To assess bacterioplankton production in the sea, we have developed a procedure for measuring growth based on incorporation of tritiated thymidine into DNA; the accuracy of this procedure was tested under a variety of laboratory and field conditions. By autoradiography, we have found that for all practical purposes our technique is specific for the nonphotosynthetic bacteria and that virtually all of the “active” bacteria (one-third or more of the total countable bacteria) take up thymidine. We also measured (1) the intracellular isotope dilution of thymidine assessed by parallel experiments with labeled phosphorus, and (2) DNA content of natural marine bacteria (0.2 to 0.6 μm size fraction); a conversion factor derived from these data permitted estimation of production from thymidine incorporation results. A very similar conversion factor was independently derived from the empirical relationship between thymidine incorporation and growth of natural bacterioplankton under controlled conditions. Combined results show that this technique, which can be performed rapidly and easily at sea, provides good estimates of production. Data from Southern California Bight waters, which contain oligotrophic as well as moderately eutrophic regions, show that average bacterioplankton doubling times, like those of the phytoplankton, are on the order of a few days, with fastest growth at depths just below those of greatest phytoplankton abundance. Offshore bacterial production is roughly 5 to 25% of the primary production; thus, at a 50% assimilation efficiency, the bacterioplankton would consume 10 to 50% of the total fixed carbon.

Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters : Evaluation and field results

A revised six-kingdom system of life is presented, down to the level of infraphylum. As in my 1983 system Bacteria are treated as a single kingdom, and eukaryotes are divided into only five kingdoms: Protozoa, Animalia, Fungi, Plantae and Chromista. Intermediate high level categories (superkingdom, subkingdom, branch, infrakingdom, superphylum, subphylum and infraphylum) are extensively used to avoid splitting organisms into an excessive number of kingdoms and phyla (60 only being recognized). The two 'zoological' kingdoms, Protozoa and Animalia, are subject to the International Code of Zoological Nomenclature, the kingdom Bacteria to the International Code of Bacteriological Nomenclature, and the three 'botanical' kingdoms (Plantae, Fungi, Chromista) to the International Code of Botanical Nomenclature. Circumscriptions of the kingdoms Bacteria and Plantae remain unchanged since Cavalier-Smith (1981). The kingdom Fungi is expanded by adding Microsporidia, because of protein sequence evidence that these amitochondrial intracellular parasites are related to conventional Fungi, not Protozoa. Fungi are subdivided into four phyla and 20 classes; fungal classification at the rank of subclass and above is comprehensively revised. The kingdoms Protozoa and Animalia are modified in the light of molecular phylogenetic evidence that Myxozoa are actually Animalia, not Protozoa, and that mesozoans are related to bilaterian animals. Animalia are divided into four subkingdoms: Radiata (phyla Porifera, Cnidaria, Placozoa, Ctenophora), Myxozoa, Mesozoa and Bilateria (bilateral animals: all other phyla). Several new higher level groupings are made in the animal kingdom including three new phyla: Acanthognatha (rotifers, acanthocephalans, gastrotrichs, gnathostomulids), Brachiozoa (brachiopods and phoronids) and Lobopoda (onychophorans and tardigrades), so only 23 animal phyla are recognized. Archezoa, here restricted to the phyla Metamonada and Trichozoa, are treated as a subkingdom within Protozoa, as in my 1983 six-kingdom system, not as a separate kingdom. The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some 'rhizopods' and is therefore renamed Cercozoa. The number of protozoan phyla is reduced by grouping Mycetozoa and Archamoebae (both now infraphyla) as a new subphylum Conosa within the phylum Amoebozoa alongside the subphylum Lobosa, which now includes both the traditional aerobic lobosean amoebae and Multicilia. Haplosporidia and the (formerly microsporidian) metchnikovellids are now both placed within the phylum Sporozoa. These changes make a total of only 13 currently recognized protozoan phyla, which are grouped into two subkingdoms: Archezoa and Neozoa the latter is modified in circumscription by adding the Discicristata, a new infrakingdom comprising the phyla Percolozoa and Euglenozoa). These changes are discussed in relation to the principles of megasystematics, here defined as systematics that concentrates on the higher levels of classes, phyla, and kingdoms. These principles also make it desirable to rank Archaebacteria as an infrakingdom of the kingdom Bacteria, not as a separate kingdom. Archaebacteria are grouped with the infrakingdom Posibacteria to form a new subkingdom, Unibacteria, comprising all bacteria bounded by a single membrane. The bacterial subkingdom Negibacteria, with separate cytoplasmic and outer membranes, is subdivided into two infrakingdoms: Lipobacteria, which lack lipopolysaccharide and have only phospholipids in the outer membrane, and Glycobacteria, with lipopolysaccharides in the outer leaflet of the outer membrane and phospholipids in its inner leaflet. (ABSTRACT TRUNCATED)

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A revised six-kingdom system of life.

