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Genome Size of Cyanobacteria
Abstract
The genome sizes of 128 strains of cyanobacteria, representative of all major taxonomic groups, lie in the range 1.6 x lo9 to 8.6 x lo9 daltons. The majority of unicellular cyano-bacteria contain genomes of 1.6 x lo9 to 2-7 x lo9 daltons, comparable in size to those of other bacteria, whereas most pleurocapsalean and filamentous strains possess larger genomes. The genome sizes are discontinuously distributed into four distinct groups which have means of 2.2 x lo9, 3-6 x lo9, 5.0 x lo9 and 7.4 x lo9 daltons. The data suggest that genome evolution in cyanobacteria occurred by a series of duplications of a small ancestral genome, and that the complex morphological organization characteristic of many cyano-bacteria may have arisen as a result of this process.
... The enrichment culture technique was applied to isolate cyanobacteria from the collected water samples. Twenty-five mL of each sample were aseptically added to 100 ml of BG-11 broth [26] in 250 conical flasks. Afterwards, the inoculated flasks were incubated at 30 o C under continuous illumination from Philips fluorescent white lamps at light intensity of 400 -500 lux. ...
... Wet mount preparation was used to characterize the isolated cyanobacteria morphologically. According to Rippka, et al. [26]. the cyanobacteria morphotypes such as filamentous nature, size, shape of vegetative cells, presence of heterocyst and akinetes were identified and photographed using light microscope. ...
... 64, No. 1 (2021) 205 identified through characterization of their morphological attributes and molecular profile. Morphologically, according to Rippka et al. [26], the microscopic examination revealed that the isolates could be categorized into two groups. Isolates MN2, MN5 and MN6 of the first group were filamentous non heterocystous cyanobacteria (Fig. 2a), whereas the isolates MN1, MN3 and MN4 were filamentous heterocystous cyanobacteria (Fig. 2b). ...
... However, more recently Rippka and co-workers (134) emphasized that the helical shape of Spirulina "is a stable and constant property" of the genus that permits its differentiation from the other groups of filamentous, non-heterocystous cyanobacteria: Oscillatoria, Pseudanabaena, and the LPP (Lyngbia, Phormidium, and Plectonema) group (135). In addition, differences between Spirulina and Oscillatoria have been reported in the genome size (59), chemical composition (especially in the case of fatty acids [see later]), antigenicity (22), and ultrastructure (154). Thus, it does not seem unreasonable to maintain the genus Spirulina for at least the cyanobacteria characterized by highly spiralized trichomes living in freshwaters with high salt concentrations and alkaline pH; that is the object of this review. ...
... The genome sizes of 128 strains representing all major taxonomic groups of cyanobacteria have been determined by renaturation kinetics analysis (59). The genome sizes could be grouped into four classes that could correspond to a progressive duplication of an "ancestral genome' of ca. ...
... The studied 6 Anabaena sp. strains had genome size in arranging between 3.17 and 3.89 × 10 − 9 Da [47,48]. ...
Cyanobacteria (blue-green algae) are well-known for the ability to excrete extra-cellular products, as a variety of cyanochemicals (phycocompounds) of curio with several extensive therapeutic applications. Among these phycocompound, the cyanotoxins from certain water-bloom forming taxa are toxic to biota, including crocodiles. Failure of current non-renewable source compounds in producing sustainable and non-toxic therapeutics led the urgency of discovering products from natural sources. Particularly, compounds of the filamentous N2-fixing Anabaena sp. have effective antibacterial, antifungal, antioxidant, and anticancer properties. Today, such newer compounds are the potential targets for the possible novel chemical scaffolds, suitable for mainstream-drug development cascades. Bioactive compounds of Anabaena sp. such as, anatoxins, hassallidins and phycobiliproteins have proven their inherent antibacterial, antifungal, and antineoplastic activities, respectively. Herein, the available details of the biomass production and the inherent phyco-constituents namely, alkaloids, lipids, phenols, peptides, proteins, polysaccharides, terpenoids and cyanotoxins are considered, along with geographical distributions and morphological characteristics of the cyanobacterium. The acquisitions of cyanochemicals in recent years have newly addressed several pharmaceutical aliments, and the understanding of the associated molecular interactions of phycochemicals have been considered, for plausible use in drug developments in future.
... and pH levels (Havens, 2008), conditions likely to affect nearby bacteria. One hypothesis for such a close-knit relationship is that Cyanobacteria have small genomes compared to eukaryotic organisms (Herdman et al., 1979;Humbert et al., 2013). While this benefits Cyanobacteria for rapid reproduction and evolution, it is not automatically constructive for cyanobacterial bloom formation as some functions are lost (Giovannoni et al., 2014). ...
The presence of taste and odour compounds (T&O) in drinking water lead to numerous complaints to water companies worldwide. Geosmin and 2-MIB are common T&O compounds, with Cyanobacteria being the primary biological source in drinking water reservoirs. Both compounds have low odour thresholds in humans and require expensive additional treatment. This thesis used molecular and statistical analysis of water from Welsh Water reservoirs, to provide a framework for predicting and monitoring T&O events and understanding their causes.
Elevated T&O concentrations were confined to warmer months, except for a one geosmin event in winter 2019. There was no correlation between cyanobacterial abundance and T&O concentrations, but qPCR analysis based on eDNA sampling demonstrated that geosmin synthase (geoA) was a suitable proxy for predicting geosmin concentrations. Abundances of geoA and 2-MIB cyclase (mic) were significantly non-linearly associated with high ammonium-to-nitrate ratios, identifying thresholds for heightened T&O risk. The ratio of total inorganic nitrogen to total phosphorous was significantly non-linearly associated with increases in geoA. Increased geoA was also significantly negatively associated with temperature and dissolved reactive silicate in all reservoirs. Next-generation sequencing of bacterial and algal communities showed that community compositions clustered according to T&O concentrations. Bacterial and algal co-occurrence networks uncovered significant positive and negative associations, highlighting cyanospheres in all reservoirs. Random Forest models were developed for geosmin (Alaw) and 2-MIB (Pentwyn) using significantly co-occurring taxa exposing indicative T&O taxa and the probable Cyanobacteria causing the T&O. Cyanobacteria had more negative than positive associations in their cyanospheres.
This thesis illustrates the importance of nutrient ratios in triggering potential geosmin and 2-MIB events. It also indicates that Cyanobacteria subjected to environmental stress (negative biotic interactions and low temperatures) increase their T&O-production. These findings provide a useful framework for water monitoring to enable the prediction and possible prevention of T&O events.
... Exceptions to this obviously exist. For instance, filamentous cyanobacteria species exhibit larger genomes in comparison to their unicellular cyanobacteria relatives due to the increase in genome size at the origin of filaments [38][39][40][41]. ALE, in its default 1:1 T:D setting, indicates instead that the general tendency of an average bacterial genome is to become larger in size, yielding a low L:G value of 0.76 which, in other words, means that gene gains are 24% more frequent than gene losses, contrary to observations in real data. ...
The rooting of phylogenetic trees permits important inferences about ancestral states and the polarity of evolutionary events. Recently, methods that reconcile discordance between gene-trees and species-trees—tree reconciliation methods—are becoming increasingly popular for rooting species trees. Rooting via reconciliation requires values for a particular parameter, the gene transfer to gene duplication ratio (T:D), which in current practice is estimated on the fly from discordances observed in the trees. To date, the accuracy of T:D estimates obtained by reconciliation analyses has not been compared to T:D estimates obtained by independent means, hence the effect of T:D upon inferences of species tree roots is altogether unexplored. Here we investigated the issue in detail by performing tree reconciliations of more than 10,000 gene trees under a variety of T:D ratios for two phylogenetic cases: a bacterial (prokaryotic) tree with 265 species and a fungal-metazoan (eukaryotic) tree with 31 species. We show that the T:D ratios automatically estimated by a current tree reconciliation method, ALE, generate virtually identical T:D ratios across bacterial genes and fungal-metazoan genes. The T:D ratios estimated by ALE differ 10- to 100-fold from robust, ALE-independent estimates from real data. More important is our finding that the root inferences using ALE in both datasets are strongly dependent upon T:D. Using more realistic T:D ratios, the number of roots inferred by ALE consistently increases and, in some cases, clearly incorrect roots are inferred. Furthermore, our analyses reveal that gene duplications have a far greater impact on ALE’s preferences for phylogenetic root placement than gene transfers or gene losses do. Overall, we show that obtaining reliable species tree roots with ALE is only possible when gene duplications are abundant in the data and the number of falsely inferred gene duplications is low. Finding a sufficient sample of true gene duplications for rooting species trees critically depends on the T:D ratios used in the analyses. T:D ratios, while being important parameters of genome evolution in their own right, affect the root inferences with tree reconciliations to an unanticipated degree.
