulatory roles compared with H₂S in living organisms, especially mammals. In prokaryotes, even in bacteria, investigations into generation and physiology of RSS remain preliminary and an understanding of the relevant biological processes is still in its infancy. Despite this, recent and exciting advances in the fields are many. Here, we discuss abiotic and biotic generation of H₂S/RSS, sulfur-transforming enzymes and their functioning mechanisms, and their physiological roles as well as the sensing and regulation of H₂S/RSS.

Defending Earth's terrestrial microbiome

Microbial life represents the majority of Earth's biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth's microbial biodiversity is under threat. Here we advocate for the conservation and restoration of soil microbial life, as well as active incorporation of microbial biodiversity into managed food and forest landscapes, with an emphasis on soil fungi. We analyse 80 experiments to show that native soil microbiome restoration can accelerate plant biomass production by 64% on average, across ecosystems. Enormous potential also exists within managed landscapes, as agriculture and forestry are the dominant uses of land on Earth. Along with improving and stabilizing yields, enhancing microbial biodiversity in managed landscapes is a critical and underappreciated opportunity to build reservoirs, rather than deserts, of microbial life across our planet. As markets emerge to engineer the ecosystem microbiome, we can avert the mistakes of aboveground ecosystem management and avoid microbial monocultures of single high-performing microbial strains, which can exacerbate ecosystem vulnerability to pathogens and extreme events. Harnessing the planet's breadth of microbial life has the potential to transform ecosystem management, but it requires that we understand how to monitor and conserve the Earth's microbiome.

Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time

The earliest geochemical indicators of microbes-and the enzymes that powered them-extend back ∼3.8 Ga on Earth. Paleobiologists often attempt to understand these indicators by assuming that the behaviors of extant microbes and enzymes are uniform with those of their predecessors. This consistency in behavior seems at odds with our understanding of the inherent variability of living systems. Here, we examine whether a uniformitarian assumption for an enzyme thought to generate carbon isotope indicators of biological activity, RuBisCO, can be corroborated by independently studying the history of changes recorded within RuBisCO's genetic sequences. We resurrected a Precambrian-age RuBisCO by engineering its ancient DNA inside a cyanobacterium genome and measured the engineered organism's fitness and carbon-isotope-discrimination profile. Results indicate that Precambrian uniformitarian assumptions may be warranted but with important caveats. Experimental studies illuminating early innovations are crucial to explore the molecular foundations of life's earliest traces.

Precambrian Paleobiology: Precedents, Progress, and Prospects

In 1859, C. R. Darwin highlighted the “inexplicable” absence of evidence of life prior to the beginning of the Cambrian. Given this lack of evidence and the natural rather than theological unfolding of life’s development Darwin espoused, over the following 50 years his newly minted theory was disputed. At the turn of the 19th century, beginning with the discoveries of C. D. Walcott, glimmerings of the previously “unknown and unknowable” early fossil record came to light – but Walcott’s Precambrian finds were also discounted. It was not until the breakthrough advances of the 1950’s and the identification of modern stromatolites (1956), Precambrian phytoplankton in shales (1950’s), stromatolitic microbes in cherts (1953), and terminal-Precambrian soft-bodied animal fossils (1950’s) that the field was placed on firm footing. Over the following half-century, the development and application of new analytical techniques coupled with the groundbreaking contributions of the Precambrian Paleobiology Research Group spurred the field to its international and distinctly interdisciplinary status. Significant progress has been made worldwide. Among these advances, the known fossil record has been extended sevenfold (from ∼0.5 to ∼3.5 Ga); the fossil record has been shown consistent with rRNA phylogenies (adding credence to both); and the timing and evolutionary significance of an increase of environmental oxygen (∼2.3 Ga), of eukaryotic organisms (∼2.0 Ga), and of evolution-speeding and biota-diversifying eukaryotic sexual reproduction (∼1.2 Ga) have been identified. Nevertheless, much remains to be learned. Such major unsolved problems include the absence of definitive evidence of the widely assumed life-generating “primordial soup”; the timing of the origin of oxygenic photosynthesis; the veracity of postulated changes in global photic-zone temperature from 3.5 Ga to the present; the bases of the advent of eukaryotic sexuality-requiring gametogenesis and syngamy; and the timing of origin and affinities of the small soft-bodied precursors of the Ediacaran Fauna.

Eco-evolutionary feedbacks mediated by bacterial membrane vesicles

Bacterial membrane vesicles (BMVs) are spherical extracellular organelles whose cargo is enclosed by a biological membrane. The cargo can be delivered to distant parts of a given habitat in a protected and concentrated manner. This review presents current knowledge about BMVs in the context of bacterial eco-evolutionary dynamics among different environments and hosts. BMVs may play an important role in establishing and stabilizing bacterial communities in such environments; for example, bacterial populations may benefit from BMVs to delay the negative effect of certain evolutionary trade-offs that can result in deleterious phenotypes. BMVs can also perform ecosystem engineering by serving as detergents, mediators in biochemical cycles, components of different biofilms, substrates for cross-feeding, defense systems against different dangers and enzyme-delivery mechanisms that can change substrate availability. BMVs further contribute to bacteria as mediators in different interactions, with either other bacterial species or their hosts. In short, BMVs extend and deliver phenotypic traits that can have ecological and evolutionary value to both their producers and the ecosystem as a whole.

