Journal articles: 'Synechococcus ecotypes'

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Ahlgren, Nathan A., and Gabrielle Rocap. "Culture Isolation and Culture-Independent Clone Libraries Reveal New Marine Synechococcus Ecotypes with Distinctive Light and N Physiologies." Applied and Environmental Microbiology 72, no. 11 (August 25, 2006): 7193–204. http://dx.doi.org/10.1128/aem.00358-06.

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ABSTRACT Marine microbial communities often contain multiple closely related phylogenetic clades, but in many cases, it is still unclear what physiological traits differentiate these putative ecotypes. The numerically abundant marine cyanobacterium Synechococcus can be divided into at least 14 clades. In order to better understand ecotype differentiation in this genus, we assessed the diversity of a Synechococcus community from a well-mixed water column in the Sargasso Sea during March 2002, a time of year when this genus typically reaches its annual peak in abundance. Diversity was estimated from water sampled at three depths (approximately 5, 70, and 170 m) using both culture isolation and construction of cyanobacterial 16S-23S rRNA internal transcribed sequence clone libraries. Clonal isolates were obtained by enrichment with ammonium, nitrite, or nitrate as the sole N source, followed by pour plating. Each method sampled the in situ diversity differently. The combined methods revealed a total of seven Synechococcus phylotypes including two new putative ecotypes, labeled XV and XVI. Although most other isolates grow on nitrate, clade XV exhibited a reduced efficiency in nitrate utilization, and both clade XV and XVI are capable of chromatic adaptation, demonstrating that this trait is more widely distributed among Synechococcus strains than previously known. Thus, as in its sister genus Prochlorococcus, light and nitrogen utilization are important factors in ecotype differentiation in the marine Synechococcus lineage.

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Becraft, Eric D., Frederick M. Cohan, Michael Kühl, Sheila I. Jensen, and David M. Ward. "Fine-Scale Distribution Patterns of Synechococcus Ecological Diversity in Microbial Mats of Mushroom Spring, Yellowstone National Park." Applied and Environmental Microbiology 77, no. 21 (September 2, 2011): 7689–97. http://dx.doi.org/10.1128/aem.05927-11.

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ABSTRACTPast analyses of sequence diversity in high-resolution protein-encoding genes have identified putative ecological species of unicellular cyanobacteria in the genusSynechococcus, which are specialized to 60°C but not 65°C in Mushroom Spring microbial mats. Because these studies were limited to only two habitats, we studied the distribution ofSynechococcussequence variants at 1°C intervals along the effluent flow channel and at 80-μm vertical-depth intervals throughout the upper photic layer of the microbial mat. Diversity at thepsaAlocus, which encodes a photosynthetic reaction center protein (PsaA), was sampled by PCR amplification, cloning, and sequencing methods at 60, 63, and 65°C sites. The evolutionary simulation programs Ecotype Simulation and AdaptML were used to identify putative ecologically distinct populations (ecotypes). Ecotype Simulation predicted a higher number of putative ecotypes in cases where habitat variation was limited, while AdaptML predicted a higher number of ecologically distinct phylogenetic clades in cases where habitat variation was high. Denaturing gradient gel electrophoresis was used to track the distribution of dominant sequence variants of ecotype populations relative to temperature variation and to O2, pH, and spectral irradiance variation, as measured using microsensors. Different distributions along effluent channel flow and vertical gradients, where temperature, light, and O2concentrations are known to vary, confirmed the ecological distinctness of putative ecotypes.

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Kupczok, Anne, and Tal Dagan. "Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage." Viruses 11, no. 8 (August 6, 2019): 720. http://dx.doi.org/10.3390/v11080720.

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Cyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and horizontal processes to short-term evolution of marine cyanophages. Analyzing time series data of Synechococcus-infecting Myoviridae ecotypes spanning up to 17 years, we found a high contribution of recombination relative to mutation (r/m) in all ecotypes. Additionally, we found a molecular clock of substitution and recombination in one ecotype, RIM8. The estimated RIM8 evolutionary rates are 2.2 genome-wide substitutions per year (1.275 × 10−5 substitutions/site/year) and 29 genome-wide nucleotide alterations due to recombination per year. We found 26 variable protein families, of which only two families have a predicted functional annotation, suggesting that they are auxiliary metabolic genes with bacterial homologs. A comparison of our rate estimates to other phage evolutionary rate estimates in the literature reveals a negative correlation of phage substitution rates with their genome size. A comparison to evolutionary rates in bacterial organisms further shows that phages have high rates of mutation and recombination compared to their bacterial hosts. We conclude that the increased recombination rate in phages likely contributes to their vast genomic diversity.