... At the beginning of hormogonium differentiation, a change in some environmental factors, such as an increase or decrease in a nutrient or a change in the quantity or quality of light, stimulates production (Meeks, Elhai 2002). In the laboratory, induction is performed by transferring the strain from a dense culture, close to the stationary growth phase, to a new medium , which involves several changes, such as in the amount of available nutrients and in the quality and quantity of light, in addition to the decrease in endogenous hormogonium-inhibiting substances (Gantar et al. 1993;Herdman et al. 1979;Meeks, Elhai 2002). In the treatments with nutrient addition, there was a predominance of homocytous strains, and it is precisely in these that hormogonia are more visible. ...
In epiphytic associations, cyanobacteria form the periphyton with phytoplanktonic algae and with aquatic macrophytes. In this study, we found homocytous and heterocytous filamentous strains of epiphytic cyanobacteria associated with submerged leaves of the aquatic fern Salvinia auriculata. Fila-mentous morphotypes can produce adaptive structures such as heterocysts, akinetes, and hormogonia. Based on the premise that light limitation and nutrient limitation affect the adaptive strategies of cyanobac-teria epiphytic we hypothesized that the heterocysts production would be greater under nutrient scarcity and full sunlight conditions, akinetes would be predominantly produced under growth-limiting conditions , such as nutrient scarcity and shade, and hormogonia would be abundantly produced under shade. In addition, for purposes of recording, identification and assembling a collection, we carry out the isolation of cultivable cyanobacteria. We conducted an experiment in a greenhouse applying a shade cloth and Hoagland's solution to manipulate, respectively, the light intensity and the concentration of nutrients. Both factors, light and nutrients, affected the production of adaptive structures. Heterocysts were produced in greater numbers when no nutrient was added and under full light. Akinetes were produced mainly in the treatments under shade and no nutrient addition. In its turn, hormogonia were produced in the treatments with nutrients and mainly in the shade. Accordingly, akinete differentiation was negatively correlated with that of hormogonia. We conclude that the non-addition of nutrients stimulates heterocysts production, as well as akinete production. Therefore, due to the BFN BNF performed in heterocysts, we suggest that in olig-otrophic aquatic environments, cyanobacteria epi-phytic on the roots of aquatic macrophytes can supply fixed nitrogen to the aquatic ecosystem. Besides, with the shading produced by macrophytes, and available nutrients, the production of hormogonia is stimulated due to positive phototaxis. At the end of the experiment, nine morphologically distinct strains were isolated and taxonomically classified, up to the level of family and genus, and will allow us to assemble a collection for future research.
... At the beginning of hormogonium differentiation, a change in some environmental factors, such as an increase or decrease in a nutrient or a change in the quantity or quality of light, stimulates production (Meeks, Elhai 2002). In the laboratory, induction is performed by transferring the strain from a dense culture, close to the stationary growth phase, to a new medium , which involves several changes, such as in the amount of available nutrients and in the quality and quantity of light, in addition to the decrease in endogenous hormogonium-inhibiting substances (Gantar et al. 1993;Herdman et al. 1979;Meeks, Elhai 2002). In the treatments with nutrient addition, there was a predominance of homocytous strains, and it is precisely in these that hormogonia are more visible. ...
In epiphytic associations, cyanobacteria form the periphyton with phytoplanktonic algae and with aquatic macrophytes. In this study, we found homocytous and heterocytous filamentous strains of epiphytic cyanobacteria associated with submerged leaves of the aquatic fern Salvinia auriculata. Filamentous morphotypes can produce adaptive structures such as heterocysts, akinetes, and hormogonia. Based on the premise that light limitation and nutrient limitation affect the adaptive strategies of cyanobacteria epiphytic we hypothesized that the heterocysts production would be greater under nutrient scarcity and full sunlight conditions, akinetes would be predominantly produced under growth-limiting conditions, such as nutrient scarcity and shade, and hormogonia would be abundantly produced under shade. In addition, for purposes of recording, identification and assembling a collection, we carry out the isolation of cultivable cyanobacteria. We conducted an experiment in a greenhouse applying a shade cloth and Hoagland’s solution to manipulate, respectively, the light intensity and the concentration of nutrients. Both factors, light and nutrients, affected the production of adaptive structures. Heterocysts were produced in greater numbers when no nutrient was added and under full light. Akinetes were produced mainly in the treatments under shade and no nutrient addition. In its turn, hormogonia were produced in the treatments with nutrients and mainly in the shade. Accordingly, akinete differentiation was negatively correlated with that of hormogonia. We conclude that the non-addition of nutrients stimulates heterocysts production, as well as akinete production. Therefore, due to the BFN BNF performed in heterocysts, we suggest that in oligotrophic aquatic environments, cyanobacteria epiphytic on the roots of aquatic macrophytes can supply fixed nitrogen to the aquatic ecosystem. Besides, with the shading produced by macrophytes, and available nutrients, the production of hormogonia is stimulated due to positive phototaxis. At the end of the experiment, nine morphologically distinct strains were isolated and taxonomically classified, up to the level of family and genus, and will allow us to assemble a collection for future research.
... One reason for this close association could be that, like other Bacteria and Archaea (Swan et al. 2013; Giovannoni et al. 2014), Cyanobacteria have small genomes compared with eukaryotes (Herdman et al. 1979;Humbert et al. 2013). While this may be beneficial for rapid reproduction and evolution, it is not necessarily conducive for cyanoHAB formation. ...
... Genome sizes for members of these three kingdoms are compared in Fig. 12. Archaebacterial genomes have a relatively narrow size distribution, ranging from 1.6 x 106 to 4.3 x 106 bp (118,164,165). The eubacteria have a much wider size distribution, with several Mycoplasma species (196) and Chlamydia trachomatis (83) having genomes as small as 6 x 105 bp while heterocyst-forming cyanobacteria such as Calothrix species (84,131) have genomes as large as 1.3 x 107 bp. Eucaryotic organisms have the largest range of genome sizes, extending from 1.4 x 107 to more than 1 x 1011 bp (23,168). ...
Myxobacteria are soil bacteria whose unusually social behavior distinguishes them from other groups of procaryotes. Perhaps the most remarkable aspect of their social behavior occurs during development, when tens of thousands of cells aggregate and form a colorful fruiting body. Inside the fruiting body the vegetative cells convert into dormant, resistant myxospores. However, myxobacterial social behavior is not restricted to the developmental cycle, and three other social behaviors have been described. Vegetative cells have a multigene social motility system in which cell-cell contact is essential for gliding in multicellular swarms. Cell growth on protein is cooperative in that the growth rate increases with the cell density. Rippling is a periodic behavior in which the cells align themselves in ridges and move in waves. These social behaviors indicate that myxobacterial colonies are not merely collections of individual cells but are societies in which cell behavior is synchronized by cell-cell interactions. The molecular basis of these social behaviors is becoming clear through the use of a combination of behavioral, biochemical, and genetic experimental approaches.
... For Nostoc DNA, a rate of depurination at 37°C of -20 per genome per day can be estimated from the median genome size measured for several Nostoc spp. (5 x 103 MDa = 7.6 x 106 bp [166]), assuming an internal pH of 7.4 for the cytoplasm (note that the thylakoid space may have a different pH and that the pHs of the two compartments vary with light intensity [398]), and an in vitro rate of depurination of k = 2.58 x 10-6 day- (227). The rate of depurination of a desiccated Nostoc cell would achieve a 1% depurination of the genome after storage of the cells at 37°C for 10 years. ...
