Cyanobacteria

“ The differences in the ratio of photosynthetic pigments in individual genera could explain the different amplitude of the electrogenic response between Nostoc and Lyngbya under the blue light (Fig. 6) .
While it is tempting to speculate electrogenic activity may provide a means of shedding excess energy under intense light, other functions, such as a role in carbon fixation, might also be possible. For efficient carbon fixation, cyanobacteria actively import HCO3− using membrane-spanning transporters [27] . ”

“ The mechanism responsible for electrogenic activity in cyanobacteria appears to be fundamentally different from the one exploited in previously discovered electrogenic bacteria, such as Geobacter, where electrons are derived from oxidation of organic compounds and transported via a respiratory electron transfer chain (R-ETC) [3] , [4] . The electrogenic pathway of cyanobacteria might be exploited to develop light-sensitive devices or future technologies that convert solar energy into limited amounts of electricity in a self-sustainable, CO2-free manner. ”

“ The anode potential was found to oscillate as a function of illumination cycles providing direct evidence that cyanobacteria deposit electrons onto anode surface when exposed to light. Light-dependent deposition of electrons makes the anode potential less positive compared to the potential in the dark which results in the increase in MFC voltage during the light phase. The control anode devoid of photosynthetic biofilm showed no response to illumination (Fig. 3) . ”

“ Chemistry of individual proteins is important to life, but the organism must be put back into bacteriology and evolutionary biology, which have recently been dominated by fragmentary gene-, sequence-, and molecule-oriented oversimplifications [ [1] . Cyanobacteria is an excellent example of a bacterial phylum enduringly defined on organismal grounds a century before sequencing was invented and which retained its organismal integrity, essential physiological properties, and typical cell structure for at least 2.4, and probable over 2.7 billion years despite lateral gene transfer ”

“ All other relations of major groups on their tree have only moderate support. Of my 10 bacterial phyla one (Chlorobacteria) is represented by only one sequence and five are clearly monophyletic (Archaebacteria, Spirochaetes, Hadobacteria, Cyanobacteria with strong support, and Sphingobacteria with moderate (40–80%) support) . Planctobacteria appear polyphyletic with Chlamydiae and Planctomycetes not grouping together ”

“ Their advantages, despite lower specificity, are much higher turnover rates and saturation levels that could cope with greatly increased levels of peroxide after the early Proterozoic 'great oxygenation event' caused by cyanobacteria and their immediate ancestors [132] . Monofunctional catalases probably evolved soon after oxygenic photosynthesis. They would have originated in the common ancestor of Hadobacteria and Cyanobacteria: all organisms except Chlorobacteria (Figs 3, 7) . ”

“ The second key criterion that is used to polarize the evolutionary transition and place the root of the tree within negibacteria is the distribution of the proteasome core particle. It is present in archaea (20S proteasome) , in eukaryotes (26S proteasome) and in some, but not all, actinobacteria (high GC Gram positive) . The two, α and β subunits, are distantly related to HslV, a protein widely distributed in bacteria, although absent from cyanobacteria and chlorobacteria (chloroflexi) . ”

“ Even were it true, that would be no reason for preferring their theory, for no genome-wide data, or any other data, implicate mineral compartments as the immediate ancestors of archaebacteria! In fact, to his frequent embarrassment, Martin himself showed by analyzing 24,990 genes of the flowering plant Arabidopsis that more of them are related both by BLAST and tree criteria to posibacteria than to any other phylum of eubacteria except cyanobacteria (which we know were enslaved as chloroplasts) ”

“ It was also found that a very well conserved operon, the MFIcc operon, is widely found in negibacteria from Chlorobacteria upwards on the tree of Figs 3, 7, but not in cyanobacteria or Unibacteria. This operon appears ancestrally to have comprised a multihaem cytochrome c (M) , a MoCo subunit and an FeS subunit of a multidomain protein (F) , an integral membrane protein (I) , an uncharacterised protein, a 1-haem cytochrome c and another integral membrane protein. ”

“ Even if a very modest yield is used for estimating the average rate of electron discharge, the transfer of solar energy to the environment via cyanobacterial electrogenic pathway could proceed at the rate of ∼9 TW on a global scale. Therefore, the electrogenic pathway appears to be an important microbiological conduit of solar energy into the biosphere and could have significant impact on a global scale. ”

“ Furthermore, the yield of electrogenic activity appears to be underestimated because dissolved oxygen can react with electrons and protons to form water thereby interfering with electron harvesting by extracellular acceptors. Therefore, the yield of electron discharge depends not only on the physiology of the particular genus, but also on the immediate environment and the chemical composition and physical structure of the substrate that supports biofilm formation. ”

“ The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
References 1 2 3 Waterbury JB, Watson SW, Guillard RRL, Brand LE. Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium. Nature. ”

“ In ordinary arable soil there exist motile rod-like bacteria, Bacterium radicicola. These enter the root-hairs of leguminous plants, and passing down the hair in the form of a long, slimy (zoogloea) thread, penetrate the tissues of the root. As a result the tissues become hypertrophied, producing the well-known nodule. In the cells of the nodule the bacteria multiply and develop, drawing material from their host. Many of the bacteria exhibit curious involution forms (“bacteroids”) , which are finally broken down and their products absorbed by the plant. ”

“ The Desiccation of the air, if prolonged, kills many forms when in the vegetative condition. The spores however can bear a much longer period of dryness, some even several years.
Oxygen. Some species cannot live without a supply of free oxygen (Aerobic) , e.g. the Vinegar-bacteria, the Hay-bacilli, the Anthrax-bacilli, the Cholera-Microspira. Other species again thrive vigorously without supply of free oxygen, and are even checked in their development by the admission of air (Anaerobic) , e.g. the butyric acid Bacterium (Clostridium butyricium = Bacillus amylobacter) . ”

