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Creators/Authors contains: "Fu, Fei-Xue"

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  1. Free, publicly-accessible full text available December 1, 2023
  2. Abstract

    The colony-forming cyanobacteriaTrichodesmiumspp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describeTrichodesmiumpangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% completeTrichodesmiummetagenome-assembled genomes from hand-picked,Trichodesmiumcolonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2fixing clades ofTrichodesmiumacross the transect, withT. thiebautiidominating the colony-specific reads. Pangenomic analyses showed that allT. thiebautiiMAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in allT. erythraeumgenomes, vertically inherited byT. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limitedT. erythraeumis expected to be a ‘winner’ of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared toT. thiebautii, could put this outcome in question. Thus, the clear demarcation ofT. thiebautiimaintaining CRISPR-Cas systems, whileT. erythraeumdoes not, identifiesTrichodesmiumas an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmiuminteractions.

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  3. null (Ed.)
    Abstract A major challenge in modern biology is understanding how the effects of short-term biological responses influence long-term evolutionary adaptation, defined as a genetically determined increase in fitness to novel environments. This is particularly important in globally important microbes experiencing rapid global change, due to their influence on food webs, biogeochemical cycles, and climate. Epigenetic modifications like methylation have been demonstrated to influence short-term plastic responses, which ultimately impact long-term adaptive responses to environmental change. However, there remains a paucity of empirical research examining long-term methylation dynamics during environmental adaptation in nonmodel, ecologically important microbes. Here, we show the first empirical evidence in a marine prokaryote for long-term m5C methylome modifications correlated with phenotypic adaptation to CO2, using a 7-year evolution experiment (1,000+ generations) with the biogeochemically important marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly changed in response to high (750 µatm) CO2 exposure and were maintained for at least 4.5 years of CO2 selection. After 7 years of CO2 selection, however, m5C methylation levels that initially responded to high-CO2 returned to ancestral, ambient CO2 levels. Concurrently, high-CO2 adapted growth and N2 fixation rates remained significantly higher than those of ambient CO2 adapted cell lines irrespective of CO2 concentration, a trend consistent with genetic assimilation theory. These data demonstrate the maintenance of CO2-responsive m5C methylation for 4.5 years alongside phenotypic adaptation before returning to ancestral methylation levels. These observations in a globally distributed marine prokaryote provide critical evolutionary insights into biogeochemically important traits under global change. 
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  4. null (Ed.)
    Primary productivity in the nutrient-poor subtropical ocean gyres depends on new nitrogen inputs from nitrogen fixers that convert inert dinitrogen gas into bioavailable forms. Temperature and iron (Fe) availability constrain marine nitrogen fixation, and both are changing due to anthropogenic ocean warming. We examined the physiological responses of the globally important marine nitrogen fixer, Crocosphaera watsonii across its full thermal range as a function of iron availability. At the lower end of its thermal range, from 22 to 27°C, Crocosphaera growth, nitrogen fixation, and Nitrogen-specific Iron Use Efficiencies (N-IUEs, mol N fixed hour –1 mol Fe –1 ) increased with temperature. At an optimal growth temperature of 27°C, N-IUEs were 66% higher under iron-limited conditions than iron-replete conditions, indicating that low-iron availability increases metabolic efficiency. However, Crocosphaera growth and function decrease from 27 to 32°C, temperatures that are predicted for an increasing fraction of tropical oceans in the future. Altogether, this suggests that Crocosphaera are well adapted to iron-limited, warm waters, within prescribed limits. A model incorporating these results under the IPCC RCP 8.5 warming scenario predicts that Crocosphaera N-IUEs could increase by a net 47% by 2100, particularly in higher-latitude waters. These results contrast with published responses of another dominant nitrogen fixer ( Trichodesmium ), with predicted N-IUEs that increase most in low-latitude, tropical waters. These models project that differing responses of Crocosphaera and Trichodesmium N-IUEs to future warming of iron-limited oceans could enhance their current contributions to global marine nitrogen fixation with rates increasing by ∼91 and ∼22%, respectively, thereby shifting their relative importance to marine new production and also intensifying their regional divergence. Thus, interactive temperature and iron effects may profoundly transform existing paradigms of nitrogen biogeochemistry and primary productivity in open ocean regimes. 
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  5. 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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