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1. Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy

   https://doi.org/10.1093/ismejo/wrae184  

   Pierpont, C_Logan; Baroch, Jacob_J; Church, Matthew_J; Miller, Scott_R (September 2024, The ISME Journal)

   Abstract Thermophilic microorganisms are expected to have smaller cells and genomes compared with mesophiles, a higher proportion of horizontally acquired genes, and distinct nucleotide and amino acid composition signatures. Here, we took an integrative approach to investigate these apparent correlates of thermophily for Synechococcus A/B cyanobacteria, which include the most heat-tolerant phototrophs on the planet. Phylogenomics confirmed a unique origin of different thermotolerance ecotypes, with low levels of continued gene flow between ecologically divergent but overlapping populations, which has shaped the distribution of phenotypic traits along these geothermal gradients. More thermotolerant strains do have smaller genomes, but genome reduction is associated with a decrease in community richness and metabolic diversity, rather than with cell size. Horizontal gene transfer played only a limited role during Synechococcus evolution, but, the most thermotolerant strains have acquired a Thermus tRNA modification enzyme that may stabilize translation at high temperatures. Although nucleotide base composition was not associated with thermotolerance, we found a general replacement of aspartate with glutamate, as well as a dramatic remodeling of amino acid composition at the highest temperatures that substantially differed from previous predictions. We conclude that Synechococcus A/B genome diversification largely does not conform to the standard view of temperature adaptation. In addition, carbon fixation was more thermolabile than photosynthetic oxygen evolution for the most thermotolerant strains compared with less tolerant lineages. This suggests that increased flow of reducing power generated during the light reactions to an electron sink(s) beyond carbon dioxide has emerged during temperature adaptation of these bacteria. 

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2. Data report: the DNA event horizon in the Guaymas Basin subsurface biosphere: technical advances and redefined limits in bulk extractions of nucleic acids from deep marine sediments, IODP Expedition 385

   https://doi.org/10.14379/iodp.proc.385.204.2024  

   Ramírez, GA; Mara, P; Beaudoin, D; Bojanova, D; Hinkle, JE; Kingham, B; Edgcomb, VP; Morono, Y; Teske, A (October 2024, Proceedings of the International Ocean Discovery Program Expedition reports)

   We compiled DNA and RNA isolation protocols for sediment bulk extraction and their yields from Guaymas Basin subsurface sediments recovered during International Ocean Discovery Program Expedition 385 and evaluated their sensitivity for metagenomic and amplicon analyses of subsurface microbial communities. Guaymas Basin sediments present a challenge for DNA and RNA recovery due to high concentrations of hydrocarbons, steep thermal gradients, and rapidly declining cell numbers downhole. Metagenomic library construction and sequencing was possible from as little as 0.2 to 0.5 ng DNA/cm3 sediment; polymerase chain reaction (PCR) amplification of 16S rRNA genes required in most cases approximately 1–2 ng DNA/cm3 sediment. At in situ temperatures of 50° to 60°C, decreasing DNA recovery leads to increasingly uncertain hit or miss outcomes and failures for metagenomic and amplicon analyses. DNA concentration profiles show that, even before these hot temperatures are reached, relatively moderate temperatures (near 40°C) have a major effect on microbial abundance and DNA yield. Comparison with cell count profiles shows that hydrothermal influence reduces downhole cell densities by multiple orders of magnitude compared to nonhydrothermal sediments. This effect is also visible at relatively moderate temperatures. RNA recovery is highly sensitive to downhole increasing temperatures and decreasing cell numbers, and was most efficient for microbial communities in cool, relatively shallow subsurface sediments. 

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3. Epigenetic Modifier Supplementation Improves Mitochondrial Respiration and Growth Rates and Alters DNA Methylation of Bovine Embryonic Fibroblast Cells Cultured in Divergent Energy Supply

   https://doi.org/10.3389/fgene.2022.812764  

   Crouse, Matthew S.; Caton, Joel S.; Claycombe-Larson, Kate J.; Diniz, Wellison J.; Lindholm-Perry, Amanda K.; Reynolds, Lawrence P.; Dahlen, Carl R.; Borowicz, Pawel P.; Ward, Alison K. (February 2022, Frontiers in Genetics)

