Oxygen-Dependent Morphogenesis of Modern Clumped Photosynthetic Mats and Implications for the Archean Stromatolite Record

A Biofilm Channel Origin for Vermiform Microstructure in Carbonate Microbialites

A three-dimensional tubular fabric known as "vermiform microstructure" in Phanerozoic and Neoproterozoic carbonate microbialites has been hypothesized to represent the body fossil of nonspicular keratose demosponges. If correct, this interpretation extends the sponge body fossil record and origin of animals to ~890 Ma. However, the veracity of the keratose sponge interpretation for vermiform microstructure remains in question, and the origin of the tubular fabric is enigmatic. Here we compare exceptionally well-preserved microbialite textures from the Upper Triassic to channel networks created by modern microbial biofilms. We demonstrate that anastomosing channel networks of similar size and geometries are produced by microbial biofilms in the absence of sponges, suggesting the origin for vermiform microstructure in ancient carbonates is not unique to sponges and perhaps best interpreted conservatively as likely microbial in origin. We present a taphonomic model of early biofilm lithification in seawater with anomalously high carbonate saturation necessary to preserve delicate microbial textures. This work has implications for the understanding of three-dimensional biofilm architecture that goes beyond the current micro-scale observations available from living biofilm experiments and suggests that biofilm channel networks have an extensive fossil record.

Initial type and abundance of cyanobacteria determine morphotype development of phototrophic ecosystems

Phototrophic aggregates containing filamentous cyanobacteria occur naturally, for example, as cryoconite on glaciers and microbialites in fresh or marine waters, but their formation is not fully understood. Laboratory models are now available to reproduce aggregation, that is, the formation of different morphotypes like hemispheroids, microbial mats or sphere-like aggregates we call photogranules. In the model, activated sludge as starting matrix is transformed into aggregates enclosed by a phototrophic layer of growing cyanobacteria. These cyanobacteria were either enriched from the matrix or we added them intentionally. We hypothesize that the resulting morphotype depends on the type and concentration of the added cyanobacteria. When cyanobacteria from mature photogranules were added to activated sludge, photogranulation was not observed, but microbial mats were formed. Photogranulation of sludge could be promoted when adding sufficient quantities of cyanobacterial strains that form clumps when grown as isolates. The cyanobacteria putatively responsible for photogranulation were undetectable or only present in low abundance in the final communities of photogranules, which were always dominated by mat-forming cyanobacteria. We suggest that, in a temporal succession, the ecosystem engineer initiating photogranulation eventually disappears, leaving behind its structural legacy. We conclude that understanding phototrophic aggregate formation requires considering the initial succession stages of the ecosystem development.

The Archean origin of oxygenic photosynthesis and extant cyanobacterial lineages

The record of the coevolution of oxygenic phototrophs and the environment is preserved in three forms: genomes of modern organisms, diverse geochemical signals of surface oxidation and diagnostic Proterozoic microfossils. When calibrated by fossils, genomic data form the basis of molecular clock analyses. However, different interpretations of the geochemical record, fossil calibrations and evolutionary models produce a wide range of age estimates that are often conflicting. Here, we show that multiple interpretations of the cyanobacterial fossil record are consistent with an Archean origin of crown-group Cyanobacteria. We further show that incorporating relative dating information from horizontal gene transfers greatly improves the precision of these age estimates, by both providing a novel empirical criterion for selecting evolutionary models, and increasing the stringency of sampling of posterior age estimates. Independent of any geochemical evidence or hypotheses, these results support oxygenic photosynthesis evolving at least several hundred million years before the Great Oxygenation Event (GOE), a rapid diversification of major cyanobacterial lineages around the time of the GOE, and a post-Cryogenian origin of extant marine picocyanobacterial diversity.

