Proterozoic photosynthesis – a critical review

Chlorophyll‐based photosynthesis has fuelled the biosphere since at least the early Archean, but it was the ecological takeover of oxygenic cyanobacteria in the early Palaeoproterozoic, and of photosynthetic eukaryotes in the late Neoproterozoic, that gave rise to a recognizably modern ocean–atmosphere system. The fossil record offers a unique view of photosynthesis in deep time, but is deeply compromised by differential preservation and non‐diagnostic morphologies. The pervasively polyphyletic expression of modern cyanobacterial phenotypes means that few Proterozoic fossils are likely to be members of extant clades; rather than billion‐year stasis, their similarity to modern counterparts is better interpreted as a combination of serial convergence and extinction, facilitated by high levels of horizontal gene transfer. There are few grounds for identifying cyanobacterial akinetes or crown‐group Nostocales in the Proterozoic record. Such recognition undermines the results of various ancestral state reconstruction analyses, as well as molecular clock estimates calibrated against demonstrably problematic Proterozoic fossils. Eukaryotic organisms are likely to have acquired their (stem‐group nostocalean) photoendosymbionts/plastids by at least the Palaeoproterozoic, but remained ecologically marginalized by incumbent cyanobacteria until the late Neoproterozoic appearance of suspension‐feeding animals.     

Proterozoic phytoplankton and timing of Chlorophyte algae origins

Abstract: Morphological and reproductive features and cell wall ultrastructure and biochemistry of Proterozoic acritarchs are used to determine their affinity to modern algae. The first appearance datum of these microbiota is traced to infer a minimum age of the divergence of the algal classes to which they may belong. The chronological appearance of microfossils that represent phycoma‐like and zygotic cysts and vegetative cells and/or aplanospores, respectively, interpreted as prasinophyceaen and chlorophyceaen microalgae is related to the Viridiplantae phylogeny. An inferred minimum age of the Chlorophyte origin is before c. 1800 Ma, the Prasinophyceae at c. 1650 Ma and the Chlorophyceae at c. 1450 Ma. These divergence times differ from molecular clock estimates, and the palaeontological evidence suggests that they are older.     

Prasinophyceae (Green Algae) from the Lower Proterozoic of the Kola Peninsula

Eukaryotic organisms discovered from the earliest Lower Proterozoic phosphorites (2.04 Ga) of the Kola Peninsula are described. These are fossil forms Pechengia melezhiki gen. et sp. nov., which are tentatively assigned to green algae of the class Prasinophyceae.     

Petsamomyces, a new genus of organic-walled microfossils from the coal-bearing deposits of the Early Proterozoic, Kola Peninsula

A new genus of organic-walled microfossils of supposed fungal origin, Petsamomyces Belova gen. nov., is described from the black shales of the Pechenga complex of the Early Proterozoic (Kola Peninsula). The find testifies to the development of eukaryotic heterotrophic microorganisms as early as 2 Ga ago.     

Proterozoic microfossils from the Mara Dolomite Member, Emmerugga Dolomite, McArthur Group, from the Northern Territory, Australia

An assemblage of microfossils from the mid-Proterozoic Mara Dolomite Member of the Emmerugga Dolomite, McArthur Group, Northern Territory, Australia, has been studied. The assemblage contains 10 species, of which one is new. The classification of Proterozoic microfossils is reviewed and a morphographic scheme adopted. The new assemblage is compared with other McArthur Group assemblages, and the differences between the assemblages are explained in terms of environmental differences. Comparison with other microfossil assemblages world-wide, suggests that these assemblages have stratigraphic potential.     

Towards a 'natural' time scale for the Precambrian – A proposal

A proposal is put forward to redefine the geological time scale for the Precambrian. Flaws of the present, chronometrically defined, time scale are discussed and illustrated. It is concluded that we need to go back to the rock record to define a “natural” time scale, in which major divisions (eons, eras, etc.) are defined in terms of first-order events and transitions in the observable stratigraphic record. For the earliest part of Earth history, we need a time scale, including a formalized Hadean eon, that is fully consistent with rapidly evolving insights from planetary science.     

