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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. 

Abstract Uncertainties in the temporal and spatial patterns of marine primary production and respiration limit our understanding of the ocean carbon (C) cycle and our ability to predict its response to environmental changes. Here we present a comprehensive time‐series analysis of plankton metabolism at the Hawaii Ocean Time‐series program site, Station ALOHA, in the North Pacific Subtropical Gyre. Vertical profiles of gross oxygen production (GOP) and community respiration (CR) were quantified using the¹⁸O‐labeled water method together with net changes in O₂to Ar ratios during dawn to dusk in situ incubations. Rates of¹⁴C‐bicarbonate assimilation (¹⁴C‐based primary production [¹⁴C‐PP]) were also determined concurrently. During the observational period (April 2015 to July 2020), euphotic zone depth‐integrated (0–125 m) GOP and¹⁴C‐PP ranged from 35 to 134 mmol O₂m⁻²d⁻¹and 18 to 75 mmol C m⁻²d⁻¹, respectively, while CR ranged from 37 to 187 mmol O₂m⁻²d⁻¹. All biological rates varied with depth and season, with seasonality most pronounced in the lower portion of the euphotic zone (75–125 m). The mean annual ratio of GOP to¹⁴C‐PP was 1.7 ± 0.1 mol O₂(mol C)⁻¹. While previous studies have reported convergence of GOP and¹⁴C‐PP with depth, we find a less pronounced vertical decline in the GOP to¹⁴C‐PP ratios, with GOP exceeding¹⁴C‐PP by 50% or more in the lower euphotic zone. Variability in CR was higher than for GOP, driving most of the variability in the balance between the two. 

Abstract In oligotrophic oceans, the smallest eukaryotic phytoplankton are both significant primary producers and predators of abundant bacteria such asProchlorococcus. However, the drivers and consequences of community dynamics among these diverse protists are not well understood. Here, we investigated how trophic strategies along the autotrophy‐mixotrophy spectrum vary in importance over time and across depths at Station ALOHA in the North Pacific Subtropical Gyre. We combined picoeukaryote community composition from a 28‐month time‐series with traits of diverse phytoplankton isolates from the same location, to examine trophic strategies across 13 operational taxonomic units and 8 taxonomic classes. We found that autotrophs and slower‐grazing mixotrophs tended to prevail deeper in the photic zone, while the most voracious mixotrophs were relatively abundant near the surface. Within the mixed layer, there was greater phagotrophy when conditions were most stratified and when Chlaconcentrations were lowest, although the greatest temporal variation in trophic strategy occurred at intermediate depths (45–100 m). Dynamics at this site are consistent with previously described spatial patterns of trophic strategies. The success of relatively phagotrophic phytoplankton at shallower depths in the most stratified waters suggests that phagotrophy is a competitive strategy for acquiring nutrients when energy from light is plentiful. 

Abstract Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia‐oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite‐oxidizing bacteria (NOB)Nitrotogadominate at depth in the summer, the ammonia‐oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.