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Rocap, Gabrielle, Daniel L. Distel, John B. Waterbury, and Sallie W. Chisholm. "Resolution of Prochlorococcus and Synechococcus Ecotypes by Using 16S-23S Ribosomal DNA Internal Transcribed Spacer Sequences." Applied and Environmental Microbiology 68, no. 3 (March 2002): 1180–91. http://dx.doi.org/10.1128/aem.68.3.1180-1191.2002.

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ABSTRACT Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S-23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary-structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low-B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high-B/A ecotype into four genetically distinct clades. ITS-based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin). The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world's oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.

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Six, Christophe, Morgane Ratin, Dominique Marie, and Erwan Corre. "Marine Synechococcus picocyanobacteria: Light utilization across latitudes." Proceedings of the National Academy of Sciences 118, no. 38 (September 13, 2021): e2111300118. http://dx.doi.org/10.1073/pnas.2111300118.

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The most ubiquitous cyanobacteria, Synechococcus, have colonized different marine thermal niches through the evolutionary specialization of lineages adapted to different ranges of temperature seawater. We used the strains of Synechococcus temperature ecotypes to study how light utilization has evolved in the function of temperature. The tropical Synechococcus (clade II) was unable to grow under 16 °C but, at temperatures >25 °C, induced very high growth rates that relied on a strong synthesis of the components of the photosynthetic machinery, leading to a large increase in photosystem cross-section and electron flux. By contrast, the Synechococcus adapted to subpolar habitats (clade I) grew more slowly but was able to cope with temperatures <10 °C. We show that growth at such temperatures was accompanied by a large increase of the photoprotection capacities using the orange carotenoid protein (OCP). Metagenomic analyzes revealed that Synechococcus natural communities show the highest prevalence of the ocp genes in low-temperature niches, whereas most tropical clade II Synechococcus have lost the gene. Moreover, bioinformatic analyzes suggested that the OCP variants of the two cold-adapted Synechococcus clades I and IV have undergone evolutionary convergence through the adaptation of the molecular flexibility. Our study points to an important role of temperature in the evolution of the OCP. We, furthermore, discuss the implications of the different metabolic cost of these physiological strategies on the competitiveness of Synechococcus in a warming ocean. This study can help improve the current hypotheses and models aimed at predicting the changes in ocean carbon fluxes in response to global warming.

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Šantić, Danijela, and Mladen Šolić. "Factors affecting the distribution of two Synechococcus ecotypes in the coastal Adriatic Sea." Acta Adriatica 59, no. 1 (June 28, 2018): 51–60. http://dx.doi.org/10.32582/aa.59.1.4.

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U radu je istražena raspodjela i brojnost dva ekotipa roda Synechococcus, tzv. stanice bogate fikocijaninom (PC-SYN) i stanice bogate fikoeritrinom (PE-SYN) u površinskom sloju vodenog stupca, tijekom 2015. i 2016. godine. Područje istraživanja obuhvaćalo je nekoliko estuarijskih područja te područje trofičkog gradijenta od obale prema otvorenom moru, širokog raspona temperature mora \((11.82 - 20.75 ^oC)\), saliniteta (4.47-38.84) i koncentracije hranjiva. Brojnost PC-SYN bila je u rasponu od \( 0 to 79.79 x 10^ 3 cell mL^-1\), a PE-SYN od \(5.01 x 10^3 to 76.74 x 10^3 cell mL^-1\). Utvrđeno je istovremeno obitavanje oba ekotipa na istraživanom području, s prevladavanjem PC-SYN tijekom proljeća te PE-SYN tijekom zime i jeseni. Pokazana je statistički značajna povezanost između PC-SYN i temperature te njegova jaka pozitivna povezanost s dušikovim spojevima, dok su PE-SYN stanice pozitivno odgovorile na dostupnost fosfata. Relativni omjer dostupnosti fosfora i ukupnih hranjiva dušika (N/P omjer) utjecao je na prostornu raspodjelu oba ekotipa roda Synechococcus.