Carbon isotope evidence for the global physiology of Proterozoic cyanobacteria

Ancestral cyanobacteria are assumed to be prominent primary producers after the Great Oxidation Event [≈2.4 to 2.0 billion years (Ga) ago], but carbon isotope fractionation by extant marine cyanobacteria (α-cyanobacteria) is inconsistent with isotopic records of carbon fixation by primary producers in the mid-Proterozoic eon (1.8 to 1.0 Ga ago). To resolve this disagreement, we quantified carbon isotope fractionation by a wild-type planktic β-cyanobacterium (Synechococcus sp. PCC 7002), an engineered Proterozoic analog lacking a CO₂-concentrating mechanism, and cyanobacterial mats. At mid-Proterozoic pH and pCO₂ values, carbon isotope fractionation by the wild-type β-cyanobacterium is fully consistent with the Proterozoic carbon isotope record, suggesting that cyanobacteria with CO₂-concentrating mechanisms were apparently the major primary producers in the pelagic Proterozoic ocean, despite atmospheric CO₂ levels up to 100 times modern. The selectively permeable microcompartments central to cyanobacterial CO₂-concentrating mechanisms ("carboxysomes") likely emerged to shield rubisco from O₂ during the Great Oxidation Event.

How to resurrect ancestral proteins as proxies for ancient biogeochemistry

Throughout the history of life, enzymes have served as the primary molecular mediators of biogeochemical cycles by catalyzing the metabolic pathways that interact with geochemical substrates. The byproducts of enzymatic activities have been preserved as chemical and isotopic signatures in the geologic record. However, interpretations of these signatures are limited by the assumption that such enzymes have remained functionally conserved over billions of years of molecular evolution. By reconstructing ancient genetic sequences in conjunction with laboratory enzyme resurrection, preserved biogeochemical signatures can instead be related to experimentally constrained, ancestral enzymatic properties. We may thereby investigate instances within molecular evolutionary trajectories potentially tied to significant biogeochemical transitions evidenced in the geologic record. Here, we survey recent enzyme resurrection studies to provide a reasoned assessment of areas of success and common pitfalls relevant to ancient biogeochemical applications. We conclude by considering the Great Oxidation Event, which provides a constructive example of a significant biogeochemical transition that warrants investigation with ancestral enzyme resurrection. This event also serves to highlight the pitfalls of facile interpretation of paleophenotype models and data, as applied to two examples of enzymes that likely both influenced and were influenced by the rise of atmospheric oxygen - RuBisCO and nitrogenase.

A census-based estimate of Earth's bacterial and archaeal diversity

The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8–1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%–96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%–93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2–4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.

A massive survey of Earth's Bacteria and Archaea reveals that their diversity is orders of magnitude lower than previously thought. The study also indicates that extinctions played an important role in prokaryotic evolution.

The global diversity of Bacteria and Archaea ("prokaryotes"), the most ancient and most widespread forms of life on Earth, is subject to high uncertainty. Here, to estimate the global diversity of prokaryotes, we analyzed a large number of 16S ribosomal RNA gene sequences, found in all prokaryotes and commonly used to catalogue prokaryotic diversity. Sequences were obtained from a multitude of environments across thousands of geographic locations worldwide. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs), i.e., 16S gene clusters sharing 97% similarity, roughly corresponding to prokaryotic species. Using several statistical approaches and through comparison with existing databases and previous independent surveys, we estimate that there exist globally between 0.8 and 1.6 million prokaryotic OTUs. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar estimates as for the global data set, suggesting that most OTUs are not restricted to a single continent but are instead globally distributed. Our estimates constrain the extent of a commonly hypothesized but poorly quantified rare prokaryotic biosphere and refute recent predictions that there exists trillions of prokaryotic OTUs. Our findings also indicate that, contrary to common speculation, extinctions may strongly influence global prokaryotic diversity.

Information transmission in microbial and fungal communication: from classical to quantum

Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication. In particular, we highlight bacterial collective behavior with classical and quantum mechanical approaches (including quantum information). Moreover, we shed a new light to introduce the concept of quantum synthetic biology and possible cellular quantum Turing test.

Sulfur-cycling fossil bacteria from the 1.8-Ga Duck Creek Formation provide promising evidence of evolution's null hypothesis

The recent discovery of a deep-water sulfur-cycling microbial biota in the ∼ 2.3-Ga Western Australian Turee Creek Group opened a new window to life's early history. We now report a second such subseafloor-inhabiting community from the Western Australian ∼ 1.8-Ga Duck Creek Formation. Permineralized in cherts formed during and soon after the 2.4- to 2.2-Ga "Great Oxidation Event," these two biotas may evidence an opportunistic response to the mid-Precambrian increase of environmental oxygen that resulted in increased production of metabolically useable sulfate and nitrate. The marked similarity of microbial morphology, habitat, and organization of these fossil communities to their modern counterparts documents exceptionally slow (hypobradytelic) change that, if paralleled by their molecular biology, would evidence extreme evolutionary stasis.