Metabolic versatility in a modern lineage of cyanobacteria from terrestrial hot springs

The extent of oxygenated environments on the early Earth was much lower than today, and cyanobacteria were critical players in Earth's shift from widespread anoxia to oxygenated surface environments. Extant cyanobacteria that aggregate into cones, tufts and ridges are used to understand the long record of photosynthesis and microbe-mineral interactions during times when oxygen was much lower, i.e., the Archean and the Proterozoic. To better understand the metabolic versatility and physiological properties of these organisms, we examined publicly available genomes of cyanobacteria from modern terrestrial hydrothermal systems and a newly sequenced genome of a cyanobacterium isolated from conical and ridged microbialites that grow in occasionally sulfidic hydrothermal springs in Yellowstone National Park, USA. Phylogenomic analyses reveal that cyanobacteria from globally distributed terrestrial and shallow marine hydrothermal systems form a monophyletic clade within the Cyanobacteria phylum. Comparative genomics of this clade reveals the genetic capacity for oxygenic photosynthesis that uses photosystems I and II, and anoxygenic photosynthesis that uses a putative sulfide quinone reductase to oxidize sulfide and bypass photosystem II. Surprisingly large proportions of the newly sequenced genome from Yellowstone National Park are also dedicated to secondary metabolite production (15.1-15.6%), of which ∼6% can be attributed to antibiotic production and resistance genes. All this may be advantageous to benthic, mat-forming photosynthesizers that have to compete for light and nutrients in sporadically or permanently sulfidic environments, and may have also improved the tolerance of ancient counterparts of these cyanobacteria to sulfidic conditions in benthic communities that colonized the coastal margins in the Archean and the Proterozoic.

How did the evolution of oxygenic photosynthesis influence the temporal and spatial development of the microbial iron cycle on ancient Earth?

Iron is the most abundant redox active metal on Earth and thus provides one of the most important records of the redox state of Earth's ancient atmosphere, oceans and landmasses over geological time. The most dramatic shifts in the Earth's iron cycle occurred during the oxidation of Earth's atmosphere. However, tracking the spatial and temporal development of the iron cycle is complicated by uncertainties about both the timing and location of the evolution of oxygenic photosynthesis, and by the myriad of microbial processes that act to cycle iron between redox states. In this review, we piece together the geological evidence to assess where and when oxygenic photosynthesis likely evolved, and attempt to evaluate the influence of this innovation on the microbial iron cycle.

Mechanistic Morphogenesis of Organo-Sedimentary Structures Growing Under Geochemically Stressed Conditions: Keystone to Proving the Biogenicity of Some Archaean Stromatolites?

Morphologically diverse organo-sedimentary structures (including microbial mats and stromatolites) provide a palaeobiological record through more than three billion years of Earth history. Since understanding much of the Archaean fossil record is contingent upon proving the biogenicity of such structures, mechanistic interpretations of well-preserved fossil microbialites can reinforce our understanding of their biogeochemistry and distinguish unambiguous biological characteristics in these structures, which represent some of the earliest records of life. Mechanistic morphogenetic understanding relies upon the analysis of geomicrobiological experiments. Herein, we report morphological-biogeochemical comparisons between micromorphologies observed in growth experiments using photosynthetic mats built by the cyanobacterium Coleofasciculus chthonoplastes (formerly Microcoleus) and green anoxygenic phototrophic Chloroflexus spp. (i.e., Coleofasciculus–Chloroflexus mats), and Precambrian organo-sedimentary structures, demonstrating parallels between them. In elevated ambient concentrations of Cu (toxic to Coleofasciculus), Coleofasciculus–Chloroflexus mats respond by forming centimetre-scale pinnacle-like structures (supra-lamina complexities) associated with large quantities of EPS at their surfaces. µPIXE mapping shows that Cu and other metals become concentrated within surficial sheath-EPS-Chloroflexus-rich layers, producing density-differential micromorphologies with distinct fabric orientations that are detectable using X-ray computed micro-tomography (X-ray µCT). Similar micromorphologies are also detectable in stromatolites from the 3.481 Ga Dresser Formation (Pilbara, Western Australia). The cause and response link between the presence of toxic elements (geochemical stress) and the development of multi-layered topographical complexities in organo-sedimentary structures may thus be considered an indicator of biogenicity, being an indisputably biological and predictable morphogenetic response reflecting, in this case, the differential responses of Coleofasciculus and Chloroflexus to Cu. Growth models for microbialite morphogenesis rely upon linking morphology to intrinsic (biological) and extrinsic (environmental) influences. Since the pinnacles of Coleofasciculus–Chloroflexus mats have an unambiguously biological origin linked to extrinsic geochemistry, we suggest that similar micromorphologies observed in ancient organo-sedimentary structures are indicative of biogenesis. An identical Coleofasciculus–Chloroflexus community subjected to salinity stress also produced supra-lamina complexities (tufts) but did not produce identifiable micromorphologies in three dimensions since salinity seems not to negatively impact either organism, and therefore cannot be used as a morphogenetic tool for the interpretation of density-homogeneous micro-tufted mats—for example, those of the 3.472 Ga Middle Marker horizon. Thus, although correlative microscopy is the keystone to confirming the biogenicity of certain Precambrian stromatolites, it remains crucial to separately interrogate each putative trace of ancient life, ideally using three-dimensional analyses, to determine, where possible, palaeoenvironmental influences on morphologies. Widespread volcanism and hydrothermal effusion into the early oceans likely concentrated toxic elements in early biomes. Morphological diversity in fossil microbialites could, therefore, reflect either (or both of) differential exposure to ambient fluids enriched in toxic elements and/or changing ecosystem structure and tolerance to elements through evolutionary time—for example, after incorporation into enzymes. Proof of biogenicity by deducing morphogenesis (i.e., a process preserved in the fossil record) overcomes many of the shortcomings inherent to the proof of biogenicity by descriptions of morphology alone.

