Synechococcus Species Research Articles

Metagenomic exploration of Andaman region of the Indian Ocean

Ocean microbiome is crucial for global biogeochemical cycles and primary productivity. Despite numerous studies investigating the global ocean microbiomes, the microbiome composition of the Andaman region of the Indian Ocean remains largely unexplored. While this region harbors pristine biological diversity, the escalating anthropogenic activities along coastal habitats exert an influence on the microbial ecology and impact the aquatic ecosystems. We investigated the microbiome composition in the coastal waters of the Andaman Islands by 16S rRNA gene amplicon and metagenomic shotgun sequencing approaches and compared it with the Tara Oceans Consortium. In the coastal waters of the Andaman Islands, a significantly higher abundance and diversity of Synechococcus species was observed with a higher abundance of photosynthesis pigment-related genes to adapt to variable light conditions and nutrition. In contrast, Prochlorococcus species showed higher abundance in open ocean water samples of the Indian Ocean region, with a relatively limited functional diversity. A higher abundance of antibiotic-resistance genes was also noted in the coastal waters region. We also updated the ocean microbiome gene catalog with 93,172 unique genes from the Andaman coastal water microbiome. This study provides valuable insights into the Indian Ocean microbiome and supplements the global marine microbial ecosystem studies.

Engineering Cyanobacterial Cell Factories for Photosynthetic Production of Fructose.

Fructose is an important monosaccharide product widely applied in the food, medicine, and chemical industries. Currently, fructose is mainly manufactured with plant biomass-sourced polysaccharides through multiple steps of digestion, conversion, separation, and purification. The development of cyanobacterial metabolic engineering provides an attractive alternative route for the one-step direct production of fructose utilizing carbon dioxide and solar energy. In this work, we developed a paradigm for engineering cyanobacterial chassis cells into efficient cell factories for the photosynthetic production of fructose. In a representative cyanobacterial strain, Synechococcus elongatus PCC 7942, knockout of fructokinase effectively activated the synthesis and secretion of fructose in hypersaline conditions, independent of any heterologous transporters. The native sucrose synthesis pathway was identified as playing a primary role in fructose synthesis. Through combinatory optimizations on the levels of metabolism, physiology, and cultivation, the fructose yield of the Synechococcus cell factories was stepwise improved to 3.9 g/L. Such a paradigm was also adopted to engineer another Synechococcus strain, the marine species Synechococcus sp. PCC 7002, and facilitated an even higher fructose yield of over 6 g/L. Finally, the fructose synthesized and secreted by the cyanobacterial photosynthetic cell factories was successfully extracted and prepared from the culture broth in the form of products with 86% purity through multistep separation-purification operations. This work demonstrated a paradigm for systematically engineering cyanobacteria for photosynthetic production of desired metabolites, and it also confirmed the feasibility and potential of cyanobacterial photosynthetic biomanufacturing as a simple and efficient route for fructose production.

The impact of aggregation between clay and phytoplanktonic cyanobacteria on trace elemental cycling in coastal environments