Kingdom protozoa and its 18 phyla.

Cyanobacteria have evolved an extremely effective single-cell CO(2) concentrating mechanism (CCM). Recent molecular, biochemical and physiological studies have significantly extended current knowledge about the genes and protein components of this system and how they operate to elevate CO(2) around Rubisco during photosynthesis. The CCM components include at least four modes of active inorganic carbon uptake, including two bicarbonate transporters and two CO(2) uptake systems associated with the operation of specialized NDH-1 complexes. All these uptake systems serve to accumulate HCO(3)(-) in the cytosol of the cell, which is subsequently used by the Rubisco-containing carboxysome protein micro-compartment within the cell to elevate CO(2) around Rubisco. A specialized carbonic anhydrase is also generally present in this compartment. The recent availability of at least nine cyanobacterial genomes has made it possible to begin to undertake comparative genomics of the CCM in cyanobacteria. Analyses have revealed a number of surprising findings. Firstly, cyanobacteria have evolved two types of carboxysomes, correlated with the form of Rubisco present (Form 1A and 1B). Secondly, the two HCO(3)(-) and CO(2) transport systems are distributed variably, with some cyanobacteria (Prochlorococcus marinus species) appearing to lack CO(2) uptake systems entirely. Finally, there are multiple carbonic anhydrases in many cyanobacteria, but, surprisingly, several cyanobacterial genomes appear to lack any identifiable CA genes. A pathway for the evolution of CCM components is suggested.

CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution

INTRODUCTION 369THE REQUIREMENT FOR CARBONIC ANHYDRASES IN DIFFERENTORGANISMS 370CYANOBACTERIA 371Carboxysomal Carbonic Anhydrase 373Is the Ci Pump a Membrane Carbonic Anhydrase? 374MICROALGAE 374Chloroplast Carbonic Anhydrase 375Periplasmie Carbonic Anhydrase 376Cytosolic Carbonic Anhydrase 377Induction of Carbonic Anhydrase at Low-C02 378AQUATIC MACROALGAE AND ANGIOSPERMS 379External Carbonic Anhydrose 379Internal Carbonic Anhydrase 380C4 PLANTS 381CAM PLANTS 382C3 PLANTS 382EVOLUTION OF PHOTOSYNTHETIC CARBONIC ANHYDRASES 385CONCLUSIONS 387

The Role of Carbonic Anhydrase in Photosynthesis

The chloroplasts of some algal groups may have evolved from endosymbiotic eukaryotic algae

In Ochromonas danica and two related species (Chrysophyceae) and in Rhodomonas lens and Cryptomonas sp. (Cryptophyceae), the chloroplast is surrounded by an outer double-membraned envelope which lies outside the usual double-membraned chloroplast envelope. At the borders of the area where the chloroplast lies adjacent to the nucleus, this outer envelope is continuous with the outer membrane of the nuclear envelope as a double-membraned outfolding, so that the entire chloroplast in these species lies within a double-membraned sac, one wall of which is the nuclear envelope. In Olisthodiscus sp. (Chrysophyceae ?), each of the small peripheral chloroplasts is surrounded by a similar double-membraned outer envelope, but in this species no connections with the nuclear envelope were observed. In the Ochromonadaceae, a characteristic array of tubules is present within the sac in the narrow space which separates the chloroplast from the nucleus. In the other species studied, tubules are present at places between the chloroplast envelope and the outer envelope. In the Cryptophyceae, the starch grains lie outside the chloroplast envelope, but within the outer double-membraned sac. A double-membraned outer envelope appears to be present outside the chloroplasts of the Phaeophyta and Euglenophyta, but seems to be absent in the other groups of algae.