The oldest records of photosynthesis

There is diverse, yet controversial fossil evidence for the existence of photosynthesis 3500 million years ago. Among the most persuasive evidence is the stromatolites described from low grade metasedimentary rocks in Western Australia and South Africa. Based on the understanding of the paleobiology of stromatolites and using pertinent fossil and Recent analogs, these Early Archean stromatolites suggest that phototrophs evolved by 3500 million years ago. The evidence allows further interpretation that cyanobacteria were involved. Besides stromatolites, microbial and chemical fossils are also known from the same rock units. Some microfossils morphologically resemble cyanobacteria and thus complement the adduced cyanobacterial involvement in stromatolite construction. If cyanobacteria had evolved by 3500 million years ago, this would indicate that nearly all prokaryotic phyla had already evolved and that prokaryotes diversified rapidly on the early Earth.     

Nanotechnology and Potential of Microorganisms

ABSTRACT

There is a growing need to develop clean, nontoxic and environmentally friendly (“green chemistry”) procedures for synthesis and assembly of nanoparticles. The use of biological organisms in this area is rapidly gaining importance due to its growing success and ease of formation of nanoparticles. Presently, the potential of bio-organisms ranges from simple prokaryotic bacterial cells to eukaryotic fungus and even live plants. In this article we have reviewed some of these biological systems, which have revolutionized the art of nano-material synthesis.     

The Size of Cells and Organisms in Relation to the Evolution of Embryophytes

Abstract: The earliest O₂-_-evolvers were marine cyanobacteria (3.5 billion years ago) with marine eukaryotic phototrophs from 2.0 billion years ago. These organisms were, and are, poikilo-hydric, i.e., cannot remain hydrated when exposed to a desiccating atmosphere (as can occur for intertidal benthic algae and cy anobacteria at low tide). The smallest marine primarily poikilo-hydric O₂-_-evolvers are close to the lower size limit imposed by non-scaleable components such as minimum genome size and constant membrane thickness, with cyanobacterial unicells 0.65 μn in diameter and eukaryotic unicells 0.95 μm in diameter. The largest (multicellular) marine primarily aquatic poikilohydric O₂-_-evolvers are brown algae at least 60 m long and over 100 kg fresh mass; there are no obvious constraints on the max imum size of such organisms. In freshwaters the size range for primarily poikilohydric O₂-_-evolving organisms is smaller, due to the absence of very large organisms. An even smaller size range characterizes terrestrial algae and cyanobacteria which have occurred for about 1 billion years. Desiccation-tolerant cyanobacterium and algae (intertidal, freshwater, terrestrial) are at the lower end of the size ranges. Embryophytic terrestrial O₂-_-evolvers arose some 450 million years ago and were than all poikilohydric and (probably) desiccation-tolerant. Embryophytic defining structural features re quire organisms of at least 100 μm equivalent spherical diameter for both gametophyte and sporophyte phases. Primarily poi kilohydric embryophytes are not more than 1 m tall as a result of a mechanistically mysterious size limit for desiccation-tolerant organisms. Homoiohydric embryophytes evolved some 420 mil lion years ago in the sporophyte phase (later to become the dominant terrestrial vegetation) and possibly in the gameto phyte phase (although no such homoiohydric gametophytes are known today). The homoiohydric features of gas spaces, stomata, cuticle, endohydric water conducting system and water and nutrient uptake structures require an organism at least 5 mm high; this has implications for the minimum size of mega-spores and seeds. The tallest homoiohydric plants are (or were within historic times) 130 m high, with height constrained by re source costs of the synthesis and maintenance of the mechanical and water conduction systems, andbr of xylem water trans port. Secondarily poikilohydric embryophytes in aquatic, or very damp terrestrial, habitats are derived from homoiohydric plants; they retain most homoiohydric features but are not functionally homoiohydric. The smaller secondarily poikilohydric plants are less than one tenth of the size of the smallest functionally homoiohydric plants.     

