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1. Synechococcus nitrogen gene loss in iron-limited ocean regions

   https://doi.org/10.1038/s43705-023-00314-9  

   Sharpe, Garrett; Zhao, Liang; Meyer, Meredith G.; Gong, Weida; Burns, Shannon M.; Tagliabue, Allesandro; Buck, Kristen N.; Santoro, Alyson E.; Graff, Jason R.; Marchetti, Adrian; et al (October 2023, ISME Communications)

   Abstract Synechococcus are the most abundant cyanobacteria in high latitude regions and are responsible for an estimated 17% of annual marine net primary productivity. Despite their biogeochemical importance, Synechococcus populations have been unevenly sampled across the ocean, with most studies focused on low-latitude strains. In particular, the near absence of Synechococcus genomes from high-latitude, High Nutrient Low Chlorophyll (HNLC) regions leaves a gap in our knowledge of picocyanobacterial adaptations to iron limitation and their influence on carbon, nitrogen, and iron cycles. We examined Synechococcus populations from the subarctic North Pacific, a well-characterized HNLC region, with quantitative metagenomics. Assembly with short and long reads produced two near complete Synechococcus metagenome-assembled genomes (MAGs). Quantitative metagenome-derived abundances of these populations matched well with flow cytometry counts, and the Synechococcus MAGs were estimated to comprise >99% of the Synechococcus at Station P. Whereas the Station P Synechococcus MAGs contained multiple genes for adaptation to iron limitation, both genomes lacked genes for uptake and assimilation of nitrate and nitrite, suggesting a dependence on ammonium, urea, and other forms of recycled nitrogen leading to reduced iron requirements. A global analysis of Synechococcus nitrate reductase abundance in the TARA Oceans dataset found nitrate assimilation genes are also lower in other HNLC regions. We propose that nitrate and nitrite assimilation gene loss in Synechococcus may represent an adaptation to severe iron limitation in high-latitude regions where ammonium availability is higher. Our findings have implications for models that quantify the contribution of cyanobacteria to primary production and subsequent carbon export. 

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2. Presence of toxin-antitoxin systems in picocyanobacteria and their ecological implications

   https://doi.org/10.1038/s41396-020-00746-4  

   Fucich, Daniel; Chen, Feng (August 2020, The ISME Journal)

   Abstract Picocyanobacteria (mainly Synechococcus and Prochlorococcus) contribute significantly to ocean’s primary production. Toxin-Antitoxin (TA) systems present in bacteria and archaea are known to regulate cell growth in response to environmental stresses. However, little is known about the presence of TA systems in picocyanobacteria. This study investigated complete genomes of Synechococcus and Prochlorococcus to understand the prevalence of TA systems in picocyanobacteria. Using the TAfinder software, Type II TA systems were predicted in 27 of 33 (81%) Synechococcus strains, but none of 38 Prochlorococcus strains contain TA genes. Synechococcus strains with larger genomes tend to contain more putative type II TA systems. The number of TA pairs varies from 0 to 42 in Synechococcus strains isolated from various environments. A linear correlation between the genome size and the number of putative TA systems in both coastal and freshwater Synechococcus was established. In general, open ocean Synechococcus contain no or few TA systems, while coastal and freshwater Synechococcus contain more TA systems. The type II TA systems inhibit microbial translation via ribonucleases and allow cells to enter the “dormant” stage in adverse environments. Inheritance of TA genes in freshwater and coastal Synechococcus could confer a recoverable persister mechanism important to survive in variable environments. 

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3. A Ubiquitously Conserved Cyanobacterial Protein Phosphatase Essential for High Light Tolerance in a Fast-Growing Cyanobacterium

   https://doi.org/10.1128/spectrum.01008-22  

   Walker, Patricia L.; Pakrasi, Himadri B. (August 2022, Microbiology Spectrum)

   Youssef, Noha H. (Ed.)