The removal of cell-bound water through air drying and the addition of water to air-dried cells are forces that have played a pivotal role in the evolution of the prokaryotes. In bacterial cells that have been subjected to air drying, the evaporation of free cytoplasmic water (Vf) can be instantaneous, and an equilibrium between cell-bound water (Vb) and the environmental water (vapor) potential (psi wv) may be achieved rapidly. In the air-dried state some bacteria survive only for seconds whereas others can tolerate desiccation for thousands, perhaps millions, of years. The desiccated (anhydrobiotic) cell is characterized by its singular lack of water--with contents as low as 0.02 g of H2O g (dry weight)-1. At these levels the monolayer coverage by water of macromolecules, including DNA and proteins, is disturbed. As a consequence the mechanisms that confer desiccation tolerance upon air-dried bacteria are markedly different from those, such as the mechanism of preferential exclusion of compatible solutes, that preserve the integrity of salt-, osmotically, and freeze-thaw-stressed cells. Desiccation tolerance reflects a complex array of interactions at the structural, physiological, and molecular levels. Many of the mechanisms remain cryptic, but it is clear that they involve interactions, such as those between proteins and co-solvents, that derive from the unique properties of the water molecule. A water replacement hypothesis accounts for how the nonreducing disaccharides trehalose and sucrose preserve the integrity of membranes and proteins. Nevertheless, we have virtually no insight into the state of the cytoplasm of an air-dried cell. There is no evidence for any obvious adaptations of proteins that can counter the effects of air drying or for the occurrence of any proteins that provide a direct and a tangible contribution to cell stability. Among the prokaryotes that can exist as anhydrobiotic cells, the cyanobacteria have a marked capacity to do so. One form, Nostoc commune, encompasses a number of the features that appear to be critical to the withstanding of a long-term water deficit, including the elaboration of a conspicuous extracellular glycan, synthesis of abundant UV-absorbing pigments, and maintenance of protein stability and structural integrity. There are indications of a growing technology for air-dried cells and enzymes. Paradoxically, desiccation tolerance of bacteria has virtually been ignored for the past quarter century. The present review considers what is known, and what is not known, about desiccation, a phenomenon that impinges upon every facet of the distributions and activities of prokaryotic cells.
... One reason for this close association could be that, like other Bacteria and Archaea (Swan et al. 2013; Giovannoni et al. 2014), Cyanobacteria have small genomes compared with eukaryotes (Herdman et al. 1979;Humbert et al. 2013). While this may be beneficial for rapid reproduction and evolution, it is not necessarily conducive for cyanoHAB formation. ...
Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280° longitudinal and 90° latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole‐community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.
... In order to quantify potential microcystin producers among genera Microcystis, Planktothrix and Dolichospermum in the samples, genus-specific qPCR was performed using an absolute quantification method with an internal standard curve, constructed as described before by Vaitomaa et al. (2003) and Koskenniemi et al. (2007). For the standard curve construction, information about the approximate genome size of Microcystis, Dolichospermum (Castenholz, 2001) and Planktothrix (Herdman et al., 1979) strains was used. The qPCR amplifications of the mcyE synthase genes (primers are shown in Table 1) were performed with ESCO Swift™ Spectrum 96 Real Time Thermal Cycler (ESCO, Singapore) in 3 replicates. ...
The coexistence of potentially toxic bloom-forming cyanobacteria (CY) and generally smaller-sized grazer communities has raised the question of zooplankton (ZP) ability to control harmful cyanobacterial blooms and highlighted the need for species-specific research on ZP-CY trophic interactions in naturally occurring communities.
A combination of HPLC, molecular and stable isotope analyses was used to assess in situ the importance of CY as a food source for dominant crustacean ZP species and to quantify the grazing on potentially toxic strains of Microcystis during bloom formation in large eutrophic Lake Peipsi (Estonia). Aphanizomenon, Dolichospermum, Gloeotrichia and Microcystis dominated bloom-forming CY, while Microcystis was the major genus producing cyanotoxins all over the lake. Grazing studies showed that CY, and especially colonial CY, formed a significant, and also preferred component of algae ingested by the cladocerans Bosmina spp. and Daphnia spp. while this was not the case for the more selective calanoid copepod Eudiaptomus gracilis. Molecular analyses confirmed the
presence of CY, including Microcystis, in ZP guts. Further analyses using qPCR targeting cyanobacterial genus-specific mcyE synthase genes indicated that potentially toxic strains of Microcystis can be ingested directly or indirectly by all the dominant crustacean grazers. However, stable isotope analyses indicated that little, if any, assimilation from ingested bloom-forming CY occurred. The study suggests that CY, and particularly Microcystis with both potentially toxic and non-toxic strains, can be widely ingested by cladoceran grazers during a bloom event with implications for control of CY abundance and for transfer of CY toxins through the food web.
... Phylogeny record supplementary to the morphology based quasi-taxonomic attribution in "Oscillatoriales" CALU strains, and the resultant identification algorithm. lthough form-genera old diagnoses dealt with genotypic characters, such as DNA base composition and genome size (Herdman et al., 1979a(Herdman et al., , 1979b, they did not include phylogeny records which at that time were absent in PCC type strains. In our study, 16S rRNA gene sequences (16S) in "Oscillatoriales" CALU strains were amplified with cyanobacterial primers, and Sanger sequenced. ...
In “Oscillatoriales” cyanobacteria (Cyanophyceae), relatively simple and uniform morphology superimposes on high genetic diversity that impedes reliable identification. The system of Cyanobacteria set forth in Bergey’s Manual of Systematic Bacteriology-2001/Systematics of Archaea and Bacteria-2015 deals with operational taxa—form-genera (“larger” genera represented by strains) unlike true cyanophycean genera represented by species. Form-genera were established on morphological criteria shared with Cyanophyceae, although they were typified by Pasteur Culture Collection (PCC) strains. Despite being important in determinative cyanobacteriology, old diagnoses of form-genera should be reappraised because, in them: (i) vague and/or ephemeral morphological characters are considered taxonomically significant; (ii) phylogenetic character, such as 16S rRNA gene sequence (16S) is missing. We identified 32 “Oscillatoriales” strains from CALU collection (St. Petersburg University, Russia) basing on core morphology traits, 16S of PCC type strains, and 16S from GenBank database. We proposed that, in experimentally oriented and ecology oriented studies, unequivocal identification can be attained via triple match: streamlined form-genus diagnosis— 16S of PCC reference strain—GenBank most similar 16S. Additionally, we traced the phylogeny of “Oscillatoriales” form-genera via 16S clustering and HIP1 fingerprinting, and suggested that these operational taxa should be replaced with monophyletic assemblages. Nucleotide sequence data reported are available in the GenBank database under the accession numbers KX263921−KX263950.
... Redundancies of the 16S rRNA sequences in a single genome vary among different cyanobacteria. As well, a single cyanobacterial cell can have more than one genome copy (polyploidy) depending on the environmental conditions ( Herdman et al., 1979;Labarre et al., 1987;Becker et al., 2002). Therefore, all cell abundances calculated from the two standard curves were interpreted as M. aeruginosa CPCC 299 cell equivalents. ...
Two Great Lake embayments, Bay of Quinte (Lake Ontario) and Maumee Bay (Lake Erie) prone to toxic cyanobacteria blooms were sampled in early and late summer in 2006 to determine which cyanobacteria genotypes were present and how many of those were capable of producing microcystins. Microcystins, chlorophyll a, soluble reactive phosphorus and stoichiometric seston ratios of carbon, nitrogen and phosphorus were measured on the same samples to provide an ecological characterization of the phytoplankton. The V3 hypervariable region of the 16S rRNA and aminotransferase (AMT) genes, microcystin (mcyE) and nodularin (nda) were analyzed with PCR-DGGE and quantitative real-time PCR to describe cyanobacterial communities. DGGE results indicated species capable of producing microcystins were present at some point in all study sites and were most likely from species within the genus Microcystis. Concentrations of microcystins were greatest when hepatotoxic cell numbers were highest and when seston stoichiometry indicated cells were not nutrient stressed. This study demonstrated the effective use of a combination of molecular and ecological monitoring of cyanobacterial communities in regions that are susceptible to toxic cyanobacteria blooms.