Geological evidence of oxygenic photosynthesis and the biotic response to the 2400-2200 ma "great oxidation event"

Fossil evidence of photosynthesis, documented in the geological record by microbially laminated stromatolites, microscopic fossils, and carbon isotopic data consistent with the presence of Rubisco-mediated CO2-fixation, extends to ~3500 million years ago. Such evidence, however, does not resolve the time of origin of oxygenic photosynthesis from its anoxygenic photosynthetic evolutionary precursor. Though it is evident that cyanobacteria, the earliest-evolved O2-producing photoautotrophs, existed before ~2450 million years ago - the onset of the "Great Oxidation Event" (GOE) that forever altered Earth's environment - O2-producing photosynthesis seems certain to have originated hundreds of millions of years earlier. How did Earth's biota respond to the GOE? Four lines of evidence are here suggested to reflect this major environmental transition: (1) rRNA phylogeny-correlated metabolic and biosynthetic pathways document evolution from an anaerobic (pre-GOE) to a dominantly oxygen-requiring (post-GOE) biosphere; (2) consistent with the rRNA phylogeny of cyanobacteria, their fossil record evidences the immediately post-GOE presence of cyanobacterial nostocaceans characterized by specialized cells that protect their oxygen-labile nitrogenase enzyme system; (3) the earliest known fossil eukaryotes, obligately aerobic phytoplankton and putative algae, closely post-date the GOE; and (4) microbial sulfuretums are earliest known from rocks deposited during and immediately after the GOE, their apparent proliferation evidently spurred by an increase of environmental oxygen and a resulting upsurge of metabolically useable sulfate and nitrate. Though the biotic response to the GOE is a question new to paleobiology that is yet largely unexplored, additional evidence of its impact seems certain to be uncovered.

Synechococcus: 3 billion years of global dominance

Cyanobacteria are among the most important primary producers on the Earth. However, the evolutionary forces driving cyanobacterial species diversity remain largely enigmatic due to both their distinction from macro-organisms and an undersampling of sequenced genomes. Thus, we present a new genome of a Synechococcus-like cyanobacterium from a novel evolutionary lineage. Further, we analyse all existing 16S rRNA sequences and genomes of Synechococcus-like cyanobacteria. Chronograms showed extremely polyphyletic relationships in Synechococcus, which has not been observed in any other cyanobacteria. Moreover, most Synechococcus lineages bifurcated after the Great Oxidation Event, including the most abundant marine picoplankton lineage. Quantification of horizontal gene transfer among 70 cyanobacterial genomes revealed significant differences among studied genomes. Horizontal gene transfer levels were not correlated with ecology, genome size or phenotype, but were correlated with the age of divergence. All findings were synthetized into a novel model of cyanobacterial evolution, characterized by serial convergence of the features, that is multicellularity and ecology.

Molecular bases and role of viruses in the human microbiome

Viruses are dependent biological entities that interact with the genetic material of most cells on the planet, including the trillions within the human microbiome. Their tremendous diversity renders analysis of human viral communities ("viromes") to be highly complex. Because many of the viruses in humans are bacteriophage, their dynamic interactions with their cellular hosts add greatly to the complexities observed in examining human microbial ecosystems. We are only beginning to be able to study human viral communities on a large scale, mostly as a result of recent and continued advancements in sequencing and bioinformatic technologies. Bacteriophage community diversity in humans not only is inexorably linked to the diversity of their cellular hosts but also is due to their rapid evolution, horizontal gene transfers, and intimate interactions with host nucleic acids. There are vast numbers of observed viral genotypes on many body surfaces studied, including the oral, gastrointestinal, and respiratory tracts, and even in the human bloodstream, which previously was considered a purely sterile environment. The presence of viruses in blood suggests that virome members can traverse mucosal barriers, as indeed these communities are substantially altered when mucosal defenses are weakened. Perhaps the most interesting aspect of human viral communities is the extent to which they can carry gene functions involved in the pathogenesis of their hosts, particularly antibiotic resistance. Persons in close contact with each other have been shown to share a fraction of oral virobiota, which could potentially have important implications for the spread of antibiotic resistance to healthy individuals. Because viruses can have a large impact on ecosystem dynamics through mechanisms such as the transfers of beneficial gene functions or the lysis of certain populations of cellular hosts, they may have both beneficial and detrimental roles that affect human health, including improvements in microbial resilience to disturbances, immune evasion, maintenance of physiologic processes, and altering the microbial community in ways that promote or prevent pathogen colonization.