Unusual microbial mat-related structural diversity 2.1 billion years ago and implications for the Francevillian biota

The 2.1-billion-year-old (Ga) Francevillian series in Gabon hosts some of the oldest reported macroscopic fossils of various sizes and shapes, stimulating new debates on the origin, evolution and organization of early complex life. Here, we document ten representative types of exceptionally well-preserved mat-related structures, comprising "elephant-skin" textures, putative macro-tufted microbial mats, domal buildups, flat pyritized structures, discoidal microbial colonies, horizontal mat growth patterns, wrinkle structures, "kinneyia" structures, linear patterns and nodule-like structures. A combination of petrographic analyses, scanning electron microscopy, Raman spectroscopy and organic elemental analyses of carbon-rich laminae and microtexture, indicate a biological origin for these structures. The observed microtextures encompass oriented grains, floating silt-sized quartz grains, concentrated heavy minerals, randomly oriented clays, wavy-crinkly laminae and pyritized structures. Based on comparisons with modern analogues, as well as an average δ¹³ C organic matter (C_org ) composition of -32.94 ± 1.17‰ (1 standard deviation, SD) with an outlier of -41.26‰, we argue that the mat-related structures contain relicts of multiple carbon pathways including heterotrophic recycling of photosynthetically derived C_org . Moreover, the relatively close association of the macroscopic fossil assemblages to the microbial mats may imply that microbial communities acted as potential benthic O₂ oases linked to oxyphototrophic cyanobacterial mats and grazing grounds. In addition, the mat's presence likely improved the preservation of the oldest large colonial organisms, as they are known to strongly biostabilize sediments. Our findings highlight the oldest community assemblage of microscopic and macroscopic biota in the aftermath of the "Great Oxidation Event," widening our understanding of biological organization during Earth's middle age.

A Field Guide to Finding Fossils on Mars

The Martian surface is cold, dry, exposed to biologically harmful radiation and apparently barren today. Nevertheless, there is clear geological evidence for warmer, wetter intervals in the past that could have supported life at or near the surface. This evidence has motivated National Aeronautics and Space Administration and European Space Agency to prioritize the search for any remains or traces of organisms from early Mars in forthcoming missions. Informed by (1) stratigraphic, mineralogical and geochemical data collected by previous and current missions, (2) Earth's fossil record, and (3) experimental studies of organic decay and preservation, we here consider whether, how, and where fossils and isotopic biosignatures could have been preserved in the depositional environments and mineralizing media thought to have been present in habitable settings on early Mars. We conclude that Noachian-Hesperian Fe-bearing clay-rich fluvio-lacustrine siliciclastic deposits, especially where enriched in silica, currently represent the most promising and best understood astropaleontological targets. Siliceous sinters would also be an excellent target, but their presence on Mars awaits confirmation. More work is needed to improve our understanding of fossil preservation in the context of other environments specific to Mars, particularly within evaporative salts and pore/fracture-filling subsurface minerals.