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Ferris, Mike J., Michael Kühl, Andrea Wieland, and David M. Ward. "Cyanobacterial Ecotypes in Different Optical Microenvironments of a 68°C Hot Spring Mat Community Revealed by 16S-23S rRNA Internal Transcribed Spacer Region Variation." Applied and Environmental Microbiology 69, no. 5 (May 2003): 2893–98. http://dx.doi.org/10.1128/aem.69.5.2893-2898.2003.

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ABSTRACT We examined the population of unicellular cyanobacteria (Synechococcus) in the upper 3-mm vertical interval of a 68°C region of a microbial mat in a hot spring effluent channel (Yellowstone National Park, Wyoming). Fluorescence microscopy and microsensor measurements of O2 and oxygenic photosynthesis demonstrated the existence of physiologically distinct Synechococcus populations at different depths along a light gradient quantified by scalar irradiance microprobes. Molecular methods were used to evaluate whether physiologically distinct populations could be correlated with genetically distinct populations over the vertical interval. We were unable to identify patterns in genetic variation in Synechococcus 16S rRNA sequences that correlate with different vertically distributed populations. However, patterns of variation at the internal transcribed spacer locus separating 16S and 23S rRNA genes suggested the existence of closely related but genetically distinct populations corresponding to different functional populations occurring at different depths.

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Scanlan, D. J., M. Ostrowski, S. Mazard, A. Dufresne, L. Garczarek, W. R. Hess, A. F. Post, M. Hagemann, I. Paulsen, and F. Partensky. "Ecological Genomics of Marine Picocyanobacteria." Microbiology and Molecular Biology Reviews 73, no. 2 (June 2009): 249–99. http://dx.doi.org/10.1128/mmbr.00035-08.

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SUMMARY Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.

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Grébert, Théophile, Hugo Doré, Frédéric Partensky, Gregory K. Farrant, Emmanuel S. Boss, Marc Picheral, Lionel Guidi, et al. "Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria." Proceedings of the National Academy of Sciences 115, no. 9 (February 12, 2018): E2010—E2019. http://dx.doi.org/10.1073/pnas.1717069115.

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Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined due to the lack of a single-genetic marker resolving all pigment types (PTs). Here, we developed and employed a robust method based on three distinct marker genes (cpcBA, mpeBA, and mpeW) to estimate the relative abundance of all known Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to reveal the global distribution of Synechococcus PTs and to define their environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified populations in which CA4 might be nonfunctional due to the lack of specific CA4 genes, notably in warm high-nutrient low-chlorophyll areas. Major ecotypes within clades I–IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study provides important insights into the ecology of Synechococcus and highlights the complex interactions between vertical phylogeny, pigmentation, and environmental parameters that shape Synechococcus community structure and evolution.

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Ahlgren, Nathan A., Bernard Shafer Belisle, and Michael D. Lee. "Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches." Environmental Microbiology 22, no. 5 (December 27, 2019): 1801–15. http://dx.doi.org/10.1111/1462-2920.14893.

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Sohm, Jill A., Nathan A. Ahlgren, Zachary J. Thomson, Cheryl Williams, James W. Moffett, Mak A. Saito, Eric A. Webb, and Gabrielle Rocap. "Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron." ISME Journal 10, no. 2 (July 24, 2015): 333–45. http://dx.doi.org/10.1038/ismej.2015.115.

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Mella-Flores, D., S. Mazard, F. Humily, F. Partensky, F. Mahé, L. Bariat, C. Courties, et al. "Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming?" Biogeosciences 8, no. 9 (September 29, 2011): 2785–804. http://dx.doi.org/10.5194/bg-8-2785-2011.