The role of clay minerals in the preservation of Precambrian organic-walled microfossils

Precambrian organic-walled microfossils (OWMs) are primarily preserved in mudstones and shales that are low in total organic carbon (TOC). Recent work suggests that high TOC may hinder OWM preservation, perhaps because it interferes with chemical interactions involving certain clay minerals that inhibit the decay of microorganisms. To test if clay mineralogy controls OWM preservation, and if TOC moderates the effect of clay minerals, we compared OWM preservational quality (measured by pitting on fossil surfaces and the deterioration of wall margins) to TOC, total clay, and specific clay mineral concentrations in 78 shale samples from 11 lithologic units ranging in age from ca. 1650 to 650 million years ago. We found that the probability of finding well-preserved microfossils positively correlates with total clay concentrations and confirmed that it negatively correlates with TOC concentrations. However, we found no evidence that TOC influences the effect of clay mineral concentrations on OWM preservation, supporting an independent role of both factors on preservation. Within the total clay fraction, well-preserved microfossils are more likely to occur in shales with high illite concentrations and low berthierine/chamosite concentrations; however, the magnitude of their effect on preservation is small. Therefore, there is little evidence that bulk clay chemistry is important in OWM preservation. Instead, we propose that OWM preservation is largely regulated by physical properties that isolate organic remains from microbial degradation such as food scarcity (low TOC) and low sediment permeability (high total clay content): low TOC increases the diffusive distances between potential carbon sources and heterotrophic microbes (or their degradative enzymes), while high clay concentrations reduce sediment pore space, thereby limiting the diffusion of oxidants and degradative enzymes to the sites of decay.     

On the species-specificity of DNA: Fifty years later

Modern approaches in DNA-based species identification are considered. Long used methods of species identification in procaryotes (G+C ratio, 16S rRNA nucleotide sequence, DNA-DNA hybridization) have recently been supplemented by the method of multilocus sequence analysis based on comparison of nucleotide sequences of fragments of several genes. Species identification in eukaryotes also employs one or two standard short fragments of the genome (known as DNA-barcodes). Potential benefits of new approaches and some difficulties during their practical realization are discussed.     

蓝藻无菌化方法研究进展

随着微藻产业的蓬勃发展,蓝藻作为具有重要经济价值的资源受到人们越来越多的关注,其多糖和蛋白的开发已被应用于多个领域。为了更深入清晰地挖掘蓝藻的特性和功能,研究者首先需获得无菌的纯种藻株,这是深入开展蓝藻生理生化、遗传和毒性等研究的基础。重点综述了如何根据蓝藻的结构及生理特性选择合适的无菌化方法,介绍了基于蓝藻与污染菌之间差异性的无菌化方法,以期为蓝藻的无菌化工作提供参考。     

Structure and molecular phylogeny of sasA genes in cyanobacteria: insights into evolution of the prokaryotic circadian system

Cyanobacteria are the simplest organisms known to have a circadian system. In addition to the three well-studied kai genes, kaiA, kaiB, and kaiC, an important element of this system is a two-component sensory transduction histidine kinase sasA. Using publicly available data of complete prokaryotic genomes, we performed structural and phylogenetic analyses of the sasA genes. Results show that this gene has a triple-domain structure, and the domains are under different selective constraints. The sasA gene originated in cyanobacteria probably through the fusion of the ancestral kaiB gene with a double-domain, two-component sensory transduction histidine kinase. The results of the phylogenetic analyses suggest that sasA emerged before the kaiA gene, about 3,000-2,500 MYA, and has evolved in parallel with the evolution of the kaiBC cluster. The observed concordant patterns of the sasA and kaiBC evolution suggest that these genes might compose an ancient KaiBC-SasA-based circadian system, without the kaiA gene, and that such a system still exists in some unicellular cyanobacteria.     