The earliest records of internally stratified cyanobacterial and algal lichens from the Lower Devonian of the Welsh Borderland

Lichenization is assumed to be a very ancient mode of fungal nutrition, but fossil records are rare. Here we describe two fragments of exceptionally preserved, probably charred, lichen thalli with internal stratification. Cyanolichenomycites devonicus has a cyanobacterial and Chlorolichenomycites salopensis a unicellular, presumably green algal photobiont. Fruiting bodies are missing. Cyanolichenomycites devonicus forms asexual spores in a pycnidium. All specimens were examined with scanning electron microscopy techniques. The fossils were extracted by maceration. Extant lichens and free-living cyanobacteria were either experimentally charcoalified for comparison or conventionally prepared. Based on their septate hyphal structure, both specimens are tentatively interpreted as representatives of the Pezizomycotina (Ascomycota). Their presence in 415 million yr (Myr) old rocks from the Welsh Borderland predates existing Late Cretaceous records of pycnidial conidiomata by some 325 Myr and Triassic records of lichens with broadly similar organization by some 195 Myr. These fossils represent the oldest known record of lichens with symbionts and anatomy as typically found in morphologically advanced taxa today. The latter does not apply to Winfrenatia reticulata, the enigmatic crustose lichen fossil from the Lower Devonian, nor to presumed lichen-like organisms such as the Cambrian Farghera robusta or to the Lower Devonian Spongiophyton minutissimum.

Gene copy number variation and its significance in cyanobacterial phylogeny

Background

In eukaryotes, variation in gene copy numbers is often associated with deleterious effects, but may also have positive effects. For prokaryotes, studies on gene copy number variation are rare. Previous studies have suggested that high numbers of rRNA gene copies can be advantageous in environments with changing resource availability, but further association of gene copies and phenotypic traits are not documented. We used one of the morphologically most diverse prokaryotic phyla to test whether numbers of gene copies are associated with levels of cell differentiation.

Results

We implemented a search algorithm that identified 44 genes with highly conserved copies across 22 fully sequenced cyanobacterial taxa. For two very basal cyanobacterial species, Gloeobacter violaceus and a thermophilic Synechococcus species, distinct phylogenetic positions previously found were supported by identical protein coding gene copy numbers. Furthermore, we found that increased ribosomal gene copy numbers showed a strong correlation to cyanobacteria capable of terminal cell differentiation. Additionally, we detected extremely low variation of 16S rRNA sequence copies within the cyanobacteria. We compared our results for 16S rRNA to three other eubacterial phyla (Chroroflexi, Spirochaetes and Bacteroidetes). Based on Bayesian phylogenetic inference and the comparisons of genetic distances, we could confirm that cyanobacterial 16S rRNA paralogs and orthologs show significantly stronger conservation than found in other eubacterial phyla.

Conclusions

A higher number of ribosomal operons could potentially provide an advantage to terminally differentiated cyanobacteria. Furthermore, we suggest that 16S rRNA gene copies in cyanobacteria are homogenized by both concerted evolution and purifying selection. In addition, the small ribosomal subunit in cyanobacteria appears to evolve at extraordinary slow evolutionary rates, an observation that has been made previously for morphological characteristics of cyanobacteria.

Gypsum-permineralized microfossils and their relevance to the search for life on Mars

Orbital and in situ analyses establish that aerially extensive deposits of evaporitic sulfates, including gypsum, are present on the surface of Mars. Although comparable gypsiferous sediments on Earth have been largely ignored by paleontologists, we here report the finding of diverse fossil microscopic organisms permineralized in bottom-nucleated gypsums of seven deposits: two from the Permian (∼260 Ma) of New Mexico, USA; one from the Miocene (∼6 Ma) of Italy; and four from Recent lacustrine and saltern deposits of Australia, Mexico, and Peru. In addition to presenting the first report of the widespread occurrence of microscopic fossils in bottom-nucleated primary gypsum, we show the striking morphological similarity of the majority of the benthic filamentous fossils of these units to the microorganisms of a modern sulfuretum biocoenose. Based on such similarity, in morphology as well as habitat, these findings suggest that anaerobic sulfur-metabolizing microbial assemblages have changed relatively little over hundreds of millions of years. Their discovery as fossilized components of the seven gypsiferous units reported suggests that primary bottom-nucleated gypsum represents a promising target in the search for evidence of past life on Mars. Key Words: Confocal laser scanning microscopy-Gypsum fossils-Mars sample return missions-Raman spectroscopy-Sample Analysis at Mars (SAM) instrument-Sulfuretum.

Where did bone come from?

Bone is specific to vertebrates, and originated as mineralization around the basal membrane of the throat or skin, giving rise to tooth-like structures and protective shields in animals with a soft cartilage-like endoskeleton. A combination of fossil anatomy and genetic information from modern species has improved our understanding of the evolution of bone. Thus, even in man, there are still similarities in the molecular regulation of skin appendages and bone. This article gives a brief overview of the major milestones in skeletal evolution. Some molecular machineries involving members of core genetic networks and their interactions are described in the context of both old theories and modern genetic approaches.

