Prochlorococcus: advantages and limits of minimalism

Cyanobacteria-cyanophage interactions between freshwater and marine ecosystems based on large-scale cyanophage genomic analysis

The disparities in harmful algal blooms dynamics are largely attributed to variations in cyanobacteria populations within aquatic ecosystems. However, cyanobacteria-cyanophage interactions and their role in shaping cyanobacterial populations has been previously underappreciated. To address this knowledge gap, we isolated and sequenced 42 cyanophages from diverse water sources in China, with the majority (n = 35) originating from freshwater sources. We designated these sequences as the "Novel Cyanophage Genome sequence Collection" (NCGC). NCGC displayed notable genetic variations, with 95 % (40/42) of the sequences representing previously unidentified taxonomic ranks. By integrating NCGC with public data of cyanophages and cyanobacteria, we found evidence for more frequent historical cyanobacteria-cyanophage interactions in freshwater ecosystems. This was evidenced by a higher prevalence of prophage integrase-related genes in freshwater cyanophages (37.97 %) than marine cyanophages (7.42 %). In addition, freshwater cyanophages could infect a broader range of cyanobacteria orders (n = 4) than marine ones (n = 0). Correspondingly, freshwater cyanobacteria harbored more defense systems per million base pairs in their genomes, indicating more frequent phage infections. Evolutionary and cyanophage epidemiological studies suggest that interactions between cyanobacteria and cyanophages in freshwater and marine ecosystems are interconnected, and that brackish water can act as a transitional zone for freshwater and marine cyanophages. In conclusion, our research significantly expands the genetic information database of cyanophage, offering a wider selection of cyanophages to control harmful cyanobacterial blooms. Additionally, we represent a pioneering large-scale and comprehensive analysis of cyanobacteria and cyanophage sequencing data, and it provides theoretical guidance for the application of cyanophages in different environments.

Prochlorococcus marinus responses to light and oxygen

Prochlorococcus marinus, the smallest picocyanobacterium, comprises multiple clades occupying distinct niches, currently across tropical and sub-tropical oligotrophic ocean regions, including Oxygen Minimum Zones. Ocean warming may open growth-permissive temperatures in new, poleward photic regimes, along with expanded Oxygen Minimum Zones. We used ocean metaproteomic data on current Prochlorococcus marinus niches, to guide testing of Prochlorococcus marinus growth across a matrix of peak irradiances, photoperiods, spectral bands and dissolved oxygen. MED4 from Clade HLI requires greater than 4 h photoperiod, grows at 25 μmol O2 L-1 and above, and exploits high cumulative diel photon doses. MED4, however, relies upon an alternative oxidase to balance electron transport, which may exclude it from growth under our lowest, 2.5 μmol O2 L-1, condition. SS120 from clade LLII/III is restricted to low light under full 250 μmol O2 L-1, shows expanded light exploitation under 25 μmol O2 L-1, but is excluded from growth under 2.5 μmol O2 L-1. Intermediate oxygen suppresses the cost of PSII photoinactivation, and possibly the enzymatic production of H2O2 in SS120, which has limitations on genomic capacity for PSII and DNA repair. MIT9313 from Clade LLIV is restricted to low blue irradiance under 250 μmol O2 L-1, but exploits much higher irradiance under red light, or under lower O2 concentrations, conditions which slow photoinactivation of PSII and production of reactive oxygen species. In warming oceans, range expansions and competition among clades will be governed not only by light levels. Short photoperiods governed by latitude, temperate winters, and depth attenuation of light, will exclude clade HLI (including MED4) from some habitats. In contrast, clade LLII/III (including SS120), and particularly clade LLIV (including MIT9313), may exploit higher light niches nearer the surface, under expanding OMZ conditions, where low O2 relieves the stresses of oxidation stress and PSII photoinhibition.

Shaping of microbial phenotypes by trade-offs

Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.