Evidence of oxygenic phototrophy in ancient phosphatic stromatolites from the Paleoproterozoic Vindhyan and Aravalli Supergroups, India

Fossil microbiotas are rare in the early rock record, limiting the type of ecological information extractable from ancient microbialites. In the absence of body fossils, emphasis may instead be given to microbially derived features, such as microbialite growth patterns, microbial mat morphologies, and the presence of fossilized gas bubbles in lithified mats. The metabolic affinity of micro-organisms associated with phosphatization may reveal important clues to the nature and accretion of apatite-rich microbialites. Stromatolites from the 1.6 Ga Chitrakoot Formation (Semri Group, Vindhyan Supergroup) in central India contain abundant fossilized bubbles interspersed within fine-grained in situ-precipitated apatite mats with average δ¹³ C_org indicative of carbon fixation by the Calvin cycle. In addition, the mats hold a synsedimentary fossil biota characteristic of cyanobacterial and rhodophyte morphotypes. Phosphatic oncoid cone-like stromatolites from the Paleoproterozoic Aravalli Supergroup (Jhamarkotra Formation) comprise abundant mineralized bubbles enmeshed within tufted filamentous mat fabrics. Construction of these tufts is considered to be the result of filamentous bacteria gliding within microbial mats, and as fossilized bubbles within pristine mat laminae can be used as a proxy for oxygenic phototrophy, this provides a strong indication for cyanobacterial activity in the Aravalli mounds. We suggest that the activity of oxygenic phototrophs may have been significant for the formation of apatite in both Vindhyan and Aravalli stromatolites, mainly by concentrating phosphate and creating steep diurnal redox gradients within mat pore spaces, promoting apatite precipitation. The presence in the Indian stromatolites of alternating apatite-carbonate lamina may result from local variations in pH and oxygen levels caused by photosynthesis-respiration in the mats. Altogether, this study presents new insights into the ecology of ancient phosphatic stromatolites and warrants further exploration into the role of oxygen-producing biotas in the formation of Paleoproterozoic shallow-basin phosphorites.

Carbonate-rich dendrolitic cones: insights into a modern analog for incipient microbialite formation, Little Hot Creek, Long Valley Caldera, California

Ancient putative microbial structures that appear in the rock record commonly serve as evidence of early life on Earth, but the details of their formation remain unclear. The study of modern microbial mat structures can help inform the properties of their ancient counterparts, but modern mineralizing mat systems with morphological similarity to ancient structures are rare. Here, we characterize partially lithified microbial mats containing cm-scale dendrolitic coniform structures from a geothermal pool ("Cone Pool") at Little Hot Creek, California, that if fully lithified, would resemble ancient dendrolitic structures known from the rock record. Light and electron microscopy revealed that the cm-scale 'dendrolitic cones' were comprised of intertwined microbial filaments and grains of calcium carbonate. The degree of mineralization (carbonate content) increased with depth in the dendrolitic cones. Sequencing of 16S rRNA gene libraries revealed that the dendrolitic cone tips were enriched in OTUs most closely related to the genera Phormidium, Leptolyngbya, and Leptospira, whereas mats at the base and adjacent to the dendrolitic cones were enriched in Synechococcus. We hypothesize that the consumption of nutrients during autotrophic and heterotrophic growth may promote movement of microbes along diffusive nutrient gradients, and thus microbialite growth. Hour-glass shaped filamentous structures present in the dendrolitic cones may have formed around photosynthetically-produced oxygen bubbles-suggesting that mineralization occurs rapidly and on timescales of the lifetime of a bubble. The dendrolitic-conical structures in Cone Pool constitute a modern analog of incipient microbialite formation by filamentous microbiota that are morphologically distinct from any structure described previously. Thus, we provide a new model system to address how microbial mats may be preserved over geological timescales.