Clay minerals and cyanobacteria occur ubiquitously in nature, and both independently influence trace metal cycling due to their high specific surface areas and reactivity. Although the surface reactivity of each is well-studied, the reactivity of clay-cyanobacterial aggregates has received less attention. Here, we performed potentiometric acid-base titrations and Cd adsorption experiments on various concentrations of clay-cyanobacterial aggregates using three clay minerals (kaolinite, illite, and montmorillonite) and two model planktonic cyanobacteria, the freshwater species Synechocystis sp. PCC 6803 and marine species Synechococcus sp. PCC 7002. A component additivity surface complexation modeling (CA-SCM) approach was applied to study the impacts of the aggregation processes on the total surface reactivity. Results demonstrate that the CA-SCM approach effectively predicted the acid-base titration and Cd adsorption behaviors of aggregates at low aggregate concentrations (up to 2.5 g of clay/L for acid-base titration and 0.1 g of clay/L for Cd adsorption), indicating the additivity of the reactivity for the two components. However, at higher aggregate concentrations (25 g of clay/L for acid-base titration and 10 g of clay/L for Cd adsorption), the CA-SCM approach overestimates the acid-base titration and Cd adsorption behaviors for the aggregates, indicating significant surface site blockage during aggregation. Our SEM images show that both cyanobacterial species were covered by layered clay minerals at the surfaces and formed relatively larger aggregates at high aggregate concentrations than at low aggregate concentrations. Based on the combined results, we propose that the interaction between clays and cyanobacteria is relatively weak at low aggregate concentrations (e.g., <10 g of aggregate/L), but that significant obstruction of surface adsorption sites occurs at high aggregate concentrations (e.g., >10 g of aggregate/L), possibly due to the encrustation of bacteria by clay minerals. The implication of this work is that where turbid rivers discharge into estuaries or deltas with high primary phytoplankton productivity, aggregation (or flocculation) processes will cause the depression of surface reactivity of the aggregates and lead to a decrease in metal-binding capacity. Therefore, depending on whether the trace elements are nutrients (e.g., phosphorous) or potentially toxic (e.g., cadmium), this process has the potential to impact the marine biosphere. To ground truth this hypothesis, we further analyzed the correlation between total organic carbon (TOC) content and trace metal compositions in a compiled shale database and the results show clear negative correlation between Cd concentration and the concentration of TOC, Al and Si. Although this offers only an indirect assessment of the role of clay-plankton aggregation, as a first-order test it does indeed show that the aggregation between clay minerals and phytoplanktonic bacteria in estuaries is an essential factor that influences trace-elemental cycling.

Do anti-HIV drugs pose a threat to photosynthetic microorganisms?

We investigated the occurrence and risk assessment of three anti-HIV drugs [(tenofovir (TNF), lamivudine (LMV) and efavirenz (EFV)] in urban rivers from Curitiba (Brazil), as well as the individual and combined effects of their environmental representative concentrations on the freshwater periphytic species Synechococcus elongatus (Cyanobacteria) and Chlorococcum infusionum (Chlorophyta). The three studied drugs, except TNF, were found in 100% of the samples, and concentrations in samples ranged from 165 to 412 ng TNF L−1, 173–874 ng LMV L−1 and 13–1250 ng EFV L−1. Bioassays using artificial contaminated water showed that at environmental concentrations, TNF and LMV did not represent environmental risks to the studied photosynthetic organisms. However, EFV was shown to be toxic, affecting photosynthesis, respiration, and oxidative metabolism. The studied drugs demonstrated interactive effects. Indeed, when submitted to the combination of TNF and LMV, decreased photosynthesis was observed in C. infusionum cells. Moreover, the toxic effects of EFV were amplified in both species when TNF and/or LMV were added to the media. The simultaneous presence of TNF, LMV and EFV in environmental matrices associated with their interactive effects, lead to increased toxicological effects of water contaminated by anti-HIV drugs and thus to an ecological threat to photosynthetic microorganisms.

Periphytic Algae and Cyanobacteria from the Rio Doce Basin Respond Differently to Metals and Salinity, Showing Different Potential for Bioremediation.

We have studied the isolated and combined effects of metals (Fe and Mn) and NaCl the on growth, physiology, and metal-uptake capacity of two photosynthetic periphytic species—Synechococcus elongatus (Cyanobacteria) and Chlorococcum infusionum (Chlorophyta)—isolated from an impacted area of the Rio Doce River (Brazil) after the Fundão dam collapse. The effective concentrations found to reduce 10 and 50% growth were 15.2 and 31.6 mg Fe L−1, and 2.5 and 7.9 mg Mn L−1 for S. elongatus and 53.9 and 61.6 mg Fe L−1, and 53.2 and 60.9 mg Mn L−1 for C. infusionum. Although the metal toxicity was related to oxidative stress, both species showed activation of antioxidant systems under phytotoxic concentrations of Fe and Mn. By binding large concentrations of metals on its cell surface and thus avoiding their entrance into the cells, C. infusionum presents greater resistance to Fe and Mn than S. elongatus. Under environmental realistic concentrations of Fe and Mn in river water from the Rio Doce Basin, S. elongatus and C. infusionum showed a metal removal efficiency of 42 and 65% and 53 and 79%, respectively after 96 h. These species were insensitive to increased NaCl concentrations which, in addition, did not disrupt the metal removal capacity of the species. Due to their salt and metal tolerance, S. elongatus and C. infusionum can be used for the remediation of waters contaminated with Fe and Mn.