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Abstract. Biological communities populating the Mediterranean Sea, which is situated at the northern boundary of the subtropics, are often claimed to be particularly affected by global warming. This is indicated, for instance, by the introduction of (sub)tropical species of fish or invertebrates that can displace local species. This raises the question of whether microbial communities are similarly affected, especially in the Levantine basin where sea surface temperatures have significantly risen over the last 25 years (0.50 ± 0.11 °C in average per decade, P < 0.01). In this paper, the genetic diversity of the two most abundant members of the phytoplankton community, the picocyanobacteria Prochlorococcus and Synechococcus, was examined during two cruises through both eastern and western Mediterranean Sea basins held in September 1999 (PROSOPE cruise) and in June–July 2008 (BOUM cruise). Diversity was studied using dot blot hybridization with clade-specific 16S rRNA oligonucleotide probes and/or clone libraries of the 16S-23S ribosomal DNA Internal Transcribed Spacer (ITS) region, with a focus on the abundance of clades that may constitute bioindicators of warm waters. During both cruises, the dominant Prochlorococcus clade in the upper mixed layer at all stations was HLI, a clade typical of temperate waters, whereas the HLII clade, the dominant group in (sub)tropical waters, was only present at very low concentrations. The Synechococcus community was dominated by clades I, III and IV in the northwestern waters of the Gulf of Lions and by clade III and groups genetically related to clades WPC1 and VI in the rest of the Mediterranean Sea. In contrast, only a few sequences of clade II, a group typical of warm waters, were observed. These data indicate that local cyanobacterial populations have not yet been displaced by their (sub)tropical counterparts.

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García-Fernández, Jose Manuel, Nicole Tandeau de Marsac, and Jesús Diez. "Streamlined Regulation and Gene Loss as Adaptive Mechanisms in Prochlorococcus for Optimized Nitrogen Utilization in Oligotrophic Environments." Microbiology and Molecular Biology Reviews 68, no. 4 (December 2004): 630–38. http://dx.doi.org/10.1128/mmbr.68.4.630-638.2004.

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SUMMARY Prochlorococcus is one of the dominant cyanobacteria and a key primary producer in oligotrophic intertropical oceans. Here we present an overview of the pathways of nitrogen assimilation in Prochlorococcus, which have been significantly modified in these microorganisms for adaptation to the natural limitations of their habitats, leading to the appearance of different ecotypes lacking key enzymes, such as nitrate reductase, nitrite reductase, or urease, and to the simplification of the metabolic regulation systems. The only nitrogen source utilizable by all studied isolates is ammonia, which is incorporated into glutamate by glutamine synthetase. However, this enzyme shows unusual regulatory features, although its structural and kinetic features are unchanged. Similarly, urease activities remain fairly constant under different conditions. The signal transduction protein PII is apparently not phosphorylated in Prochlorococcus, despite its conserved amino acid sequence. The genes amt1 and ntcA (coding for an ammonium transporter and a global nitrogen regulator, respectively) show noncorrelated expression in Prochlorococcus under nitrogen stress; furthermore, high rates of organic nitrogen uptake have been observed. All of these unusual features could provide a physiological basis for the predominance of Prochlorococcus over Synechococcus in oligotrophic oceans.

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Mella-Flores, D., S. Mazard, F. Humily, F. Partensky, F. Mahé, L. Bariat, C. Courties, et al. "Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming?" Biogeosciences Discussions 8, no. 3 (May 3, 2011): 4281–330. http://dx.doi.org/10.5194/bgd-8-4281-2011.

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Abstract. Biological communities populating the Mediterranean Sea, which is situated at the northern boundary of the subtropics, are often claimed to be particularly affected by global warming. This is indicated, for instance, by the introduction of (sub)tropical species of fish or invertebrates that can displace local species. This raises the question of whether microbial communities are similarly affected, especially in the Levantine basin where sea surface temperatures have risen in recent years. In this paper, the genetic diversity of the two most abundant members of the phytoplankton community, the picocyanobacteria Prochlorococcus and Synechococcus, was examined on a transect from the South coast of France to Cyprus in the summer of 2008 (BOUM cruise). Diversity was studied using dot blot hybridization with clade-specific 16S rRNA oligonucleotide probes and clone libraries of the 16S–23S ribosomal DNA Internal Transcribed Spacer (ITS) region. Data were compared with those obtained during the PROSOPE cruise held almost a decade earlier, with a focus on the abundance of clades that may constitute bioindicators of warm waters. During both cruises, the dominant Prochlorococcus clade in the upper mixed layer at all stations was HLI, a clade typical of temperate waters, whereas the HLII clade, the dominant group in (sub)tropical waters, was only present at very low concentrations. The Synechococcus community was dominated by clades I, III and IV in the northwestern waters of the Gulf of Lions and by clade III and groups genetically related to clades WPC1 and VI in the rest of the Mediterranean Sea. In contrast, only a few sequences of clade II, a group typical of warm waters, were observed. These data indicate that local cyanobacterial populations have not yet been displaced by their (sub)tropical counterparts. This is discussed in the context of the low phosphorus concentrations found in surface waters in the eastern Mediterranean basin, as this may constitute a barrier to the colonization of these waters by alien picocyanobacterial groups.