“ The chromacea, as protophyta, are plasmodomous. They form new plasm by synthesis and reduction from simple inorganic compounds—water, carbonic acid, ammonia, nitric acid, etc. But the bacteria, as protozoa, are plasmophagous. They cannot, as a rule, form new plasm, but have to take it from other organisms (as parasites, saprophytes, etc.) ; they decompose it by analysis and oxydation. Hence the [201] colorless bacteria are without the important green, blue, or red coloring matter (phycocyan) which tints the plastids of the chromacea, and is the real instrument of the carbon-assimilation. ”

“ The cells of the Bacteria are constructed like other plant-cells in so far as their diminutive size has allowed us to observe them. The cell-wall only exceptionally shows the reactions of cellulose (in Sarcina, Leuconostoc; also in a Vinegar-bacterium, Bacterium xylinum) ; a mucilaginous external layer is always present. The body of the cell mostly appears to be an uniform or finely granulated protoplasm. Very few species (e.g. Bacillus virens) contain chlorophyll; others are coloured red (purple sulphur Bacteria) ; the majority are colourless. ”

“ The ability of these plants to fix nitrogen from the air depends on the presence of bacteria of the genus Rhizobium which infect the roots of the plant and form nodules on them. These root-nodule bacteria of the genus Rhizobium fall into at least six species. No one species will infect the roots of all species of leguminous plants. But each will infect well-defined groups of those plants. [3] Each species of root-nodule bacteria is made up of distinct strains which vary in efficiency. ”

“ These properties explain the regular distribution of bacteria in liquids exposed to the air. Thus, in water in which plants have been macerated the surface of the liquid is occupied by Bacillus subtilis. which has need of free oxygen in order to live, while in the bulk of the liquid, in the vegetable tissues, we find other bacteria, notably B. amylobacter, which lives very well by consuming oxygen in a state of combination. Bacteria, then, can only live in organic matters, now in the presence and now in the absence of air. ”

“ I hope that I have convinced the reader that the root should be on the branch from Chloroflexus to the rest of eubacteria on both the protochlorophyllide and chlorophyllide reductase subtrees. Yet both put it between the two green bacterial phyla with chlorosomes and proteobacteria. In the past this has been misinterpreted as evidence for lateral gene transfer between the green bacteria. It is not. It is just a bad tree, dimensionally hugely distorted by quantum evolution and misrooted by paralogue rooting that is necessarily misled by gross long-branch artefacts. ”

“ Probably no subject in the whole domain of cryptogamic botany has wider bearings on agricultural science than the study of the flora and changes on and in manure and soil. Nitrifying bacteria play a very important part by providing plant life with a most necessary food. They occur in the soil, and two kinds have been described—the one kind converting ammonia into nitrous acid, and the other changing nitrous into nitric acid. We are principally indebted to Winogradsky for our knowledge of these bacteria ”

“ It is further to be noted that not only is all this dead organic matter removed; but it is converted into forms which are again available for plant growth. Carbon dioxide forms the source of the carbon in all green plants, hence in all animals; the sulphates and phosphates are likewise taken up by green plants and built up again into protein compounds; the ammonia is not directly available to green plants to any large extent but is converted by the nitrifying bacteria (Chapter XI) into nitrates which is the form in which nitrogen is assimilated by these higher types. ”

“ Not only does the close resemblance of the Bacteria to unquestionable plants, such as the Oscillatorioe and the lower forms of Fungi, justify this conclusion, but the manufacturing test settles the question at once. It is only needful to add a minute drop of fluid containing Bacteria, to water in which tartrate, phosphate, and sulphate of ammonia are dissolved; and, in a very short space of time, the clear fluid becomes milky by reason of their prodigious multiplication, which, of course, implies the manufacture of living Bacterium-stuff out of these merely saline matters. ”

“ As the negibacteria most closely related to Posibacteria (Eurybacteria) are glycobacteria with much more complex OM, secretion, and import mechanisms than Chlorobacteria (which lack lipopolysaccharide, most porins, Omp85, type I, II, and III secretion machinery, and probably the LolDE lipoprotein release mechanism, of more advanced bacteria) , evolution in the reverse direction of such a complex OM in one step from a posibacteria would be practically impossible (see text) and immensely more difficult than the stepwise increase in its complexity possible with a chlorobacterial root of the tree. ”

“ In white light, the bacteria will be seen to precipitate themselves upon the grains of chlorophyl, to get the oxygen disengaged from them. They thus constitute a very delicate reagent. To witness the effect of the different colors, we let the microscopic spectrum fall upon a filament of conferva, or a transverse leaf-section. The bacteria will collect upon the plant in the red, at the point of maximum absorption, next in the blue, and the density of the population will nearly follow the absorption-curve of the coloring-matter. ”

“ This has proved to be correct, and the fixation of nitrogen by bacteria is now a well-recognised process, the conditions of which are being thoroughly worked out. Two types of organisms are known—those associated with leguminous plants, and those living in a free and independent state in the soil. Of the latter the Clostridium, isolated by Winogradsky, is anaerobic, and the Azotobacter of Beijerinck is aerobic. The essential conditions are that a source of energy must be supplied—usually given as sugar—that the medium must not be acid, and that sufficient phosphate must be present. ”

“ Contrary to molecular pessimism that neglects organismal properties of bacteria [173] , one can plant the tree of life; in my view the arguments in this and earlier papers [ [1] , [5] , [174] together unambiguously establish that the universal root is within negibacteria, and that it is most probably among the non-flagellate, photosynthetic, gliding negibacteria, and most likely of all among or beside the chlorobacteria. For understanding their evolution, bacteria (=prokaryotes) must be thought of as organisms [ [1] , not disembodied genes [ [173] . ”