Probing Individual Particles in Aquatic Suspensions by Simultaneously Measuring Polarized Light Scattering and Fluorescence.

Suspended particles play a significant role in aquatic systems. However, existing methods to probe suspended particles have several limitations. In this paper, we present a portable prototype to in situ probe individual particles in aquatic suspensions by simultaneously measuring polarized light scattering and fluorescence, aiming to obtain an effective classification of microplastics and microalgae. Results show that the obtained classification accuracy is significantly higher than that for either of these two methods. The setup also successfully measures submicron particles and discriminates two species of Synechococcus. Our study demonstrates the feasibility of simultaneously measuring polarized light scattering and fluorescence, and the promising capability of our method for further aquatic environmental monitoring.

Evolution of Superoxide Dismutases and Catalases in Cyanobacteria: Occurrence of the Antioxidant Enzyme Genes before the Rise of Atmospheric Oxygen.

Knowledge on the evolution of antioxidant systems in cyanobacteria is crucial for elucidating the cause and consequence of the rise of atmospheric oxygen in the Earth's history. In this study, to elucidate the origin and evolution of cyanobacterial antioxidant enzymes, we analyzed the occurrence of genes encoding four types of superoxide dismutases and three types of catalases in 85 complete cyanobacterial genomes, followed by phylogenetic analyses. We found that Fe superoxide dismutase (FeSOD), Mn superoxide dismutase (MnSOD), and Mn catalase (MnCat) are widely distributed among modern cyanobacteria, whereas CuZn superoxide dismutase (CuZnSOD), bifunctional catalase (KatG), and monofunctional catalase (KatE) are less common. Ni superoxide dismutase (NiSOD) is distributed among marine Prochlorococcus and Synechococcus species. Phylogenetic analyses suggested that bacterial MnSOD evolved from cambialistic Fe/MnSOD before the diversification of major bacterial lineages. The analyses suggested that FeSOD evolved from MnSOD before the origin of cyanobacteria. MnCat also evolved in the early stages of bacterial evolution, predating the emergence of cyanobacteria. KatG, KatE, and NiSOD appeared 2.3-2.5 billion years ago. Thus, almost all cyanobacterial antioxidant enzymes emerged before or during the rise of atmospheric oxygen. The loss and appearance of these enzymes in marine cyanobacteria may be also related to the change in the metal concentration induced by the increased oxygen concentration in the ocean.

Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea

Bacteria are an active and diverse component of pelagic communities. The identification of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profile, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classified the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more differentiated by depth than by area, with temperature and identified salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identified genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium-related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors affecting picoplankton in the open sea environment.

The large genome of Synechococcus moorigangaii CMS01 isolated from a mangrove ecosystem- evidences of motility and adaptive features

The whole genome of Synechococcus moorigangaii CMS01 isolated from Indian Sundarbans mangroves of Bay of Bengal is about 5.5 Mbp in size and contains approximately 0.5 Mbp plasmids. Genome annotation revealed total of 5806 genes out of which 5701 were CDSs. Of these, 5616 coding genes with 5616 protein coding CDSs were found. Along with genes coding for essential metabolic proteins, transport proteins and other cellular apparatus, genome also codes for proteins involved in flagella and pilus formation which has not been widely reported before in any coastal species of Synechococcus. The genome contains one incomplete prophage sequence. The genome analysis revealed adaptive features of S. moorigangaii CMS01 and establishes its ubiquitous distribution in coastal water of Bay of Bengal.