... The amount of DNA in unicellular cyanobacteria varies from 1.6 x 10 9 to 8.6 x 10 9 daltons. This is similar to the genome size in bacteria (1.0 x 10 9 to 3.6 x 10 9 daltons) and is larger than the genome size in mycoplasmas (0.4 x 10 9 to 0.5 x 10 9 daltons; Herdman et al., 1979). The peripheral protoplasm is composed principally of thylakoids and their associated structures, the phycobilisomes. ...
The occurrence of cyanobacterial blooms in nutrients enriched aquatic ecosystems is a widespread phenomenon. Cyanobacterial blooms synthesized several bioactive compounds, and cyanotoxin is among one of them. The most commonly reported cyanotoxin are Nodularin, Microcystins Anatoxin‐a, Saxitoxins, and Cylindrospermopsin. Biochemically, cyanotoxins are polyketides, alkaloids, nonribosomal peptides, potent toxins, and trypsin inhibitors. Pharmaceutically and neutraceutically these are significant, and exhibits, a diverse range of bioactivity, mainly antiviral, antibacterial, antitumor, anticancerous, antifungal, etc. Several oligopeptides are synthesized through nonribosomal peptide synthetase (NRPSs) in prokaryotes and lower eukaryotes. Cyanobacterial bioactive compounds are not utilized in growth and developments but are a promising source for the novel compounds. Nutrient composition especially nitrogen and phosphorus significantly influences types of bioactive compounds. The common cyanotoxin frequently occurred in cyanobacterial blooms is Microcystin, and is encoded by mcy gene cluster in freshwater and brackish water ecosystems. There are several methods used for purification and characterizations of the bioactive compounds from blooms forming cyanobacterial such as HPLC, UPLC, LC‐MS‐MS, and MALDI‐TOF‐MS. This review mainly focused on novel bioactive compounds obtained from cyanobacteria.
Recent progress in studies on the bacterial chromosome is summarized. Although the greatest amount of information comes from studies on Escherichia coli, reports on studies of many other bacteria are also included. A compilation of the sizes of chromosomal DNAs as determined by pulsed-field electrophoresis is given, as well as a discussion of factors that affect gene dosage, including redundancy of chromosomes on the one hand and inactivation of chromosomes on the other hand. The distinction between a large plasmid and a second chromosome is discussed. Recent information on repeated sequences and chromosomal rearrangements is presented. The growing understanding of limitations on the rearrangements that can be tolerated by bacteria and those that cannot is summarized, and the sensitive region flanking the terminator loci is described. Sources and types of genetic variation in bacteria are listed, from simple single nucleotide mutations to intragenic and intergenic recombinations. A model depicting the dynamics of the evolution and genetic activity of the bacterial chromosome is described which entails acquisition by recombination of clonal segments within the chromosome. The model is consistent with the existence of only a few genetic types of E. coli worldwide. Finally, there is a summary of recent reports on lateral genetic exchange across great taxonomic distances, yet another source of genetic variation and innovation.
Viruses are integral to ecological and evolutionary processes, but we have a poor understanding of what drives variation in key traits across diverse viruses. For lytic viruses, burst size, latent period, and genome size are primary characteristics controlling host-virus dynamics. Burst size and latent period are analogous to organismal traits of fecundity and generation time, and genome size affects the size of the virion as well as viral control of host metabolism. Here we synthesize data on these traits for 75 strains of phytoplankton viruses, which play an important role in global biogeochemistry. We find that primary traits of the host (genome size, growth rate) are major ecological drivers, explaining 40-50% of variation in burst size and latent period. We analyze an eco-evolutionary model to explore mechanisms underlying these patterns. We find that burst size may be set by the host genomic resources available for viral construction, while latent period evolves to permit this maximal burst size, modulated by host metabolic rate. These results suggest that general mechanisms may underlie the evolution of diverse viruses, which will facilitate our understanding of viral community processes, ecosystem impacts, and coevolutionary dynamics.
Viruses are integral to ecological and evolutionary processes, but we have a poor understanding of what drives variation in key traits across diverse viruses. For lytic viruses, burst size, latent period, and genome size are primary characteristics controlling host-virus dynamics. Here we synthesize data on these traits for 75 strains of phytoplankton viruses, which play an important role in global biogeochemistry. We find that primary traits of the host (genome size, growth rate) explain 40%–50% of variation in burst size and latent period. Specifically, burst size and latent period both exhibit saturating relationships versus the host∶virus genome size ratio, with both traits increasing at low genome size ratios while showing no relationship at high size ratios. In addition, latent period declines as host growth rate increases. We analyze a model of latent period evolution to explore mechanisms that could cause these patterns. The model predicts that burst size may often be set by the host genomic resources available for viral construction, while latent period evolves to permit this maximal burst size, modulated by host metabolic rate. These results suggest that general mechanisms may underlie the evolution of diverse viruses. Future extensions of this work could help explain viral regulation of host populations, viral influence on community structure and diversity, and viral roles in biogeochemical cycles.
Mi.cro.co' le.us . Gr. adj. mikros small (or thin); Gr. n. koleos sheath; M.L. masc. n. Microcoleus small or thin sheath.
Cyanobacteria / Subsection III / Incertae Sedis / Form‐ Microcoleus
In members assigned to this form‐genus, two to several trichomes oriented parallel , often spirally and tightly interwoven, are enclosed by a common homogeneous sheath (Figure 1). Cells (diameter 3–6 µm) composing the trichomes are longer than wide (or isodiametric); visible constrictions at the cross‐walls (but usually much less than 1/4 of the cell diameter); mature end cells are conical ; the bundles of filaments generally exhibit slow gliding motility, not involving rotation . Based on analysis of a limited number of isolates, a radial arrangement of thylakoids (in cross‐section, T.E.M.) seems to be typical .
Among the most significant conceptual advances in biology made in the twentieth century was the realization that sharp discontinuities exist, on the one hand, between cellular organisms and the noncellular entities now known as viruses and, on the other hand, between those cellular organisms that are prokaryotic and those that are eukaryotic in organization of their cells. It may seem strange to a contemporary microbiologist that nonrecognition of these discontinuities, and of the related distinctions among these kinds of life forms, persisted as long as it did. In fact, manifestations of this ignorance were still with us into the 1970s when a number of plant diseases, thought for a century to be caused by filterable viruses, were first shown actually to be caused by various deformable (and, hence, filterable) bacteria without cell walls, the mycoplasma-like entities (Whitcomb and Tully, 1979; this Handbook, Chapters 167 and 169).
Pseud' an.a.baen' a . Gr. adj. pseud false; anabaena (cf. genus Anabaena ); M.L. fem. n. Pseudanabaena false Anabaena .
Cyanobacteria / Subsection III / Incertae Sedis / Form‐ Pseudanabaena
Trichomes that divide exclusively by binary fission in one plane and have conspicuous constrictions at the crosswalls that may exceed half the cell diameter (Figure 1). In some strains, the total constriction is less but is still more than 1/8 the cell diameter (Guglielmi and Cohen‐Bazire, 1984a). Cells are longer than broad to isodiametric and are often barrel‐shaped . Trichomes of strains characterized in culture range from ∼1 to 3 µm in diameter . The formation of the transverse septum involves a partial centripetal ingrowth of all wall layers. In some cases, the remaining connection appears quite narrow, as if the cells were strung as beads. The structural (peptidoglycan) layer of the cross‐wall is 3–6 times thicker than the layer surrounding the rest of the cell (Guglielmi and Cohen‐Bazire, 1984a) (Figure 2). Another characteristic observed through T.E.M. is the consistency of peripheral thylakoids, parallel to the cell walls . Near the cross‐walls, the continuity of thylakoids may be interrupted by gas vesicle clusters. The trichomes are usually straight and, depending on the morphotype, may be quite short (consisting of less than 3 to ∼10 cells) or may be longer (>10 cells). Reproduction by intercellular trichome breakage . Single detached cells are frequently found in cultured populations and may be confused with unicellular cyanobacteria (Castenholz, unpublished). Gliding motility, probably without rotation, occurs at rates usually <1 µm/s. Gliding motility has been lost in a few cultured strains (Guglielmi and Cohen‐Bazire, 1984a).