   Epigenetic modifiers (EM; methionine, choline, folate, and vitamin B 12 ) are important for early embryonic development due to their roles as methyl donors or cofactors in methylation reactions. Additionally, they are essential for the synthesis of nucleotides, polyamines, redox equivalents, and energy metabolites. Despite their importance, investigation into the supplementation of EM in ruminants has been limited to one or two epigenetic modifiers. Like all biochemical pathways, one-carbon metabolism needs to be stoichiometrically balanced. Thus, we investigated the effects of supplementing four EM encompassing the methionine–folate cycle on bovine embryonic fibroblast growth, mitochondrial function, and DNA methylation. We hypothesized that EM supplemented to embryonic fibroblasts cultured in divergent glucose media would increase mitochondrial respiration and cell growth rate and alter DNA methylation as reflected by changes in the gene expression of enzymes involved in methylation reactions, thereby improving the growth parameters beyond Control treated cells. Bovine embryonic fibroblast cells were cultured in Eagle’s minimum essential medium with 1 g/L glucose (Low) or 4.5 g/L glucose (High). The control medium contained no additional OCM, whereas the treated media contained supplemented EM at 2.5, 5, and 10 times (×2.5, ×5, and ×10, respectively) the control media, except for methionine (limited to ×2). Therefore, the experimental design was a 2 (levels of glucose) × 4 (levels of EM) factorial arrangement of treatments. Cells were passaged three times in their respective treatment media before analysis for growth rate, cell proliferation, mitochondrial respiration, transcript abundance of methionine–folate cycle enzymes, and DNA methylation by reduced-representation bisulfite sequencing. Total cell growth was greatest in High ×10 and mitochondrial maximal respiration, and reserve capacity was greatest ( p < 0.01) for High ×2.5 and ×10 compared with all other treatments. In Low cells, the total growth rate, mitochondrial maximal respiration, and reserve capacity increased quadratically to 2.5 and ×5 and decreased to control levels at ×10. The biological processes identified due to differential methylation included the positive regulation of GTPase activity, molecular function, protein modification processes, phosphorylation, and metabolic processes. These data are interpreted to imply that EM increased the growth rate and mitochondrial function beyond Control treated cells in both Low and High cells, which may be due to changes in the methylation of genes involved with growth and energy metabolism. 

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4. Light availability modulates the effects of warming in a marine N₂ fixer

   https://doi.org/10.5194/bg-17-1169-2020  

   Yi, Xiangqi; Fu, Fei-Xue; Hutchins, David A.; Gao, Kunshan (January 2020, Biogeosciences)

   Abstract. Trichodesmium species, as a group of photosynthetic N2 fixers(diazotrophs), play an important role in the marine biogeochemical cycles ofnitrogen and carbon, especially in oligotrophic waters. How ongoing oceanwarming may interact with light availability to affect Trichodesmium is not yet clear. Wegrew Trichodesmium erythraeum IMS 101 at three temperature levels of 23, 27, and 31∘C undergrowth-limiting and growth-saturating light levels of 50 and 160 µmol quanta m−2 s−1, respectively, for at least 10 generations and thenmeasured physiological performance, including the specific growth rate, N2fixation rate, and photosynthesis. Light availability significantly modulatedthe growth response of Trichodesmium to temperature, with the specific growth ratepeaking at ∼27∘C under the light-saturatingconditions, while growth of light-limited cultures was non-responsive acrossthe tested temperatures (23, 27, and 31∘C). Short-term thermalresponses for N2 fixation indicated that both high growth temperatureand light intensity increased the optimum temperature (Topt) forN2 fixation and decreased its susceptibility to supra-optimaltemperatures (deactivation energy – Eh). Simultaneously, alllight-limited cultures with low Topt and high Eh were unable tosustain N2 fixation during short-term exposure to high temperatures (33–34∘C) that are not lethal for the cells grown underlight-saturating conditions. Our results imply that Trichodesmium spp. growing under lowlight levels while distributed deep in the euphotic zone or under cloudyweather conditions might be less sensitive to long-term temperature changesthat occur on the timescale of multiple generations but are more susceptible toabrupt (less than one generation time span) temperature changes, such asthose induced by cyclones and heat waves. 

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5. Evaluation of Genomic Sequence-Based Growth Rate Methods for Synchronized Synechococcus Cultures

   https://doi.org/10.1128/AEM.01743-21  

   Carroll, Julia; Van Oostende, Nicolas; Ward, Bess B. (January 2022, Applied and Environmental Microbiology)

   Glass, Jennifer B. (Ed.)

   ABSTRACT Standard methods for calculating microbial growth rates (μ) through the use of proxies, such as in situ fluorescence, cell cycle, or cell counts, are critical for determining the magnitude of the role bacteria play in marine carbon (C) and nitrogen (N) cycles. Taxon-specific growth rates in mixed assemblages would be useful for attributing biogeochemical processes to individual species and understanding niche differentiation among related clades, such as found in Synechococcus and Prochlorococcus . We tested three novel DNA sequencing-based methods (iRep, bPTR, and GRiD) for evaluating the growth of light-synchronized Synechococcus cultures under different light intensities and temperatures. In vivo fluorescence and cell cycle analysis were used to obtain standard estimates of growth rate for comparison with those of the sequence-based methods (SBM). None of the SBM values were correlated with growth rates calculated by standard techniques despite the fact that all three SBM were correlated with the percentage of cells in S phase (DNA replication) over the diel cycle. Inaccuracy in determining the time of maximum DNA replication is unlikely to account entirely for the absence of a relationship between SBM and growth rate, but the fact that most microbes in the surface ocean exhibit some degree of diel cyclicity is a caution for application of these methods. SBM correlate with DNA replication but cannot be interpreted quantitatively in terms of growth rate. IMPORTANCE Small but abundant, cyanobacterial strains such as the photosynthetic Synechococcus spp. are important because they contribute significantly to primary productivity in the ocean. These bacteria generate oxygen and provide biologically available carbon, which is essential for organisms at higher trophic levels. The small size and diversity of natural microbial assemblages mean that taxon-specific activities (e.g., growth rate) are difficult to obtain in the field. It has been suggested that sequence-based methods (SBM) may be able to solve this problem. We find, however, that SBM can detect DNA replication and are correlated with phases of the cell cycle but cannot be interpreted in terms of absolute growth rate for Synechococcus cultures growing under a day-night cycle, like that experienced in the ocean. 

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