A distinct, high-affinity, alkaline phosphatase facilitates occupation of P-depleted environments by marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus, the two most abundant phototrophs on Earth, thrive in oligotrophic oceanic regions. While it is well known that specific lineages are exquisitely adapted to prevailing in situ light and temperature regimes, much less is known of the molecular machinery required to facilitate occupancy of these low-nutrient environments. Here, we describe a hitherto unknown alkaline phosphatase, Psip1, that has a substantially higher affinity for phosphomonoesters than other well-known phosphatases like PhoA, PhoX, or PhoD and is restricted to clade III Synechococcus and a subset of high light I-adapted Prochlorococcus strains, suggesting niche specificity. We demonstrate that Psip1 has undergone convergent evolution with PhoX, requiring both iron and calcium for activity and likely possessing identical key residues around the active site, despite generally very low sequence homology. Interrogation of metagenomes and transcriptomes from TARA oceans and an Atlantic Meridional transect shows that psip1 is abundant and highly expressed in picocyanobacterial populations from the Mediterranean Sea and north Atlantic gyre, regions well recognized to be phosphorus (P)-deplete. Together, this identifies psip1 as an important oligotrophy-specific gene for P recycling in these organisms. Furthermore, psip1 is not restricted to picocyanobacteria and is abundant and highly transcribed in some α-proteobacteria and eukaryotic algae, suggesting that such a high-affinity phosphatase is important across the microbial taxonomic world to occupy low-P environments.

Biological interactions with Prochlorococcus: implications for the marine carbon cycle

The unicellular picocyanobacterium Prochlorococcus is the most abundant photoautotroph and contributes substantially to global CO2 fixation. In the vast euphotic zones of the open ocean, Prochlorococcus converts CO2 into organic compounds and supports diverse organisms, forming an intricate network of interactions that regulate the magnitude of carbon cycling and storage in the ocean. An understanding of the biological interactions with Prochlorococcus is critical for accurately estimating the contributions of Prochlorococcus and interacting organisms to the marine carbon cycle. This review synthesizes the primary production contributed by Prochlorococcus in the global ocean. We outline recent progress on the interactions of Prochlorococcus with heterotrophic bacteria, phages, and grazers that multifacetedly determine Prochlorococcus carbon production and fate. We discuss that climate change might affect the biological interactions with Prochlorococcus and thus the marine carbon cycle.

Genome reduction occurred in early Prochlorococcus with an unusually low effective population size

In the oligotrophic sunlit ocean, the most abundant free-living planktonic bacterial lineages evolve convergently through genome reduction. The cyanobacterium Prochlorococcus responsible for 10% global oxygen production is a prominent example. The dominant theory known as "genome streamlining" posits that they have extremely large effective population sizes (Ne) such that selection for metabolic efficiency acts to drive genome reduction. Because genome reduction largely took place anciently, this theory builds on the assumption that their ancestors' Ne was similarly large. Constraining Ne for ancient ancestors is challenging because experimental measurements of extinct organisms are impossible and alternatively reconstructing ancestral Ne with phylogenetic models gives large uncertainties. Here, we develop a new strategy that leverages agent-based modeling to simulate the changes in the genome-wide ratio of radical to conservative nonsynonymous nucleotide substitution rate (dR/dC) in a possible range of Ne in ancestral populations. This proxy shows expected increases with decreases of Ne only when Ne falls to about 10 k - 100 k or lower, magnitudes characteristic of Ne of obligate endosymbiont species where drift drives genome reduction. Our simulations therefore strongly support a scenario where the primary force of Prochlorococcus genome reduction is drift rather than selection.

A timeline of bacterial and archaeal diversification in the ocean

Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, Ca. Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades Prochlorococcus, Synechococcus, and Crocosphaera, whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.