Relationship between Microorganisms Inhabiting Alkaline Siliceous Hot Spring Mat Communities and Overflowing Water.

The compositions of Octopus Spring and Mushroom Spring (Yellowstone National Park, Wyoming, USA) microbial mats have been thoroughly studied, but the compositions of the effluent waters that flow above the mats have not. In this study, cells in the mats and overflowing waters of both springs were investigated at multiple sites where Synechococcus spp. are the dominant cyanobacteria (ca. 72°C to ca. 50°C), and on several dates. In addition to microscopic analyses of stained and autofluorescent cells, 16S rRNA gene sequencing was used to characterize the major taxa present and a protein-encoding gene (psaA) was sequenced and analyzed by ecotype simulation to predict species of Synechococcus The mats of both springs were similar in terms of the downstream distribution of predominant taxa detected previously. However, waters above these mats were predominated by taxa that reside in upstream mats or communities above the upper-temperature limit of the mat. A disturbance/recolonization study was performed at a site normally predominated by Synechococcus species adapted to low temperatures. After removing indigenous Synechococcus cells, Synechococcus species adapted to higher temperatures, which were predominant in the water overflowing this site, colonized the newly forming mat. Differences in recolonization under reduced and UV-screened irradiance suggested that, in addition to physical transport, environmental conditions likely select for species that are better adapted to these different conditions and can influence mat recovery. A transport model was developed and used to predict that, in Mushroom Spring, erosion predominates in the narrower and deeper upstream effluents and deposition predominates over erosion in wider and shallower downstream effluents.IMPORTANCE In flowing aquatic systems, cell erosion and deposition are important to the dispersal of cells from one location to another. Very little is known about microbial dispersal and the physical processes that underlie it. This study demonstrates its importance to colonization of downstream surfaces and especially to the recolonization and functioning of disturbed sites. Ecological systems in flowing environments are often, roughly speaking, pseudosteady, in that nutrients enter the system and by-products leave at relatively steady rates. Over time, material inputs and outputs must balance. Measurements of input fluxes (e.g., growth rates and proxies, such as photosynthesis rates) are frequent. However, erosion and deposition of cells are seldom measured and ecological significance is sometimes neglected. The importance of these parameters is immediately evident in any attempt to construct a model of long-time community behavior, as spatial ecological structure is significantly impacted and can be dominated by migration of organisms, even in small numbers.

Description of a new marine planktonic cyanobacterial species Synechococcus moorigangaii (Order Chroococcales) from Sundarbans mangrove ecosystem

The genus Synechococcus is widespread across marine environments globally including in coastal habitats. In this study, culture of a new isolate (CMS01) of Synechococcus has been established and described based on polyphasic taxonomy from the world’s largest mangrove ecosystem, Sundarbans. This planktonic photoautrotroph has been proposed as a new species Synechococcus moorigangaii sp. nov. belonging to the order Chroococcales. The cells representing this proposed new species are solitary and can also form chain comprising of 4–6 cells. The shape of cell is oval to cylindrical and length ranges from 1.2–3 µm while the width ranges from 0.8–2 µm. The distribution pattern of photosynthetic filaments was found to be from the periphery of cell. Based on robust phylogeny of 16S rRNA, in addition to functional genes such as psbA, ureC, rbcL, and cbbA (multi gene phylogeny), the proposed new species differed from closest described species of Synechococcus under order Chroococcales. The fatty acid analysis indicated the presence of C12 and C14 chain fatty acids exclusive to isolate CMS01. The new isolate can grow across a range of salinity and in presence of different nitrogen sources. It has the ability to fix atmospheric di-nitrogen into ammonium ion. This new isolate of Synechococcus spp. is the first marine planktonic cyanobacterium described from a mangrove ecosystem and characterized using polyphasic approaches. Based on 16S rRNA phylogeny, this proposed new species clustered with Synechococcus strains PCC 7117, PCC 73109, PCC 7002, PCC 7003, PCC 7376 and NKNG15041c belonging to the order Chroococcales. The new species Synechococcus moorigangaii sp. nov. can serve as a model organism to understand ecophysiology and adaptation of planktonic cyanobacterial communities in mangrove ecosystems.