Nos ' toc . M.L. n. Nostoc origin uncertain, supposedly invented by Paracelsus from the old English word Nosthryl (nostril) and the corresponding German word Nasenloch = Nostoch .
Cyanobacteria / Subsection IV / Subsection IV.I / Form‐ Nostoc
Ri.vu.la' ri.a . L. adj. rivularius pertaining to a small creek; M.L. fem. n. Rivularia the one of a small creek.
Cyanobacteria / Subsection IV / Subsection IV.II / Form‐Rivularia
Chro.o.coc' ci.di.op' sis . Gr. fem. n. chroa skin; Gr. n. kokkidios presumed diminutive of kokkos small seed or grain; Gr. fem. n. opsis appearance; M.L. fem. n. Chroococcidiopsis small cells appearing in skin or coating.
Cyanobacteria / Subsection II / Genera in Which Extensive Vegetative Binary Fission Precedes Multiple Fission / Form‐ Chroococcidiopsis
Cyanobacteria that undergo repeated binary fission in three planes to produce more or less regular cubical cell aggregates. Multiple fission occurs simultaneously in most cells of the aggregate and is followed by the release of nonmotile baeocytes which possess an outer fibrous wall layer. The baeocytes differ little in diameter from mature parental cells and enlarge symmetrically into a spherical vegetative cells that, just before the onset of binary fission, attain dimensions characteristic and constant for any given strain.
Nod.u.la' ri.a . L. adj. nodulus diminutive of nodus, small and knotty, knobby; L. n. arium place; M.L. fem. n. Nodularia knobby microbial filament.
Cyanobacteria / Subsection IV / Subsection IV.I / Form‐ Nodularia
The trichomes, motile or immotile, are composed of vegetative cells that are shorter than broad (“discoid” or “disk‐like”) and may be enclosed in a thin sheath layer. Terminal cells do not differ from intercalary cells. Heterocysts and akinetes are similar in shape to the vegetative cells but often appear compressed. Differentiation of heterocysts takes place predominantly in intercalary positions. Akinetes are initiated usually distant from heterocysts and may occur in short chains. Structurally distinct hormogonia not produced. Planktonic members exhibit gas vesicle clusters dispersed throughout the vegetative cells.
Lyng' by.a . M.L. fem. n. Lyngbye named after H.C. Lyngbye, Danish botanist, 1782–1837.
Cyanobacteria / Subsection III / Incertae Sedis / Form‐ Lyngbya
Filamentous organisms that share the entire range of cellular types with Oscillatoria (as here defined), but which produce a distinct, persistent, and firm sheath (Figure 1). The sheath may be thin but can be seen with phase contrast optics, particularly where it extends beyond the terminal cell of the trichome (Fig 1). The trichome diameters range from about 6 to ∼80 µm. Sheaths in some species may accrete to several µm in thickness and display laminations. Cells composing the trichomes are disk shaped (shorter than broad) , a feature also characteristic of Oscillatoria (as here defined).
Apart from sharing the basic cellular features of other Bacteria , the cyanobacteria possess unique and diagnostic characteristics that will be briefly described here, but less extensively than in the 1989 edition of Bergey's Manual of Systematic Bacteriology . The cell wall in cyanobacteria is of a Gram‐negative type. Cell division in most unicellular and colonial cyanobacteria and some filamentous forms is by binary fission. Regarding cell exterior and motility, fimbriae (or pili) occur abundantly with diverse patterns in many cyanobacteria. Although not all thylakoids in cyanobacteria appear to be invaginations of the cytoplasmic membrane, there are orderly “attachment points” or “thylakoid centers” associated with the periphery of the cytoplasm or the cytoplasmic membrane. In the cytoplasm of cyanobacteria there are many other components and “inclusions”, most of which can be visualized readily using various preparative techniques for transmission electron microscopy. They include glycogen granules, cyanophycin granules, carboxysomes (polyhedral bodies), polyphosphate (volutin) granules, and gas vacuoles. Heterocysts, akinetes, and hormogonia are some of the specialized cells and differentiation in Cyanobacteria. The chief physiological/biochemical characteristic of cyanobacteria, distinguishing them from all other procaryotes, is the dual photosystem that allows the use of H 2 O as photoreductant with the consequent liberation of O 2 . Two courses for the delimitation of genera have been followed by cyanobacterial specialists: (a) to retain “small” genera or (b) to gather many species into fewer genera.
Cyanobacteria / General Characteristics of the Cyanobacteria
A.na.bae' na . Gr. adj. ana up again; Gr. v. baino to walk, to step; M.L. fem. n. Anabaena to step up again, repeating line of units (cells).
Cyanobacteria / Subsection IV / Subsection IV.I / Form‐Anabaena
Trichomes straight or slightly sinuous, vegetative cells spherical, cylindrical, or barrel shaped, and separated by conspicuous constrictions at the crosswalls. Heterocysts predominantly intercalary, though terminal heterocysts may also occur. Akinetes located, singly or in groups (2–3), adjacent to heterocysts or occurring in chains, initiated distant from heterocysts. A firm sheath is absent, but mucilage production may be abundant. False branching generally not observed. Reproduction by random trichome fragmentation. Hormogonia, distinct in morphology from the parental trichomes, not produced.
Spi.ru.li' na . L. n. spira a coil; L. n. linea a line; M.L. fem. n. Spirulina coiled filament.
Cyanobacteria / Subsection III / Incertae Sedis / Form‐ Spirulina
Filamentous organisms that divide exclusively by binary fission and in one plane but that grow in the form of a tight to nearly tight, coiled right‐ or left‐handed helix , although this helix may become partly unwound in some trichomes of cultured populations. More loosely coiled representatives often form partial double helices composed of two individual filaments that rotated into each other. The cross‐walls are thin and barely visible even if observed by light microscopy using phase contrast objectives , a characteristic that distinguishes this genus from Arthrospira (Holmgren et al., 1971) (Figure 1). Originally Spirulina was described as being a long unicellular thread. No sheath is visible under the light microscope, and “healthy” trichomes are in constant motion. Gliding motility consists of a “turning of the screw”, thus with great transverse movement and little forward motion. Motility is by rotation around the outer surface of the helix . Free ends not in contact with a solid support may oscillate wildly as the coil turns. The terminus of the trichome is either blunt or pointed. In different species the diameter of the trichome can range from <1 µm to ∼5 µm in size. In the latter case, the width of the whole helix may be as great as 12 µm. Color is variable, blue‐green to red; the latter being typical of some marine representatives that synthesize C‐PE as the major light‐harvesting pigment, but contain relatively little PC and APC. Although C‐PE content may vary inversely with light intensity, complementary chromatic adaptation has not been observed (Tomaselli et al., 1995). Spirulina isolates seem to be stable with respect to trichome structure. Straight variants, as found often in Arthrospira (Jeeji‐Bai and Seshadri, 1980; Lewin, 1980; Rippka, unpublished), have not been observed, even after maintenance in culture for more than 30 years (Rippka, unpublished).
Ca' lo.thrix . Gr. adj. kalos beautiful; Gr. n. thrix hair; M.L. fem. n. Calothrix beautiful filament.
Cyanobacteria / Subsection IV / Subsection IV.II / Form‐Calothrix
Mature ensheathed trichomes exhibit a pronounced degree of tapering. The motile hormogonia are generally very short, exhibit a significantly reduced cell diameter, and are sheathless (or less ensheathed). They give rise to trichomes that differentiate a basal, one‐pored heterocyst. False branching frequent. Akinetes lacking in most members. All are freshwater, soil, or hot spring inhabitants.
Scy.to.ne' ma . Gr. n. skytos leather; Gr. n. nema thread; M.L. neut. n. Scytonema leather thread.