   ABSTRACT Synechococcus elongatus UTEX 2973, the fastest-growing cyanobacterial strain known, optimally grows under extreme high light (HL) intensities of 1,500–2,500 μmol photons m −2 s −1 , which is lethal to most other photosynthetic microbes. We leveraged the few genetic differences between Synechococcus 2973 and the HL sensitive strain Synechococcus elongatus PCC 7942 to unravel factors essential for the high light tolerance. We identified a novel protein in Synechococcus 2973 that we have termed HltA for H igh l ight t olerance protein A . Using bioinformatic tools, we determined that HltA contains a functional PP2C-type protein phosphatase domain. Phylogenetic analysis showed that the PP2C domain belongs to the bacterial-specific Group II family and is closely related to the environmental stress response phosphatase RsbU. Additionally, we showed that unlike any previously described phosphatases, HltA contains a single N-terminal regulatory GAF domain. We found hltA to be ubiquitous throughout cyanobacteria, indicative of its potentially important role in the photosynthetic lifestyle of these oxygenic phototrophs. Mutations in the hltA gene resulted in severe defects specific to high light growth. These results provide evidence that hltA is a key factor in the tolerance of Synechococcus 2973 to high light and will open new insights into the mechanisms of cyanobacterial light stress response. IMPORTANCE Cyanobacteria are a diverse group of photosynthetic prokaryotes. The cyanobacterium Synechococcus 2973 is a high light tolerant strain with industrial promise due to its fast growth under high light conditions and the availability of genetic modification tools. Currently, little is known about the high light tolerance mechanisms of Synechococcus 2973, and there are many unknowns overall regarding high light tolerance of cyanobacteria. In this study, a comparative genomic analysis of Synechococcus 2973 identified a single nucleotide polymorphism in a locus encoding a serine phosphatase as a key factor for high light tolerance. This novel GAF-containing phosphatase was found to be the sole Group II metal-dependent protein phosphatase that is evolutionarily conserved throughout cyanobacteria. These results shed new light on the light response mechanisms of Synechococcus 2973, improving our understanding of environmental stress response. Additionally, this work will help facilitate the development of Synechococcus 2973 as an industrially useful organism. 

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4. Genome Sequence of Synechococcus sp. Strain LA31, Isolated from a Temperate Estuary

   https://doi.org/10.1128/mra.00775-21  

   Kling, Joshua D.; Webb, Eric A.; Hutchins, David A. (February 2022, Microbiology Resource Announcements)

   Stewart, Frank J. (Ed.)

   ABSTRACT Cluster 5 Synechococcus species are widely acknowledged for their broad distribution and biogeochemical importance. In particular, subcluster 5.2 strains inhabit freshwater, estuarine, and marine environments but are understudied, compared to other subclusters. Here, we present the genome for Synechococcus sp. strain LA31, a strain that was recently isolated from Narragansett Bay, Rhode Island, USA. 

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5. Seasons of Syn

   https://doi.org/10.1002/lno.11374  

   Hunter‐Cevera, Kristen R.; Neubert, Michael G.; Olson, Robert J.; Shalapyonok, Alexi; Solow, Andrew R.; Sosik, Heidi M. (November 2019, Limnology and Oceanography)

   Abstract Synechococcusis a widespread and important marine primary producer. Time series provide critical information for identifying and understanding the factors that determine abundance patterns. Here, we present the results of analysis of a 16‐yr hourly time series ofSynechococcusat the Martha's Vineyard Coastal Observatory, obtained with an automated, in situ flow cytometer. We focus on understanding seasonal abundance patterns by examining relationships between cell division rate, loss rate, cellular properties (e.g., cell volume, phycoerythrin fluorescence), and environmental variables (e.g., temperature, light). We find that the drivers of cell division vary with season; cells are temperature‐limited in winter and spring, but light‐limited in the fall. Losses to the population also vary with season. Our results lead to testable hypotheses aboutSynechococcusecophysiology and a working framework for understanding the seasonal controls ofSynechococcuscell abundance in a temperate coastal system. 

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