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Palińska, Katarzyna A., and Wolfgang E. Krumbein. "Ecotype - Phenotype - Genotype An approach to the Synechococcus - Synechocystis Merismopedia - Eucapsis complex." Algological Studies/Archiv für Hydrobiologie, Supplement Volumes 75 (October 27, 1995): 213–27. http://dx.doi.org/10.1127/algol_stud/75/1995/213.

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Becker, Sven, Michael Fahrbach, Peter Böger, and Anneliese Ernst. "Quantitative Tracing, by Taq Nuclease Assays, of a Synechococcus Ecotype in a Highly Diversified Natural Population." Applied and Environmental Microbiology 68, no. 9 (September 2002): 4486–94. http://dx.doi.org/10.1128/aem.68.9.4486-4494.2002.

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ABSTRACT Quantitative Taq nuclease assays (TNAs) (TaqMan PCR), nested PCR in combination with denaturing gradient gel electrophoresis (DGGE), and epifluorescence microscopy were used to analyze the autotrophic picoplankton (APP) of Lake Constance. Microscopic analysis revealed dominance of phycoerythrin (PE)-rich Synechococcus spp. in the pelagic zone of this lake. Cells passing a 3-μm-pore-size filter were collected during the growth period of the years 1999 and 2000. The diversity of PE-rich Synechococcus spp. was examined using DGGE to analyze GC-clamped amplicons of a noncoding section of the 16S-23S intergenic spacer in the ribosomal operon. In both years, genotypes represented by three closely related PE-rich Synechococcus strains of our culture collection dominated the population, while other isolates were traced sporadically or were not detected in their original habitat by this method. For TNAs, primer-probe combinations for two taxonomic levels were used, one to quantify genomes of all known Synechococcus-type cyanobacteria in the APP of Lake Constance and one to enumerate genomes of a single ecotype represented by the PE-rich isolate Synechococcus sp. strain BO 8807. During the growth period, genome numbers of known Synechococcus spp. varied by 2 orders of magnitude (2.9 × 103 to 3.1 × 105 genomes per ml). The ecotype Synechococcus sp. strain BO 8807 was detected in every sample at concentrations between 1.6 × 101 and 1.3 × 104 genomes per ml, contributing 0.02 to 5.7% of the quantified cyanobacterial picoplankton. Although the quantitative approach taken in this study has disclosed several shortcomings in the sampling and detection methods, this study demonstrated for the first time the extensive internal dynamics that lie beneath the seemingly arbitrary variations of a population of microbial photoautotrophs in the pelagic habitat.

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Revsbech, Niels Peter, Erik Trampe, Mads Lichtenberg, David M. Ward, and Michael Kühl. "In SituHydrogen Dynamics in a Hot Spring Microbial Mat during a Diel Cycle." Applied and Environmental Microbiology 82, no. 14 (May 6, 2016): 4209–17. http://dx.doi.org/10.1128/aem.00710-16.