The origin of multicellularity in cyanobacteria

BACKGROUND

Cyanobacteria are one of the oldest and morphologically most diverse prokaryotic phyla on our planet. The early development of an oxygen-containing atmosphere approximately 2.45-2.22 billion years ago is attributed to the photosynthetic activity of cyanobacteria. Furthermore, they are one of the few prokaryotic phyla where multicellularity has evolved. Understanding when and how multicellularity evolved in these ancient organisms would provide fundamental information on the early history of life and further our knowledge of complex life forms.

RESULTS

We conducted and compared phylogenetic analyses of 16S rDNA sequences from a large sample of taxa representing the morphological and genetic diversity of cyanobacteria. We reconstructed ancestral character states on 10,000 phylogenetic trees. The results suggest that the majority of extant cyanobacteria descend from multicellular ancestors. Reversals to unicellularity occurred at least 5 times. Multicellularity was established again at least once within a single-celled clade. Comparison to the fossil record supports an early origin of multicellularity, possibly as early as the "Great Oxygenation Event" that occurred 2.45-2.22 billion years ago.

CONCLUSIONS

The results indicate that a multicellular morphotype evolved early in the cyanobacterial lineage and was regained at least once after a previous loss. Most of the morphological diversity exhibited in cyanobacteria today--including the majority of single-celled species--arose from ancient multicellular lineages. Multicellularity could have conferred a considerable advantage for exploring new niches and hence facilitated the diversification of new lineages.

The paleobiological record of photosynthesis

Fossil evidence of photosynthesis, documented in Precambrian sediments by microbially laminated stromatolites, cyanobacterial microscopic fossils, and carbon isotopic data consistent with the presence of Rubisco-mediated CO2-fixation, extends from the present to ~3,500 million years ago. Such data, however, do not resolve time of origin of O2-producing photoautotrophy from its anoxygenic, bacterial, evolutionary precursor. Though it is well established that Earth's ecosystem has been based on autotrophy since its very early stages, the time of origin of oxygenic photosynthesis, more than 2,450 million years ago, has yet to be established.

The tree of life viewed through the contents of genomes

A universal Tree of Life has been a longstanding goal of the biosciences. The most common Tree of Life, based on the small subunit rRNA gene, may or may not represent the phylogenetic history of microorganisms. The horizontal transfer of genes from one taxon to another provides a means by which each gene may tell of an independent history. When complete genomes became available, the extent to which horizontal gene transfer (HGT) has occurred became more evident. When using genomic data to study the Tree of Life, one can use any of the four broad approaches: (i) build lots of individual gene trees ("phylogenomics"), (ii) concatenate genes together for an analysis yielding one "supergene" tree, (iii) form a single tree based on the "gene content" within genomes using either orthologs or homologs, or (iv) investigate the order of genes within genomes to discern some aspects of microbial evolution. The application of whole genome tree building has suggested that there is a core tree, that such a core tree can be investigated using these varied methods, and that the results are largely similar to those of the rRNA universal Tree of Life. Some of the most interesting features of the rRNA tree, such as early diverging hyperthermophilic lineages are still uncertain, but remain a possibility. Genomic trees and geologic evidence together suggest that the vertical descent of genes and the horizontal transfer of genes between genetically similar lineages ultimately results in a core Tree of Life with at least some lineages that have phenotypic characteristics recognizable for billions of years.

Lineages with long durations are old and morphologically average: an analysis using multiple datasets

Lineage persistence is as central to biology as evolutionary change. Important questions regarding persistence include: why do some lineages outlive their relatives, neither becoming extinct nor evolving into separate lineages? Do these long-duration lineages have distinctive ecological or morphological traits that correlate with their geologic durations and potentially aid their survival? In this paper, I test the hypothesis that lineages (species and higher taxa) with longer geologic durations have morphologies that are more average than expected by chance alone. I evaluate this hypothesis for both individual lineages with longer durations and groups of lineages with longer durations, using more than 60 published datasets of animals with adequate fossil records. Analyses presented here show that groups of lineages with longer durations fall empirically into one of three theoretically possible scenarios, namely: (1) the morphology of groups of longer duration lineages is closer to the grand average of their inclusive group, that is, their relative morphological distance is smaller than expected by chance alone, when compared with rarified samples of their shorter duration relatives (a negative group morpho-duration distribution); (2) the relative morphological distance of groups of longer duration lineages is no different from rarified samples of their shorter duration relatives (a null group morpho-duration distribution); and (3) the relative morphological distance of groups of longer duration lineages is greater than expected when compared with rarified samples of their shorter duration relatives (a positive group morpho-duration distribution). Datasets exhibiting negative group morpho-duration distributions predominate. However, lineages with higher ranks in the Linnean hierarchy demonstrate positive morpho-duration distributions more frequently. The relative morphological distance of individual longer duration lineages is no different from that of rarified samples of their shorter duration relatives (a null individual morpho-duration distribution) for the majority of datasets studied. Contrary to the common idea that very persistent lineages are special or unique in some significant way, both the results from analyses of long-duration lineages as groups and individuals show that they are morphologically average. Persistent lineages often arise early in a group's history, even though there is no prior expectation for this tendency in datasets of extinct groups. The implications of these results for diversification histories and niche preemption are discussed.