Recovery of excreted n-butanol from genetically engineered cyanobacteria cultures: Process modelling to quantify energy and economic costs of different separation technologies

The photoautotrophic production of excreted biofuels from genetically engineered cyanobacteria and microalgae represents a new and promising alternative to conventional algal fuel technologies. N-butanol is a particularly promising fuel product, as it can be directly used in petroleum engines, and has been successfully expressed in species of Synechococcus elongates 7942 and Synechocystis sp. PCC 6803. However, the high energy requirements of recovering butanol from dilute mixtures can easily outweigh the energy content of the fuel and must be carefully assessed and optimized. Consequently, the recovery of butanol was modelled using four of the most promising butanol separation technologies (distillation, gas stripping, pervaporation and ionic liquid extraction) to calculate the minimum butanol culture concentrations required to render the process energy-positive. With a break-even concentration of only 3.7 g L−1, ionic liquid extraction proved much more efficient than the distillation base-case scenario (9.3 g L−1), whilst neither pervaporation (10.3 g L−1) nor gas stripping (16.9 g L−1) could compete on an energy basis with distillation. Despite this, due to the high costs of the ionic liquid solvent, the lowest capital costs are obtained for distillation (pilot plant scale, butanol culture concentrations of 10 g L−1), whilst pervaporation carries the lowest utility costs, as a result of its low electrical energy demand. Although currently achieved maximum n-butanol culture concentrations are significantly below the calculated break-even values for all four technologies, the present work provides an important threshold for future strain development. Moreover, the recovery of side-products from purged biomass could help to reduce the costs associated with biofuel production.

Roseicyclus marinus sp. nov., isolated from a Synechococcus culture, and emended description of the genus Roseicyclus.

A novel Gram-stain-negative, aerobic, non-flagellated, pink-pigmented and rod-shaped strain with gliding motility, designated strain CCMM001T, was isolated from a mixed culture of Synechococcus species PCC7002 and a natural bacterial community from a sample of offshore seawater from Qingdao, China, during September 2014. The strain contained bacteriochlorophyll a with a small peak at 802 nm and a large in vivo absorption band at 870 nm. Strain CCMM001T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CCMM001T is most closely related to the genus Roseicyclus and its type and only species Roseicyclus mahoneyensis ML6T with 96.9 % sequence similarity. The polar lipids of strain CCMM001T consisted of phosphatidylethanolamine, phosphatidylcholine, one unidentified aminolipid, and five unidentified lipids. The predominant isoprenoid quinone was Q-10. The major fatty acids included C18 : 1ω7c and C19 : 0cyclo ω8c. The DNA G+C content of strain CCMM001T was 63.5 mol%. These phylogenetic, physiological and chemotaxonomic data indicated that strain CCMM001T represents a novel species of the genus Roseicyclus, for which the name Roseicyclus marinus sp. nov. is proposed. The type strain is CCMM001T (=MCCC 1K03242T=KCTC 52641T).

Production of Bioplastic Compounds by Genetically Manipulated and Metabolic Engineered Cyanobacteria.

Direct conversion of carbon dioxide to valuable compounds is a desirable way to reduce the environmental burden and switch from fossil to renewable fuels. Cyanobacteria are photosynthetic bacteria that perform oxygenic photosynthesis and are able to produce valuable compounds from carbon dioxide in the air. Synechocystis and Synechococcus species, model unicellular cyanobacteria, can produce succinate and lactate, which are commodity chemicals used to generate bioplastics. Several cyanobacteria are also able to produce polyhydroxybutyrate, a biodegradable polyester that accumulates under nitrogen or phosphorus starvation. Genetic manipulation succeeded in increasing the productivity of succinate, lactate, and polyhydroxybutyrate from cyanobacteria. We summarize the recent findings in this review.