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ABSTRACTMicrobes can produce molecular hydrogen (H2) via fermentation, dinitrogen fixation, or direct photolysis, yet the H2dynamics in cyanobacterial communities has only been explored in a few natural systems and mostly in the laboratory. In this study, we investigated the dielin situH2dynamics in a hot spring microbial mat, where various ecotypes of unicellular cyanobacteria (Synechococcussp.) are the only oxygenic phototrophs. In the evening, H2accumulated rapidly after the onset of darkness, reaching peak values of up to 30 μmol H2liter−1at about 1-mm depth below the mat surface, slowly decreasing to about 11 μmol H2liter−1just before sunrise. Another pulse of H2production, reaching a peak concentration of 46 μmol H2liter−1, was found in the early morning under dim light conditions too low to induce accumulation of O2in the mat. The light stimulation of H2accumulation indicated that nitrogenase activity was an important source of H2during the morning. This is in accordance with earlier findings of a distinct early morning peak in N2fixation and expression ofSynechococcusnitrogenase genes in mat samples from the same location. Fermentation might have contributed to the formation of H2during the night, where accumulation of other fermentation products lowered the pH in the mat to less than pH 6 compared to a spring source pH of 8.3.IMPORTANCEHydrogen is a key intermediate in anaerobic metabolism, and with the development of a sulfide-insensitive microsensor for H2, it is now possible to study the microdistribution of H2in stratified microbial communities such as the photosynthetic microbial mat investigated here. The ability to measure H2profiles within the mat compared to previous measurements of H2emission gives much more detailed information about the sources and sinks of H2in such communities, and it was demonstrated that the high rates of H2formation in the early morning when the mat was exposed to low light intensities might be explained by nitrogen fixation, where H2is formed as a by-product.

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Gilbert, Naomi E., Gary R. LeCleir, Robert F. Strzepek, Michael J. Ellwood, Benjamin S. Twining, S. Roux, C. Pennacchio, Philip W. Boyd, and Steven W. Wilhelm. "Bioavailable iron titrations reveal oceanic Synechococcus ecotypes optimized for different iron availabilities." ISME Communications 2, no. 1 (July 1, 2022). http://dx.doi.org/10.1038/s43705-022-00132-5.

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AbstractThe trace metal iron (Fe) controls the diversity and activity of phytoplankton across the surface oceans, a paradigm established through decades of in situ and mesocosm experimental studies. Despite widespread Fe-limitation within high-nutrient, low chlorophyll (HNLC) waters, significant contributions of the cyanobacterium Synechococcus to the phytoplankton stock can be found. Correlations among differing strains of Synechococcus across different Fe-regimes have suggested the existence of Fe-adapted ecotypes. However, experimental evidence of high- versus low-Fe adapted strains of Synechococcus is lacking, and so we investigated the transcriptional responses of microbial communities inhabiting the HNLC, sub-Antarctic region of the Southern Ocean during the Spring of 2018. Analysis of metatranscriptomes generated from on-deck incubation experiments reflecting a gradient of Fe-availabilities reveal transcriptomic signatures indicative of co-occurring Synechococcus ecotypes adapted to differing Fe-regimes. Functional analyses comparing low-Fe and high-Fe conditions point to various Fe-acquisition mechanisms that may allow persistence of low-Fe adapted Synechococcus under Fe-limitation. Comparison of in situ surface conditions to the Fe-titrations indicate ecological relevance of these mechanisms as well as persistence of both putative ecotypes within this region. This Fe-titration approach, combined with transcriptomics, highlights the short-term responses of the in situ phytoplankton community to Fe-availability that are often overlooked by examining genomic content or bulk physiological responses alone. These findings expand our knowledge about how phytoplankton in HNLC Southern Ocean waters adapt and respond to changing Fe supply.

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Doré, Hugo, Jade Leconte, Ulysse Guyet, Solène Breton, Gregory K. Farrant, David Demory, Morgane Ratin, et al. "Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts." mSystems, December 5, 2022. http://dx.doi.org/10.1128/msystems.00656-22.

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Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of “who is where” by describing the distribution of Synechococcus clades or ecotypes in the open ocean.

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Ford, Benjamin A., Pramita Ranjit, Bridget C. Mabbutt, Ian T. Paulsen, and Bhumika S. Shah. "ProX from marine Synechococcus spp. show a sole preference for glycine‐betaine with differential affinity between ecotypes." Environmental Microbiology, August 16, 2022. http://dx.doi.org/10.1111/1462-2920.16168.

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Kearney, Sean M., Elaina Thomas, Allison Coe, and Sallie W. Chisholm. "Microbial diversity of co-occurring heterotrophs in cultures of marine picocyanobacteria." Environmental Microbiome 16, no. 1 (January 6, 2021). http://dx.doi.org/10.1186/s40793-020-00370-x.