A fresh look at the fossil evidence for early Archaean cellular life

The rock record provides us with unique evidence for testing models as to when and where cellular life first appeared on Earth. Its study, however, requires caution. The biogenicity of stromatolites and 'microfossils' older than 3.0 Gyr should not be accepted without critical analysis of morphospace and context, using multiple modern techniques, plus rejection of alternative non-biological (null) hypotheses. The previous view that the co-occurrence of biology-like morphology and carbonaceous chemistry in ancient, microfossil-like objects is a presumptive indicator of biogenicity is not enough. As with the famous Martian microfossils, we need to ask not 'what do these structures remind us of?', but 'what are these structures?' Earth's oldest putative 'microfossil' assemblages within 3.4-3.5 Gyr carbonaceous cherts, such as the Apex Chert, are likewise self-organizing structures that do not pass tests for biogenicity. There is a preservational paradox in the fossil record prior to ca 2.7 Gyr: suitable rocks (e.g. isotopically light carbonaceous cherts) are widely present, but signals of life are enigmatic and hard to decipher. One new approach includes detailed mapping of well-preserved sandstone grains in the ca 3.4 Gyr Strelley Pool Chert. These can contain endolithic microtubes showing syngenicity, grain selectivity and several levels of geochemical processing. Preliminary studies invite comparison with a class of ambient inclusion trails of putative microbial origin and with the activities of modern anaerobic proteobacteria and volcanic glass euendoliths.

Adaptation of Spirogyra insignis (Chlorophyta) to an extreme natural environment (sulphureous waters) through preselective mutations

Adaptation of Spirogyra insignis (Chlorophyceae) to growth and survival in an extreme natural environment (sulphureous waters from La Hedionda Spa, S. Spain) was analysed by using an experimental model. Photosynthesis and growth of the alga were inhibited when it was cultured in La Hedionda Spa waters (LHW), but after further incubation for several weeks, the culture survived due to the growth of a variant that was resistant to LHW. A Luria-Delbruck fluctuation analysis was carried out to distinguish between resistant filaments arising from rare spontaneous mutations and resistant filaments arising from other mechanisms of adaptation. It was demonstrated that the resistant filaments arose randomly by rare spontaneous mutations before the addition of LHW (preselective mutations). The rate of spontaneous mutation from sensitivity to resistance was 2.7 x 10(-7) mutants per cell division. Since LHW(resistant) mutants have a diminished growth rate, they are maintained in nonsulphureous natural waters as the result of a balance between new resistants arising from spontaneous mutation and resistants eliminated by natural selection. Thus, recurrence of rare spontaneous preselective mutations ensures the survival of the alga in sulphureous waters.

Chroococcidiopsis and heterocyst-differentiating cyanobacteria are each other's closest living relatives

Many filamentous cyanobacteria reduce atmospheric nitrogen in specialized differentiated cells called heterocysts. Here we present evidence that shows that members of the unicellular non-heterocyst-differentiating genus Chroococcidiopsis and the filamentous heterocyst-differentiating cyanobacteria are each other's closest living relatives. Distance, maximum-parsimony, and maximum-likelihood analyses of complete small subunit ribosomal RNA gene sequences yielded highly congruent support for the monophyly of Chroococcidiopsis and the heterocyst-differentiating cyanobacteria. Our results demonstrate that the order Pleurocapsales, which traditionally contains Chroococcidiopsis, is a polyphyletic assemblage with the ability to reproduce by multiple fission having arisen independently at least twice during the cyanobacterial radiation. Our data also reject Myxosarcina as a sister taxon to Chroococcidiopsis, indicating that the numerous presumed shared derived characters thought to unite the two genera evolved independently. The sequence divergence within the Chroococcidiopsis lineage is comparable to and probably exceeds that in the entire heterocyst-differentiating lineage. Chroococcidiopsis forms unique survival cells under nitrogen-limiting conditions, and the sister group relationship with the heterocystous cyanobacteria shown here suggests that differentiation of these cells and heterocysts may be related processes.

Daily and circadian variation in survival from ultraviolet radiation in Chlamydomonas reinhardtii

The survival of organisms depends on their ability to adapt to their environment, one important aspect of which is the daily cycle of day and night. During the day, organisms use a variety of strategies to protect themselves from deleterious ultraviolet (UV) wavelengths of sunlight. Among those strategies could be timing of UV-sensitive cellular processes to occur at night to avoid UV-induced damage. We tested whether the unicellular alga Chlamydomonas reinhardtii uses this strategy by measuring the survival of cells following exposure to UV radiation at different phases of the day. Chlamydomonas cells displayed a rhythm of survival from UV radiation where the most sensitive phases occurred during the end of the day and at the beginning of the night. This phase of sensitivity corresponds to the time of nuclear division. The rhythm continues in constant light indicating control by a circadian clock. The results presented here suggest a hypothesis of how circadian clocks may have evolved; a temporal program whereby light-sensitive processes are timed to avoid sunlight-induced damage would be advantageous and therefore selected.