&lt;i&gt;Synechococcus salsus&lt;/i&gt; sp. nov. (Cyanobacteria): A new unicellular, coccoid species from Yuncheng Salt Lake, North China

A new species of the genus Synechococcus C. Nägeli was described from extreme environment (high salinity) of the Yuncheng salt lake, North China. Morphological characteristics observed by light microscopy (LM) and transmission electron microscopy (TEM) were described. DNA barcodes (16S rRNA+ITS-1, cpcBA-IGS) were used to evaluate its taxonomic status. This species was identified as Synechococcus salsus H. Lv et S. Xie. It is characterized by unicellular, without common mucilage, cells with several dispersed or solitary polyhedral bodies, widely coccoid, sometimes curved or sigmoid, rounded at the ends, thylakoids localized along cells walls. Molecular analyses further support its systematic position as an independent branch. The new species Synechococcus salsus is closely allied to S. elongatus, C.Nägeli, but differs from it by having shorter cell with length 1.0–1.5 times of width.Bangladesh J. Plant Taxon. 24(2): 137–147.

Diversity and community structure of cyanobacteria and other microbes in recycling irrigation reservoirs.

Recycling irrigation reservoirs (RIRs) are emerging aquatic environments of global significance to crop production, water conservation and environmental sustainability. This study characterized the diversity and population structure of cyanobacteria and other detected microbes in water samples from eight RIRs and one adjacent runoff-free stream at three ornamental crop nurseries in eastern (VA1 and VA3) and central (VA2) Virginia after cloning and sequencing the 16S rRNA gene targeting cyanobacteria and chloroplast of eukaryotic phytoplankton. VA1 and VA2 utilize a multi-reservoir recycling irrigation system with runoff channeled to a sedimentation reservoir which then overflows into transition and retention reservoirs where water was pumped for irrigation. VA3 has a single sedimentation reservoir which was also used for irrigation. A total of 208 operational taxonomic units (OTU) were identified from clone libraries of the water samples. Among them, 53 OTUs (358 clones) were cyanobacteria comprising at least 12 genera dominated by Synechococcus species; 59 OTUs (387 clones) were eukaryotic phytoplankton including green algae and diatoms; and 96 were other bacteria (111 clones). Overall, cyanobacteria were dominant in sedimentation reservoirs, while eukaryotic phytoplankton and other bacteria were dominant in transition/retention reservoirs and the stream, respectively. These results are direct evidence demonstrating the negative impact of nutrient-rich horticultural runoff, if not contained, on natural water resources. They also help in understanding the dynamics of water quality in RIRs and have practical implications. Although both single- and multi-reservoir recycling irrigation systems reduce the environmental footprint of horticultural production, the former is expected to have more cyanobacterial blooming, and consequently water quality issues, than the latter. Thus, a multi-reservoir recycling irrigation system should be preferred where feasible.

Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat.

Recent studies of bacterial speciation have claimed to support the biological species concept—that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B') of Synechococcus in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B' lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B' lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.

Paulinella longichromatophora sp. nov., a New Marine Photosynthetic Testate Amoeba Containing a Chromatophore

The freshwater testate filose amoeba Paulinella chromatophora is the sole species in the genus to have plastids, usually termed "chromatophores", of a Synechococcus/Prochlorococcus-like cyanobacterial origin. Here, we report a new marine phototrophic species, Paulinella longichromatophora sp. nov., using light and electron microscopy and molecular data. This new species contains two blue-green U-shaped chromatophores reaching up to 40 μm in total length. Further, the new Paulinella species is characterized by having five oral scales surrounding the pseudostomal aperture. All trees generated using three nuclear rDNA datasets (18S rDNA, 28S rDNA, and the concatenated 18S + 28S rDNA) demonstrated that three photosynthetic Paulinella species (two freshwater species, P. chromatophora and Paulinella strain FK01, and one marine species, P. longichromatophora) congruently formed a monophyletic group with strong support (≥ 90% of ML and ≥ 0.90 of PP), but their relationship to each other within the clade remained unresolved in all trees. P. longichromatophora, nevertheless, clustered consistently together with Paulinella strain FK01 with very low support, but the clade received strong support in plastid phylogenies. Phylogenetic analyses inferred from plastid-encoded 16S rDNA and a concatenated dataset of plastid 16S+23S rDNA demonstrated that chromatophores of all photosynthetic Paulinella species were monophyletic. The monophyletic group fell within a cyanobacteria clade having a close relationship to an α-cyanobacterial clade containing Prochlorococcus and Synechococcus species with very robust support (100% of ML and 1.0 of PP). Additionally, phylogenetic analyses of nuclear 18S rDNA and plastid 16S rDNA suggested divergent evolution within the photosynthetic Paulinella population after a single acquisition of the chromatophore. After the single acquisition of the chromatophore, ancestral photosynthetic Paulinella appears to have diverged into at least two distinct clades, one containing the marine P. longichromatophora and freshwater Paulinella strain FK01, the other P. chromatophora CCAC 0185.