Cyanobacteria / Subsection IV / Subsection IV.I / Form‐Scytonema
The mature trichomes are immotile, heavily ensheathed, and form numerous false branches that exhibit upright aerial mode of growth. Constrictions between the disk‐shaped to cylindrical cells are shallow. Heterocysts generally occupy intercalary positions, although some false branches may carry at their base a terminal heterocyst. Hormogonia are less ensheathed, exhibit no or only slow motility, and differ little in cell morphology from the mature filaments. Akinetes are not produced.
The cyanobacterial photosynthetic apparatus is remarkably similar in structure and function to that found in the chloroplasts of eucaryotic algae and higher plants (Bryant, 1987). Four major multiprotein complexes of the thylakoids—the Photosystem II complex = the water-plastoquinone photo-oxidoreductase; the cytochrome b6/f complex= the plastoquinol-plastocyanin (cytochrome c553) oxidoreductase; the Photosystem I complex = plastocyanin (cytochrome c553)-ferredoxin (flavodoxin) photo-oxidoreductase; and the ATP synthase—have been shown to be rather similar in all oxygenic procaryotes and eucaryotes studied. The predominant differences among the photosynthetic apparatuses in the various algae and higher plants derives from the considerable diversity that exists in the light-harvesting antennae systems among these organisms. In eucaryotic algae and higher plants, the light-harvesting complexes for Photosystem I and Photosystem II are a diverse collection of carteno-chlorophyll protein complexes that in general are integral membrane components (Owens, 1988; Thornber et al., 1988). Such antenna systems are also found in certain procaryotes such as Prochloron sp. and Prochlorothrix hollandica (Bullerjahn et al., 1987). However, in the cyanobacteria, in the chloroplasts of the eucaryotic red algae, and in the cyanelles of certain phylogenetically ambiguous eucaryotes such as Cyanophora paradoxa, the light-harvesting antenna complexes for Photosystem II are large, multiprotein complexes composed of water-soluble proteins, the phycobilisomes, which are attached to the thylakoid surface in close proximity to the Photosystem II reaction centers (Bryant, 1987).
Cyanobacteria, a group of prokaryotes previously known as blue&;#x02010;green algae, belong to the most ancient group of photosynthetic organisms and are the only prokaryotes capable of carrying out plantlike oxygenic photosynthesis. This chapter gives a general introduction to cyanobacteria physiology as well as their genetic tools, which are important background for utilizing these organisms for industrial applications. It reviews works on the development of strains as potential cell factories for the production of commercially relevant compounds, with a focus on primary metabolites. Cyanobacteria form a phylum of bacteria that can perform plantlike photosynthesis. The physiology of cyanobacteria as a photosynthetic organism is greatly impacted by the availability of light in its environment. A few unicellular cyanobacteria are naturally competent for transformation, and can uptake foreign DNA from their environment in the form of plasmid or linear DNA.
A historical survey of studies of seedling morphology and anatomy in the palm family is given. The traditional three germination types—adjacent ligular, remote ligular, and remote tubular—that have been commonly recognized are reevaluated. The study includes seedlings of 63 species, representing the six subfamilies of palms. Morphological characteristics of germination patterns and the anatomy of the eophyll are described. The results of this survey show that germination types determined by the length of the hyperphyll (cotyledonary petiole) are not completely valid. Instead, a combination of characters such as primary root orientation, coleoptile length, number of cataphylls, and eophyll plication correspond to the most recent classification of the family, and represent a better way of describing germination.
The 32 kD-D1 protein is a chloroplast-encoded gene product that, in association with O2 and cytochrome b559, constitutes the photosystem II (PS II) reaction center. The protein has additional characteristics that have attracted considerable attention. Among these are its rapid light-dependent degradation and its being the target site for many PS II herbicides. We review the current model for the organization and function of the PS II reaction center components in analogy with the bacterial reaction center. The different steps in the life cycle of the 32 kD-D1 protein including its post-translational modifications are also described. Finally, we address the question of light regulation of the protein at the transcriptional, post-transcriptional, and post-translational levels. The various models proposed for the structure and function of the 32 kO-OJ protein are being tested by means of cyanobacterial and Chlamydomonas transformation systems. Some recent results on the bioengineering of the herbicide-binding sites of the protein are also summarized.
Cyanobacteria (blue-green algae, blue-greens) are prokaryotic organisms that contain a photosynthetic apparatus similar in structure and function to that present in the chloroplast of the phototrophic eukaryotes (Stanier, 1977). They differ from Prochloron, a prokaryote that contains chlorophyll b instead of phycobiliproteins as light-harvesting pigments. They differ from the purple and green bacteria, particularly because they carry out oxygenic photosynthesis, but also because of differences in the ultrastructure, in the chemical composition of the photosynthetic apparatus, and in nutritional requirements and growth physiology. The mechanism of cyanobacterial photosynthesis is identical to that of photosynthetic eukaryotes. Accordingly, in this discussion of oxygenic prokaryotic photosynthesis, only those areas where cyanobacteria played a role in the understanding of the process or only those details which are characteristic of blue-greens will be reviewed.
The best established physical evidence of early life forms are stromatolites which have been dated to 3.3–3.5 × 109 (Awramik et al., 1983; Schopf and Walter, 1987; Schopf, 1993). Although the phototrophic obligatory anaerobes belonging to the genus Chloroflexus can make laminated microbial mats similar to that seen in micro fossil records (Awramik et al. 1983; Giovannoni et al., 1987), these early stromatolites are generally thought to be in large part the result of the activity of cyanobacteria. Recent micro fossil evidence (Sohopf, 1993) supports this view. Molecular evidence based on ribosomal RNA sequences does not however place cyanobacteria among the earliest branchings of life but rather shows them emerging somewhat later as one of approximately twelve distinct phyla of the Domain Bacteria (Giovannoni et al., 1988). Regardless of the precise time of arrival of the cyanobacteria they are of special interest to the study of early life (Lazcano and Miller, 1994) because they are the most important group of extant microorganisms in terms of relating data from the geological and molecular approaches to the study of early life.
Two coccoid cyanobacteria isolated from South Atlantic Ocean continental shelf deep water and from a marine green algae inhabiting the Admiralty Bay, King George Island, Antarctica were investigated based on morphological and ultrastructural traits, phylogeny of 16S rRNA gene sequences, secondary structure of the 16S-23S ITS regions and phylogenomic analyses. The majority of these evaluations revealed that both strains differ from the already known cyanobacterial genera and, therefore, supported the description of the novel genus Aliterella gen. nov., under the provisions of the International Code of Nomenclature for algae, fungi and plants. Furthermore, the identity and phylogeny of 16S rRNA gene sequences together with secondary structure of D1D1' and BoxB intergenic regions sustained that the two strains are distinct species: Aliterella atlantica sp. nov. (type SP469036, strain CENA595T) and Aliterella antarctica sp. nov. (type SP469035, strain CENA408T). The phylogenomic analysis of A. atlantica CENA595T based on 21 protein sequences revealed that this genus belongs to the cyanobacterial order Chroococcidiopsidales. The isolation and cultivation of two geographically distant unicellular members of a novel cyanobacterial genus and the sequenced genome of the type strain bring new insights into the current classification of the coccoid group and in the reconstruction of their evolutionary history.
Phycological observations on field materials have led to a remarkable nomenclatural hypertrophy. About 170 genera and over 1,000 species have been described by the standard taxonomic treatment of Geitler (1932), now almost 50 years old. This field-based system of classification leads to many difficulties and ambiguities when applied to pure cultures. The necessarily provisional goal of this chapter is to redefine genera in such a way that simple and clear-cut assignments may be made for cyanobacterial pure cultures. Our approach has been conservative: insofar as possible, we have attempted to maintain the classical generic nomenclature and definitions (Bourrelly, 1970; Desikachary, 1959; Geitler, 1932).