Separation and identification of hydrocarbons and other volatile compounds from cultured blue-green alga Nostoc sp. by gas chromatography-mass spectrometry using serially coupled capillary columns with consecutive nonpolar and semipolar stationary phases

The complex hydrocarbons and volatile compounds produced by cultured blue-green alga Nostoc sp. were separated by serially coupled capillary columns with consecutive nonpolar and semipolar stationary phases. More than 130 metabolites including, cyclohexane, cyclopentane, normal saturated hydrocarbons (C7-C30), fatty acids and benzene derivatives were identified by GC-MS. The most abundant family of hydrocarbons identified were derivatives of cyclohexane (41) and cyclopentane (11). Most of these compounds have not been reported previously in blue-green algae studies.

Acritarchs and microfossils from the Mesoproterozoic Bangemall Group, northwestern Australia

Three microfossil assemblages occur in the Mesoproterozoic Bangemall Group (1625-1000 Ma) of northwestern Australia, each occupying a different environmental and taphonomic setting. In peritidal environments, benthic prokaryotic filaments and spheroids of matting habit and small size were permineralized by early diagenetic silicification of stromatolitic carbonates. In shallow subtidal environments, benthic filaments of large size and nonmatting habit and planktonic sphaeromorph acritarchs with thin walls and moderate dimensions were compressed in mildly kerogenous shale. In deeper subtidal environments, planktonic megasphaeromorph acritarchs with thick walls were initially entombed in concretionary nodules in highly kerogenous shale and then permineralized by silica during later diagenesis. Taxonomic diversity and numerical abundance evidently decrease offshore. The three assemblages have typical Mesoproterozoic aspects: peritidal benthic habitats were dominated by Siphonophycus-Sphaerophycus-Eosynechococcus-Myxococcoides-Palaeopleurocapsa, shallow subtidal settings were occupied by Siphonophycus-Leiosphaeridia-Pterosphermopsimorpha-Satka, and offshore plankton consisted solely of very large chuarid acritarchs. Because of its taphonomic restriction to mid-intertidal stromatolites, the peritidal assemblage can be equated in microenvironment with a similar assemblage in the Neoproterozoic Draken Conglomerate, suggesting that ecological stasis at the community level can last for intervals up to 900 million years. In the deeper subtidal assemblage, the common chuarid has an unusual mode of preservation, in three dimensions in early diagenetic concretions, revealing that it possesses a thick multilamellate wall. Because of this distinctive ultrastructure, the new genus Crassicorium is erected for these fossils, which are among the oldest indubitable eukaryotes. Very large (34-55 micrometers in diameter) filaments from shallow subtidal habitats are assigned to the emended species Siphonophycus punctatum.

13C-Depleted carbon microparticles in >3700-Ma sea-floor sedimentary rocks from west greenland

Turbiditic and pelagic sedimentary rocks from the Isua supracrustal belt in west Greenland [more than 3700 million years ago (Ma)] contain reduced carbon that is likely biogenic. The carbon is present as 2- to 5-micrometer graphite globules and has an isotopic composition of delta13C that is about -19 per mil (Pee Dee belemnite standard). These data and the mode of occurrence indicate that the reduced carbon represents biogenic detritus, which was perhaps derived from planktonic organisms.

Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes

The presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. An alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. In this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryotes. They are believed to be descended from the most primitive organisms. Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria, and I suggest that this evolution occurred in response to antibiotic selection pressures. Evidence is presented that diderm prokaryotes (i.e., gram-negative bacteria), which have a bilayered cell wall, are derived from monoderm prokaryotes. Signature sequences in different proteins provide a means to define a number of different taxa within prokaryotes (namely, low G+C and high G+C gram-positive, Deinococcus-Thermus, cyanobacteria, chlamydia-cytophaga related, and two different groups of Proteobacteria) and to indicate how they evolved from a common ancestor. Based on phylogenetic information from indels in different protein sequences, it is hypothesized that all eukaryotes, including amitochondriate and aplastidic organisms, received major gene contributions from both an archaebacterium and a gram-negative eubacterium. In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes.