Growth of modern branched columnar stromatolites in Lake Joyce, Antarctica

Modern decimeter-scale columnar stromatolites from Lake Joyce, Antarctica, show a change in branching pattern during a period of lake level rise. Branching patterns correspond to a change in cyanobacterial community composition as preserved in authigenic calcite crystals. The transition in stromatolite morphology is preserved by mineralized layers that contain microfossils and cylindrical molds of cyanobacterial filaments. The molds are composed of two populations with different diameters. Large diameter molds (>2.8 μm) are abundant in calcite forming the oldest stromatolite layers, but are absent from younger layers. In contrast, <2.3 μm diameter molds are common in all stromatolites layers. Loss of large diameter molds corresponds to the transition from smooth-sided stromatolitic columns to branched and irregular columns. Mold diameters are similar to trichome diameters of the four most abundant living cyanobacteria morphotypes in Lake Joyce: Phormidium autumnale morphotypes have trichome diameters >3.5 μm, whereas Leptolyngbya antarctica, L. fragilis, and Pseudanabaena frigida morphotypes have diameters <2.3 μm. P. autumnale morphotypes were only common in mats at <12 m depth. Mats containing abundant P. autumnale morphotypes were smooth, whereas mats with few P. autumnale morphotypes contained small peaks and protruding bundles of filaments, suggesting that the absence of P. autumnale morphotypes allowed small-scale topography to develop on mats. Comparisons of living filaments and mold diameters suggest that P. autumnale morphotypes were present early in stromatolite growth, but disappeared from the community through time. We hypothesize that the mat-smoothing behavior of P. autumnale morphotypes inhibited nucleation of stromatolite branches. When P. autumnale morphotypes were excluded from the community, potentially reflecting a rise in lake level, short-wavelength roughness provided nuclei for stromatolite branches. This growth history provides a conceptual model for initiation of branched stromatolite growth resulting from a change in microbial community composition.

Benthic perspective on Earth's oldest evidence for oxygenic photosynthesis

The Great Oxidation Event (GOE) is currently viewed as a protracted process during which atmospheric oxygen increased above ∼10(-5) times the present atmospheric level (PAL). This threshold represents an estimated upper limit for sulfur isotope mass-independent fractionation (S-MIF), an Archean signature of atmospheric anoxia that begins to disappear from the rock record at 2.45 Ga. However, an increasing number of papers have suggested that the timing for oxidative continental weathering, and by conventional thinking the onset of atmospheric oxygenation, was hundreds of million years earlier than previously thought despite the presence of S-MIF. We suggest that this apparent discrepancy can be resolved by the earliest oxidative-weathering reactions occurring in benthic and soil environments at profound redox disequilibrium with the atmosphere, such as biological soil crusts and freshwater microbial mats covering riverbed, lacustrine, and estuarine sediments. We calculate that oxygenic photosynthesis in these millimeter-thick ecosystems provides sufficient oxidizing equivalents to mobilize sulfate and redox-sensitive trace metals from land to the oceans while the atmosphere itself remained anoxic with its attendant S-MIF signature. As continental freeboard increased significantly between 3.0 and 2.5 Ga, the chemical and isotopic signatures of benthic oxidative weathering would have become more globally significant from a mass-balance perspective. These observations help reconcile evidence for pre-GOE oxidative weathering with the history of atmospheric chemistry, and support the plausible antiquity of a terrestrial biosphere populated by cyanobacteria well before the GOE.

Cyanophycin mediates the accumulation and storage of fixed carbon in non-heterocystous filamentous cyanobacteria from coniform mats

Thin, filamentous, non-heterocystous, benthic cyanobacteria (Subsection III) from some marine, lacustrine and thermal environments aggregate into macroscopic cones and conical stromatolites. We investigate the uptake and storage of inorganic carbon by cone-forming cyanobacteria from Yellowstone National Park using high-resolution stable isotope mapping of labeled carbon (H(13)CO3 (-)) and immunoassays. Observations and incubation experiments in actively photosynthesizing enrichment cultures and field samples reveal the presence of abundant cyanophycin granules in the active growth layer of cones. These ultrastructurally heterogeneous granules rapidly accumulate newly fixed carbon and store 18% of the total particulate labeled carbon after 120 mins of incubation. The intracellular distribution of labeled carbon during the incubation experiment demonstrates an unexpectedly large contribution of PEP carboxylase to carbon fixation, and a large flow of carbon and nitrogen toward cyanophycin in thin filamentous, non-heterocystous cyanobacteria. This pattern does not occur in obvious response to a changing N or C status. Instead, it may suggest an unusual interplay between the regulation of carbon concentration mechanisms and accumulation of photorespiratory products that facilitates uptake of inorganic C and reduces photorespiration in the dense, surface-attached communities of cyanobacteria from Subsection III.