/pdf/nuclear-envelope-chloroplast-relationships-in-algae-mnbphashau.pdf

Nuclear envelope-chloroplast relationships in algae.

In preparing this paper, I had two big decisions to make. First, whose classification of the algae should I use, and second, which terminology should I use to describe chloroplast ultrastructure? I decided to use Christensen’s classification of the algae because overall it correlates fairly well with chloroplast ultrastructure. Since Christensen’s classification of the algae has not yet been mentioned in this conference, I will summarize it briefly. Christensen separates the algae into four divisions: the Cyanophyta, comprising one class, the Cyanophyceae; the Rhodophyta, comprising one class, the Rhodophyceae; the Chromophyta, comprising nine classes, the Cryptophyceae, Dinophyceae, Raphidophyceae (the Chloromonads) , Chrysophyceae, Haptophyceae, Craspedophyceae (the collared flagellates, which I will not mention again since none are known to have chloroplasts), the Bacillariophyceae, Xanthophyceae, and Phaeophyceae; and the Chlorophyta, into which he puts four classes. These are the Euglenophyceae, the Chlorophyceae, and two groups of algae that he removed from the green algae because of ‘differences in flagellation, the Prasinophyceae and Loxophyceae. The differences between these two classes are not clear-cut, and in this paper I will follow Peterfi and Manton * and lump the Loxophyceae with the Prasinophyceae. The question of which terminology of chloroplast ultrastructure to use is a more difficult one. For all other cell organelles, electron microscopists have now more or less agreed on a standard terminology. Who, for example, would still call the endoplasmic reticulum alpha cytomembranes? However, if you want to describe only the membranes of a chloroplast, you have a dozen odd terms to choose from-discs, thylakoids, frets, partitions, lamellae, lamellations, stacks, grana, bands-despite the fact that the membranes of all chloroplasts are built on a basic structural plan. The basic unit of the chloroplast is a flattened membrane-limited sac which Menke has named a thylakoid. Others, myself included, have called these sacs discs. In the interest of a uniform terminology, I propose that we abandon the word disc and use thylakoid henceforth. I propose to use the wbrd granum specifically to refer to a stack of appressed thylakoids, many of which are short and round and of approximately equal diameter, whereas others, which are interspersed with these, extend across the stroma to form part of a neighboring granum or even of the same granum. This leaves the problem of what to call the groups of two or three appressed or loosely associated thylakoids which extend across the chloroplasts of most algae. Stacks is probably the most descriptive word, but it is not a very euphonious one, and it implies a pile of some height rather than an extended flat layer.

The comparative ultrastructure of the algal chloroplast

Publisher Summary This chapter discusses the structure, function, and evolutionary significance of the chloroplast Endoplasmic Reticulum (ER). In majority of the classes of algae a unique association exists between the rough endoplasmic reticulum of the cytoplasm and the cell's chloroplasts. The cell's chloroplasts are completely enclosed by a continuous sheet of ER that has ribosomes on its outer surface. A layer of tubules and vesicles, the periplastidal reticulum is present in the narrow space between the double-membraned chloroplast envelope and the nuclear envelope. Some algae have a specialized cytoplasmic ER cisternum that is continuous with chloroplast ER. The main function of the chloroplast ER is to synthesize nuclear-coded proteins that are destined for the chloroplast. The chapter discusses the intriguing question of biochemical composition of the nucleomorph, and if it is the vestigial nucleus of a chloroplast-containing eukaryotic symbiont. ER cisternae that are, at times, associated with the plastids of bryophytes and vascular plants are very different from chloroplast ER in algae. The clue to the theory of evolution of chloroplast ER is the nucleomorph of cryptomonads. The chapter proves that the chloroplast of cryptomonads arose from a eukaryotic endosymbiont; and the nucleomorph has the major characteristics of a nucleus.

Sarah P. Gibbs

Papers

The chloroplasts of some algal groups may have evolved from endosymbiotic eukaryotic algae

Nuclear envelope-chloroplast relationships in algae.

The comparative ultrastructure of the algal chloroplast

The Chloroplast Endoplasmic Reticulum: Structure, Function, and Evolutionary Significance

The fine structure of Euglena gracilis with special reference to the chloroplasts and pyrenoids