The proton-translocating cytochrome b6-f complex of chloroplast and cyanobacterial thylakoid membranes catalyzes electron transfer from plastoquinone to plastocyanin and is thus required for noncyclic electron flow between the two photosystems (PS) as well as for cyclic flow around PS I. The complex consists of four essential polypeptides: cytochromes f and b6, the Rieske FeS protein, and a subunit IV of unknown function. In the cyanobacterium Anabaena these have apparent molecular weights of 31, 22.5, 22, and 16kd, respectively (1). The b6-f polypeptides occur in equal stoichiometric amounts and share considerable structural homology with components of the mitochondrial-type cytochrome b-cl complex (2). In photosynthetic eukaryotes the genes encoding three of these polypeptides reside in the chloroplast whereas the one for the Rieske FeS protein is located in the nucleus (3). In a purple photosynthetic bacterium the three genes for the essential polypeptides of the b-cl complex are clustered and cotranscribed (4).
Plastids, the eukaryotic organelles responsible for photosynthesis and other biochemical tasks, are semiautonomous endosymbionts derived from previously free-living cyanobacteria (Gray, 1992; Douglas, 1994; Loiseaux-de Göer, 1994; Bhattacharya and Medlin, 1995). In this chapter we discuss, with an emphasis on molecular phylogenetic evidence, our current understanding of the origin and diversification of these organelles, provide an overview of plastid diversity in the context of endosymbiosis, and discuss the evolution of plastid genomes from that of a cyanobacterium. We place particular emphasis on the evidence from different cellular genomes—nuclear, plastid, and mitochondri al—that bears on the fundamental question of whether all plastids are derived from a single endosymbiotic event, or from two or more independent events. Although the bulk of the data support a monophyletic origin of plastids, some evidence, particularly from the nuclear genome, suggests at least two independent endosymbiotic events.
Cyanobacteria / Subsection III / Incertae Sedis / Subsection III
It is now apparent from multiple 16S rDNA sequence analyses that this subsection is not phylogenetically coherent. Some of the genera of this former order and even named species of the genus Oscillatoria , for example, are polyphyletic (see Turner, 1997; Phylogenetic relationships amongst the Cyanobacteria , p. 487). It is premature to reclassify this “oscillatorian” group of morphotypes on the basis of the still incompletely determined genetic relationships. The present treatment, therefore, will follow the older, artificial grouping of Subsection III, although the degree of genetic similarities of some genera (on the basis of nucleotide and other sequence similarities) are mentioned in the text description of each genus and also in the discussion in the chapter on phylogeny.
The flagellate Cyanophora paradoxa contains blue-greenish, organelle-like inclusions termed cyanelles which perform photosynthetic CO2-fixation in place of chloroplasts. By the use of the HPLC-technique, Cyanophora was shown to form glucose, sucrose, maltose, mannitol, ribose, glycerol and trehalose. Extracts from the whole organism and from the eucaryotic host, but not from the cyanelles, convert 14C-labelled UDP-glucose to polyglucan. Synthesis of sucrose from UDP-glucose and fructose-6-P or fructose could not be demonstrated in any extract from Cyanophora. The transfer of metabolites into cyanelles was monitored by the silicone oil filtering technique. The solute spaces for 14C-labelled sorbitol and 3H2O were the same indicating that sorbitol freely penetrated the plasma membrane of cyanelles in contrast to the situation found in chloroplasts. The measurements of the solute spaces for the different compounds showed that maltose and sucrose were not accumulated by isolated cyanelles. Other compounds like fructose, fucose, glutamine or glycine had intermediate sizes of their solute spaces. Cyanelles apparently possess a rapidly transporting glucose carrier and not a malate/oxaloacetate shuttle and also not an ATP/ADP translocator. The carrier composition at the plasma membrane of cyanelles and at the inner envelope membrane of chloroplasts seems to be totally different.
A comparative discussion of cyanellar and chloroplast genome structure and gene organization might lead to a better understanding of plastid ancestry and to new concepts about how to trace plastid evolution. This was our hypothesis and initial aim when we decided to work with the cyanelle DNA from Cyanophora paradoxa.
DNA replication and repair are two fundamental processes required in life proliferation and cellular defense and some common proteins are involved in both processes. The filamentous cyanobacterium Anabaena sp. strain PCC 7120 is capable of forming heterocysts for N2 fixation in the absence of a combined-nitrogen source. This developmental process is intimately linked to cell cycle control. In this study, we investigated the localization of the DNA double-strand break repair protein RecN during key cellular events, such as chromosome damaging, cell division, and heterocyst differentiation. Treatment by a drug causing DNA double-strand breaks (DSBs) induced reorganization of the RecN focus preferentially towards the mid-cell position. RecN-GFP was absent in most mature heterocysts. Furthermore, our results showed that HetR, a central player in heterocyst development, was involved in the proper positioning and distribution of RecN-GFP. These results showed the dynamics of RecN in DSB repair and suggested a differential regulation of DNA DSB repair in vegetative cell and heterocysts. The absence of RecN in mature heterocysts is compatible with the terminal nature of these cells.
Phosphatidylglycerol (PG) is considered to play an important role in the ordered assembly and structural maintenance of the photosynthetic apparatus in thylakoid membranes. However, its function in photosynthesis remains poorly understood. In this study we have identified a pgsA gene of Synechocystis sp. PCC6803 that encodes a PG phosphate synthase involved in the biosynthesis of PG. A disruption of the pgsA gene allowed us to manipulate the content of PG in thylakoid membranes and to investigate the function of PG in photosynthesis. The obtained pgsA mutant could grow only in the medium containing PG, and the photosynthetic activity of the pgsA mutant dramatically decreased with a concomitant decrease of PG content in thylakoid membranes when the cells grown in the presence of PG were transferred to the medium without PG. This decrease of photosynthetic activity was attributed to the decrease of photosystem (PS)II activity, but not to the decrease in PSI activity. These findings demonstrate that PG is essential for growth of Synechocystis sp. PCC6803 and provide the first direct evidence that PG plays an important role in PSII.
It has been currently estimated that the life generated about four billion years ago in the primitive sea as a result of the chemical evolution. There is no doubt that, at that time, the protoorganism was a prokaryotic monad, formed from a certain aggregate of primitive proteins, nucleic acids, and other macromolecules and wrapped with (phospho)lipid membrane. Some workers have proposed that the macromolecules involved in the formation of the life were adsorbed on surface of clay particles in the primeval soup (Cairns-Smith 1982). However, it seems very unlikely that such a simple aggregation of the macromolecules would lead to the formation of a vital cell. The reasons for such uncertainty which have been discussed (see Nakamura 1987c) are: (1) The extant cells, without exception, are wrapped by a single membrane consisting of phospholipid bilayer. (2) Life is expressed only in a closed, rather than open, system isolated from the environment by the plasma membrane.
SUMMARYA DNA-DNA hybridization membrane filter method suitable for blue-green algal DNA was developed. One of the main obstacles, the high amount of aspecific binding of the blue-green algal DNA to filters, could be resolved by means of an additional purification step involving isopycnic centrifugation of the thoroughly purified DNA. Application on DNA of several strains of blue-green algae indicates that this method is useful for taxonomic purposes.
On the basis of a comparative study of 178 strains of cyanobacteria, representative of this group of prokaryotes, revised definitions of many genera are proposed. Revisions are designed to permit the generic identification of cultures, often difficult through use of the field-based system of phycological classification. The differential characters proposed are both constant and readily determinable in cultured material. The 22 genera recognized are placed in five sections, each distinguished by a particular pattern of structure and development. Generic descriptions are accompanied by strain histories, brief accounts of strain properties, and illustrations; one or more reference strains are proposed for each genus. The collection on which this analysis was based has been deposited in the American Type Culture Collection, where strains will be listed under the generic designations proposed here.
Two strains of unicellular cyanobacteria which reproduce exclusively by budding are described and assigned to genus Chamaesiphon.
The previously discovered linear relation between the base composition of DNA, expressed in terms of percentage of guanine plus cytosine bases, and the denaturation temperature, Tm, has been further investigated. By means of measurements on 41 samples of known base composition the previously observed relation has been confirmed. It can be summarized thus : for a solvent containing 0·2 M-Na+, Tm = 69·3 + 0·41 (G-C) where Tm is in degrees Centigrade and G-C refers to the mole percentage of guanine plus cytosine. The deviations of experimental points from this relation are no more than that expected from the uncertainties of base analysis and the variations of a half degree in the reproducibility of determining the Tm. Consequently it appears that the measurement of the Tm is a satisfactory means of determining base composition in DNA. The Tm values are most simply measured by following the absorbance at 260 mμ as a function of temperature of the DNA solution and noting the midpoint of the hyperchromic rise. Only 10 to 50 μg of DNA are required.A number of other DNA samples of unknown base composition have been examined in this manner and their base compositions recorded.