Early Archean planktonic mode of life: Implications from fluid dynamics of lenticular microfossils

Lenticular, and commonly flanged, microfossils in 3.0–3.4 Ga sedimentary deposits in Western Australia and South Africa are unusually large (20–80 μm across), robust, and widespread in space and time. To gain insight into the ecology of these organisms, we performed simulations of fluid dynamics of virtual cells mimicking lenticular forms of variable sizes, oblateness, flange presence, and flange thickness. Results demonstrate that (a) the flange reduces sedimentation velocity, (b) this flange function works more effectively in larger cells, and (c) modest oblateness lowers sedimentation rate. These observations support interpretations that the lenticular microbes were planktonic—a lifestyle that could have been advantageous in an early Earth harsh environment including violent volcanic activities, repeated asteroid impacts, and relatively high UV‐radiation. Although the robustness of these organisms could have provided additional protection on the early Earth, this architecture may have impeded a planktonic lifestyle by increasing cell density. However, our data suggest that this disadvantage could have been compensated by enlargement of cell volume, which could have enhanced the ability of the flange to slow sedimentation rate, especially if coupled with vacuolation. The results of this simulation study may help to explain the unique morphology and unusually large size of these Archean microfossils.     

蓝藻生物钟分子机理的研究进展

蓝藻是具有内源性生物钟的简单生物.虽然蓝藻生物钟具有跟真核生物同样的基础特征,但其相关基因和蛋白质与真核生物没有同源性.蓝藻生物钟的核心是kai基因簇及其编码的蛋白KaiA,KaiB和KaiC.这三种Kai蛋白相互作用调节KaiC的磷酸化状态,从而产生昼夜节律信息.KaiC的磷酸化循环是昼夜节律的起博器,调控包括kai基因在内的相关基因的节律性表达.组氨酸蛋白激酶的磷酸化传递可将环境信息输入和将节律信息输出生物钟核心.     

Associative Cyanobacteria Isolated from the Roots of Epiphytic Orchids

Associative cyanobacteria were isolated from the rhizoplane and velamen of the aerial roots of the epiphytic orchids Acampe papillosa, Phalaenopsis amabilis, and Dendrobium moschatum and from the substrate roots of A. papillosa and D. moschatum. Cyanobacteria were isolated on complete and nitrogen-free variants of BG-11 medium. On all media and in all samples, cyanobacteria of the genus Nostoc predominated. Nostoc, Anabaena, and Calothrixwere isolated from the surface of the A. papillosa aerial roots, whereas the isolates from the substrate roots were Nostoc, Oscillatoria,and representatives of the LPP group (Lyngbia, Phormidium, and Plectonema, incapable of nitrogen fixation). On the D. moschatum substrate roots, Nostoc and LPP group representatives were also found, as well as Fischerella. On the aerial roots of P. amabilis and D. phalaenopsis grown in a greenhouse simulating the climate of moist tropical forest, cyanobacteria were represented by Nostoc, LPP group, and Scytonema in D. phalaenopsis and by Nostoc, Scytonema, Calothrix, Spirulina, Oscillatoria, and the LPP group in P. amabilis. For D. moschatum, the spectra of cyanobacteria populating the substrate root rhizoplane and the substrate (pine bark) were compared. In the parenchyma of the aerial roots of P. amabilis, fungal hyphae and/or their half-degraded remains were detected, which testifies to the presence of mycorrhizal fungi in this plant. This phenomenon is attributed to the presence of a sheath formed by cyanobacteria and serving as a substrate for fungi.     

Synthetic Biology Toolkits for Metabolic Engineering of Cyanobacteria

Cyanobacteria are of great importance to Earth's ecology. Due to their capability in photosynthesis and C1 metabolism, they are ideal microbial chassis that can be engineered for direct conversion of carbon dioxide and solar energy into biofuels and biochemicals. Facilitated by the elucidation of the basic biology of the photoautotrophic microbes and rapid advances in synthetic biology, genetic toolkits have been developed to enable implementation of nonnatural functionalities in engineered cyanobacteria. Hence, cyanobacteria are fast becoming an emerging platform in synthetic biology and metabolic engineering. Herein, the progress made in the synthetic biology toolkits for cyanobacteria and their utilization for transforming cyanobacteria into microbial cell factories for sustainable production of biofuels and biochemicals is outlined. Current techniques in heterologous gene expression, strategies in genome editing, and development of programmable regulatory parts and modules for engineering cyanobacteria towards biochemical production are discussed and prospected. As cyanobacteria synthetic biology is still in its infancy, apart from the achievements made, the difficulties and challenges in applying and developing genetic toolkits in cyanobacteria for biochemical production are also evaluated.