The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light

Closely related strains of thermophilic Synechococcus were cultivated from the microbial mats found in the effluent channels of Mushroom Spring, Yellowstone National Park (YNP). These strains have identical or nearly identical 16S rRNA sequences but are representative of separate, predicted putative ecotype (PE) populations, which were identified by using the more highly resolving psaA locus and which predominate at different vertical positions within the 1-mm-thick upper-green layer of the mat. Pyrosequencing confirmed that each strain contained a single, predominant psaA genotype. Strains differed in growth rate as a function of irradiance. A strain with a psaA genotype corresponding to a predicted PE that predominates near the mat surface grew fastest at high irradiances, whereas strains with psaA genotypes representative of predominant subsurface populations grew faster at low irradiance and exhibited greater sensitivity to abrupt shifts to high light. The high-light-adapted and low-light-adapted strains also exhibited differences in pigment content and the composition of the photosynthetic apparatus (photosystem ratio) when grown under different light intensities. Cells representative of the different strains had similar morphologies under low-light conditions, but under high-light conditions, cells of low-light-adapted strains became elongated and formed short chains of cells. Collectively, the results presented here are consistent with the hypothesis that closely related, but distinct, ecological species of Synechococcus occupy different light niches in the Mushroom Spring microbial mat and acclimate differently to changing light environments.

Functional Characterization of the FNT Family Nitrite Transporter of Marine Picocyanobacteria.

Many of the cyanobacterial species found in marine and saline environments have a gene encoding a putative nitrite transporter of the formate/nitrite transporter (FNT) family. The presumed function of the gene (designated nitM) was confirmed by functional expression of the gene from the coastal marine species Synechococcus sp. strain PCC7002 in the nitrite-transport-less mutant (NA4) of the freshwater cyanobacterium Synechococcus elongatus strain PCC7942. The NitM-mediated nitrite uptake showed an apparent Km (NO2−) of about 8 μM and was not inhibited by nitrate, cyanate or formate. Of the nitM orthologs from the three oceanic cyanobacterial species, which are classified as α-cyanobacteria on the basis of the occurrence of Type 1a RuBisCO, the one from Synechococcus sp. strain CC9605 conferred nitrite uptake activity on NA4, but those from Synechococcus sp. strain CC9311 and Prochlorococcus marinus strain MIT9313 did not. A strongly conserved hydrophilic amino acid sequence was found at the C-termini of the deduced NitM sequences from α-cyanobacteria, with a notable exception of the Synechococcus sp. strain CC9605 NitM protein, which entirely lacked the C-terminal amino acids. The C-terminal sequence was not conserved in the NitM proteins from β-cyanobacteria carrying the Type 1b RuBisCO, including the one from Synechococcus sp. strain PCC7002. Expression of the truncated nitM genes from Synechococcus sp. strain CC9311 and Prochlorococcus marinus strain MIT9313, encoding the proteins lacking the conserved C-terminal region, conferred nitrite uptake activity on the NA4 mutant, indicating that the C-terminal region of α-cyanobacterial NitM proteins inhibits the activity of the transporter.