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Abstract Background The cyanobacteria Prochlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; heterotrophs grow on organic carbon supplied by the photolithoautotrophs. For examining the selective pressures shaping autotroph/heterotroph interactions, we have made use of unialgal enrichment cultures of Prochlorococcus and Synechococcus maintained for hundreds to thousands of generations in the lab. We examine the diversity of heterotrophs in 74 enrichment cultures of these picocyanobacteria obtained from diverse areas of the global oceans. Results Heterotroph community composition differed between clades and ecotypes of the autotrophic ‘hosts’ but there was significant overlap in heterotroph community composition across these cultures. Collectively, the cultures were comprised of many shared taxa, even at the genus level. Yet, observed differences in community composition were associated with time since isolation, location, depth, and methods of isolation. The majority of heterotrophs in the cultures are rare in the global ocean, but enrichment conditions favor the opportunistic outgrowth of these rare bacteria. However, we found a few examples, such as bacteria in the family Rhodobacteraceae, of heterotrophs that were ubiquitous and abundant in cultures and in the global oceans. We found their abundance in the wild is also positively correlated with that of picocyanobacteria. Conclusions Particular conditions surrounding isolation have a persistent effect on long-term culture composition, likely from bottlenecking and selection that happen during the early stages of enrichment for the picocyanobacteria. We highlight the potential for examining ecologically relevant relationships by identifying patterns of distribution of culture-enriched organisms in the global oceans.

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Becraft, Eric D., Jason M. Wood, Douglas B. Rusch, Michael Kühl, Sheila I. Jensen, Donald A. Bryant, David W. Roberts, Frederick M. Cohan, and David M. Ward. "The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park." Frontiers in Microbiology 6 (June 22, 2015). http://dx.doi.org/10.3389/fmicb.2015.00590.

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Nowack, Shane, Millie T. Olsen, George A. Schaible, Eric D. Becraft, Gaozhong Shen, Isaac Klapper, Donald A. Bryant, and David M. Ward. "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." Frontiers in Microbiology 6 (June 29, 2015). http://dx.doi.org/10.3389/fmicb.2015.00626.

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Olsen, Millie T., Shane Nowack, Jason M. Wood, Eric D. Becraft, Kurt LaButti, Anna Lipzen, Joel Martin, et al. "The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat." Frontiers in Microbiology 6 (June 23, 2015). http://dx.doi.org/10.3389/fmicb.2015.00604.

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Zheng, Qiang, Yu Wang, Jiayao Lu, Wenxin Lin, Feng Chen, and Nianzhi Jiao. "Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Synechococcus Culture." mBio 11, no. 1 (February 18, 2020). http://dx.doi.org/10.1128/mbio.03261-19.

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ABSTRACT Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of cocultivation. The associated heterotrophic bacterial assembly mostly constituted five classes, including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria. The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes, including Synechococcus and the five dominant heterotrophic bacteria, were reconstructed. The only primary producer of the coculture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TonB-dependent transporters (TBDTs), glycoside hydrolase, and peptidase proteins. Polysaccharide utilization loci present in the flavobacterial genomes influence their lifestyle preferences and close associations with phytoplankton. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low-molecular-weight dissolved organic carbon (DOC) through ATP-binding cassette (ABC), tripartite ATP-independent periplasmic (TRAP), and tripartite tricarboxylate transporter (TTT) transport systems. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking might also contribute to the maintenance of the Synechococcus-heterotroph coculture system and the interactions shaping the system. IMPORTANCE The high complexity of in situ ecosystems renders it difficult to study marine microbial photoautotroph-heterotroph interactions. Two-member coculture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. In the present study, combined metagenomic and metaproteomic data supplied the metabolic potentials and activities of uncultured dominant bacterial populations in the coculture system. The results of this study shed light on the nature of interactions between photoautotrophs and heterotrophs, improving our understanding of the complexity of in situ environments.

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Becraft, Eric D., Benjamin D. Jackson, Shane Nowack, Isaac Klapper, and David M. Ward. "Relationship between Microorganisms Inhabiting Alkaline Siliceous Hot Spring Mat Communities and Overflowing Water." Applied and Environmental Microbiology 86, no. 23 (September 25, 2020). http://dx.doi.org/10.1128/aem.00194-20.

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ABSTRACT 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.

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Journal articles on the topic 'Synechococcus ecotypes'

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