Phylogenetic mapping of bacterial morphology

The availability of a meaningful molecular phylogeny for bacteria provides a context for examining the historical significance of various developments in bacterial evolution. Herein, the classical morphological descriptions of selected members of the domain Bacteria are mapped upon the genealogical ancestry deduced from comparison of small-subunit rRNA sequences. For the species examined in this study, a distinct pattern emerges which indicates that the coccus shape has arisen and accumulated independently multiple times in separate lineages and typically survived as a persistent end-state morphology. At least two other morphologies persist but have evolved only once. This study demonstrates that although bacterial morphology is not useful in defining bacterial phylogeny, it is remarkably consistent with that phylogeny once it is known. An examination of the experimental evidence available for morphogenesis as well as microbial fossil evidence corroborates these findings. It is proposed that the accumulation of persistent morphologies is a result of the biophysical properties of peptidoglycan and their genetic control, and that an evolved body-plan strategy based on peptidoglycan may have been a fate-sealing step in the evolution of Bacteria. More generally, this study illustrates that significant evolutionary insights can be obtained by examining biological and biochemical data in the context of a reliable phylogenetic structure.

Evolvability

Evolvability is an organism's capacity to generate heritable phenotypic variation. Metazoan evolution is marked by great morphological and physiological diversification, although the core genetic, cell biological, and developmental processes are largely conserved. Metazoan diversification has entailed the evolution of various regulatory processes controlling the time, place, and conditions of use of the conserved core processes. These regulatory processes, and certain of the core processes, have special properties relevant to evolutionary change. The properties of versatile protein elements, weak linkage, compartmentation, redundancy, and exploratory behavior reduce the interdependence of components and confer robustness and flexibility on processes during embryonic development and in adult physiology. They also confer evolvability on the organism by reducing constraints on change and allowing the accumulation of nonlethal variation. Evolvability may have been generally selected in the course of selection for robust, flexible processes suitable for complex development and physiology and specifically selected in lineages undergoing repeated radiations.

Solar ultraviolet and the evolutionary history of cyanobacteria

On the basis of photobiological, evolutionary, paleontological, paleoenvironmental and physiological arguments, a time course for the role of solar ultraviolet radiation (UVR, wavelengths below 400 nm) in the ecology and evolution of cyanobacteria is proposed in which three main periods can be distinguished. An initial stage, before the advent of oxygenic photosynthesis, when high environmental fluxes of UVC (wavelengths below 280 nm) and UVB (280-320 nm) may have depressed the ability of protocyanobacteria to develop large populations or restricted them to UVR refuges. A second stage lasting between 500 and 1500 Ma (million years), started with the appearance of true oxygen-evolving cyanobacteria and the concomitant formation of oxygenated (micro)environments under an oxygen free-atmosphere. In this second stage, the age of UV, the overall importance of UVR must have increased substantially, since the incident fluxes of UVC and UVB remained virtually unchanged, but additionally the UVA portion of the spectrum (320-400 nm) suddenly became biologically injurious and extremely reactive oxygen species must have formed wherever oxygen and UVR spatially coincided. The last period began with the gradual oxygenation of the atmosphere and the formation of the stratospheric ozone shield. The physiological stress due to UVC all but disappeared and the effects of UVB were reduced to a large extent. Evidence in support of this dynamics is drawn from the phylogenetic distribution of biochemical UV-defense mechanisms among cyanobacteria and other microorganisms. The specific physical characteristics of UVR and oxygen exposure in planktonic, sedimentary and terrestrial habitats are used to explore the plausible impact of UVR in each of the periods on the ecological distribution of cyanobacteria.

Evolution: when was life's first branch point?

A recent analysis of protein sequences from diverse organisms has estimated that all extant species share a common ancestor that lived only 2 billion years ago; but how can this be squared with the fossil evidence that complex cells existed up to 3.5 billion years ago?

Molecular phylogeny of Metazoa (animals): monophyletic origin

The phylogenetic relationships within the kingdom Animalia (Metazoa) have long been questioned. Focusing on the lowest eukaryotic multicellular organisms, the metazoan phylum Porifera (sponges), it remained unsolved if they evolved multicellularity independently from a separate protist lineage (polyphyly of animals) of derived from the same protist group as the other animal phyla (monophyly). After having analyzed genes typical for multicellularity (adhesion molecules/receptors and a nuclear receptor), we present evidence that Porifera should be placed in the kingdom Animalia. We therefore suggest a monophyletic origin for all animals.

Molecular evolution of viruses: an interim summary

The origin and molecular evolution of viruses in this issue is dealt with at two levels: (1) tracing the past evolutionary pathways of viruses belonging to RNA virus families, retroviruses, and small and large DNA viruses; (2) tracing current changes in the RNA and DNA viral genomes that lead to the evolution of new virus mutants. In this interim summary, a time scale for the evolutionary processes is given, based on the accumulated published knowledge concerning the postulated origins of life on planet Earth, and the hypothesis that living cells with RNA genomes may have emerged (the "RNA world hypothesis") that then developed into cells with DNA genomes in eukaryotic and prokaryotic cells (1-3). The ideas about the evolution of RNA and DNA viruses from ancient cellular RNA and DNA molecules over a period of 3.5 billion years are discussed. It may be possible that by studying virus genes and molecular processes in virus-infected cells, and their involvement in the shaping of the genomes of bacteria, yeast, plants, insects, mammals, and humans, it will be possible to understand the importance of viruses in past evolution and to predict their possible impact on current and future evolutionary trends in biology.