The following properties of the genomic DNA of the unicellular blue-green alga Agmenellum quadruplicatum have been determined: (1) buoyant density in neutral CsCl (1·7012 g/cm3); (2) thermal denaturation profile (Tm=89·2°C); (3) kinetic complexity (2·2×109 to 2·8×109 daltons); (4) quantity per cell (8×109 to 13×109 daltons); and (5) molecular weight (3·9×109).These experiments indicate that blue-green algal DNA is similar to that of bacteria in the following ways: (1) there is little base composition heterogeneity present; (2) repeated sequences are below the level of detection; and (3) the size of the chromosomal DNA is most likely equal to the kinetic complexity. Our studies do suggest, however, that Agmenellum unlike common bacteria, may have a basal DNA content of two or more chromosomes per cell.
Many pairs of genes whose gene products are functionally related lie either 90 degrees or 180 degrees apart on the circular map of the E. coli chromosome. A mechanism of evolution is proposed that involves two sequential duplications of an ancestral genome, followed by mutation and divergence of function of replicate genes.
The molecular complexity of double-stranded phage genome DNA was determined by an adaptation of the initial renaturation rate method (Gillis et al., 1970). The exact conditions, the reproducibility, the reliability and the effects of salt concentration, optimal temperature, renaturation time, DNA concentration and base composition were determined. The method is sensitive: a sample size of 20 determinations yields 4% confidence limits on the sample mean. The molecular complexity and length of genome DNA from several phages were determined. Our results agree perfectly with the most reliable values proposed by Freifelder (1970). Our method appears to offer advantages by its rapidity, reproducibility and reliability.
A statistical treatment shows that the available literature data on the molecular weight of bacterial and phage chromosome DNA, and on the length of phage chromosome DNA, of the same organisms are so widely scattered that an eventual effect of the DNA base composition on the renaturation rate is smaller than the experimental scatter. When the most reliable literature data on phage T5, T7 and λ+ genome sizes (Freifelder, 1970) are used in conjunction with our k′ measurements, the effect of the % (G+C) on the renaturation rate is negligible. We propose to disregard this effect until more precise reference data become available.
Electron microscope examination and velocity sedimentation analysis of the deoxyribonucleic acid released from Pseudomonas aeruginosa spheroplasts indicate that this organism carries the bulk of its genetic determinants in a single duplex deoxyribonucleic acid molecule having a molecular mass of 2.1 x 10(9) daltons.
The molecular weight of the genomes of the blue-green algaeAnacystis nidulans andAnabaena cylindrica have been estimated as 2.27×109 and 2.47×109 daltons respectively from the renaturation kinetics of DNA. Thus the genomes of these organisms are similar in size to that ofEscherichia coli K-12, (2.40×109 daltons) measured by the same technique. No evidence was obtained of repeated sequences in the DNA of the two blue-green algae.
The cell volume and macromolecular composition, in terms of DNA, RNA and cell mass, were examined in Anacystis nidulans at different growth rates of the organism. Both DNA and RNA increased exponentially with increasing growth rate, as has been found in several heterotrophic bacteria. However, in this blue-green alga the ratio of DNA to RNA was independent of growth rate. Cell mass and volume also increased exponentially with growth rate though at a slower rate than RNA and DNA. These results also indicate a constant ratio of tRNA and rRNA to DNA in contrast to the situation in heterotrophic bacteria so far studied.
The variation of cell volume in this organism can be related to the control of cell division, and indicates that the commencement of DNA replication and the processes of cell division are associated with the achievement of a critical cell volume, as has been demonstrated for Escherichia coli.
A new method is described for the determination of the total molecular weight of haploid genome DNA. It is based on initial optical renaturation rate measurements of precisely known concentrations of fragmented DNA. The theoretical basis of the measurement is presented. The actual state of replication of the genome has little effect. The exact conditions and the effects of DNA concentration, renaturation time, size of DNA fragments, buffer concentration, optimal temperature and % (G + C) have been determined. Several types of bacterial DNA of known genome size were included as a control. As an application, the DNA genome size have been determined of 40 different bacteria. The method appears to offer advantages by its simplicity, rapidity and reproducibility.
ELECTRON microscopic studies of the contour length of DNA from a mycoplasma species, Mycoplasma hominis (H 39)1, have shown that the DNA in this organism is organized in a single circular chromosome, 262 microns long, corresponding to a molecular weight of 5.0 × 108 daltons. The genome size of bacterial DNA is only well known for a very few bacteria (genome sizes, 0.8-3.0 × 109 daltons)2, but the genomes in mycoplasmas may well be smaller that those of most or all bacteria. If all or most mycoplasmas were to have this same low chromosomal DNA content, the findings might be taken as a strong indication for their having a common phylogenetic origin as well as justifying the placing of mycoplasmas as a separate class of organisms3.
The rate of renaturation of fully denatured DNA is kinetically a second-order reaction. The reaction rate increases as the temperature decreases below Tm†, reaching a broad flat maximum from 15 to 30 °C below Tm and then decreases with a further decrease in temperature. Let N be the complexity of the DNA or the number of base-pairs in non-repeating sequences per virus or cell for the given DNA, and L the average number of nucleotides per single strand of the denatured DNA preparation. Then, the second-order renaturation rate constants for all DNA's are given approximately by . mole−1 sec−1 at (Tm − 25) °C and at [Na+] = 1.0 mole 1.−1 in aqueous solution. The reaction rate increases slightly with the GC content of the DNA. The reaction rate at the temperature maximum (Tm − 25) °C is inversely proportional to solvent viscosity, when the viscosity is changed by the addition of components which either have a small (sucrose, glycerol, ethylene glycol) or a large (NaClO4) effect on Tm. It is proposed that the mechanism of the reaction involves the joining of short, homologous sites on the two strands followed by a fast, reversible zippering reaction with forward rate constant kt. A computer analysis for this model explains the temperature and the GC dependence. To explain the viscosity dependence it is proposed that kf is inversely proportional to viscosity; that is, the zippering reaction is hydrodynamically limited. Any simple theory predicts ; the observed L0.5 length dependence is attributed to an excluded volume or steric hindrance effect, that is, to restricted interpenetration of the two complementary denatured DNA coils.
DNA from two blue-green algae was isolated and characterized. The buoyant densities, thermal denaturation and renaturation, thermal melting values, base compositions, sedimentation coefficients, and molecular weights were determined. Blue-green algal DNA renatured extensively and at a comparable rate to that of bacterial DNA. The similarities among the kinds of DNA from bacteria and blue-green algae were interpreted to reflect a close relationship.
The syn-thesis of nitrogenase by non-heterocys tous cyano-bacteria
- R Waterbury
RIPPKA, R. & WATERBURY, J. B. (1977). The syn-thesis of nitrogenase by non-heterocys tous cyano-bacteria. FEMS Microbiology Letters 2, 83-86.
A study of the conditions and mechanism of the diphenylamine reaction for the colorinietric estimation of DNA
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Genome size of myco- plasma1 DNA
- A L Black
- F T Christiansen
- C Freundt
BAK, A. L., BLACK, F. T., CHRISTIANSEN, C. &
FREUNDT, E.A. (1969). Genome size of myco-
plasma1 DNA. Nature, London 224, 1209-1 2 10.
The synthesis of nitrogenase by non-heterocys tous cyanobacteria
- R Rippka
- J B Waterbury
RIPPKA, R. & WATERBURY, J. B. (1977). The synthesis of nitrogenase by non-heterocys tous cyanobacteria. FEMS Microbiology Letters 2, 83-86.
Proposal concerning the evolution of the genome of Escherichia coli
- D Zipkas
- M Riley
ZIPKAS, D. & RILEY, M. (1975). Proposal concerning
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