Seasonal Patterns of Picocyanobacterial Community Structure in the Kuroshio Current

The nutrient-scarce, warm, and high-salinity Kuroshio current has a profound impact on both the marine ecology of the northwestern Pacific Ocean and the global climate. This study aims to reveal the seasonal dynamics of picoplankton in the subtropical Kuroshio current. Our results showed that one of the picocyanobacteria, Synechococcus, mainly distributed in the surface water layer regardless of seasonal changes, and the cell abundance ranged from 104 to 105 cells mL-1. In contrast, the maximum concentration of the other picocyanobacteria, Prochlorococcus, was maintained at more than 105 cells mL-1 throughout the year. In the summer and the autumn, Prochlorococcus were mainly concentrated at the water layer near the bottom of the euphotic zone. They were evenly distributed in the euphotic zone in the spring and winter. The stirring effect caused by the monsoon determined their distribution in the water column. In addition, the results of 16S rRNA gene diversity analysis showed that the seasonal changes in the relative abundance of Synechococcus and Prochlorococcus in the surface water of each station accounted for 20 to 40% of the total reads. The clade II of Synechococcus and the High-light II of Prochlorococcus were the dominant strains in the waters all year round. Regarding other picoplankton, Proteobacteria and Actinobacteria occupied 45% and 10% of the total picoplankton in the four seasons. These data should be helpful for elucidating the impacts of global climate changes on marine ecology and biogeochemical cycles in the Western Boundary Currents in the future.

Selection for oligotrophy among bacteria inhabiting host microbiomes

IMPORTANCE

Understanding how natural selection has historically shaped the traits of microbial populations comprising host microbiomes would help predict how the functions of these microbes may continue to evolve over space and time. Numerous host-associated microbes have been found to adapt to their host, sometimes becoming obligate symbionts, whereas free-living microbes are best known to adapt to their surrounding environment. Our study assessed the selective pressures of both the host environment and the surrounding external environment in shaping the functional potential of host-associated bacteria. Despite residing within the resource-rich microbiome of their hosts, we demonstrate that host-associated heterotrophic bacteria show evidence of trait selection that matches the nutrient availability of their broader surrounding environment. These findings illustrate the complex mix of selective pressures that likely shape the present-day function of bacteria found inhabiting host microbiomes. Our study lends insight into the shifts in function that may occur as environments fluctuate over time.

Global scale phylogeography of functional traits and microdiversity in Prochlorococcus

Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.

Latitudinal and meridional patterns of picophytoplankton variability are contrastingly associated with Ekman pumping and the warm pool in the tropical western Pacific

Marine picophytoplankton plays a major role in marine cycling and energy conversion, and its effects on the carbon cycle and global climate change have been well documented. In this study, we investigated the response of picophytoplankton across a broad range of physicochemical conditions in two distinct regions of the tropical western Pacific. Our analysis considered the abundance, carbon biomass, size fraction, distribution, and regulatory factors of the picophytoplankton community, which included the cyanobacteria Prochlorococcus and Synechococcus, and small eukaryotic phytoplankton (picoeukaryotes). The first region was a latitudinal transect along the equator (142-163° E, 0° N), characterized by stratified oligotrophic conditions. The second region was a meridional transect (143° E, 0-22° N) known for its high-nutrient and low-chlorophyll (HNLC) conditions. Results showed that picophytoplankton contributed >80% of the chlorophyll a (Chl a), and was mainly distributed above 100 m. Prochlorococcus was the dominant organism in terms of cell abundance and estimated carbon biomass in both latitudinal and meridional transects, followed by Synechococcus and picoeukaryotes. In the warm pool, Prochlorococcus was primarily distributed below the isothermal layer, with the maximum subsurface abundance forming below it. The maximum Synechococcus abundance was restricted to the west-warm pool, due to the high temperature, and the second-highest Synechococcus abundance was associated with frontal interaction between the east-warm pool and the westward advance of Middle East Pacific water. In contrast, picoeukaryotes formed a maximum subsurface abundance corresponding to the subsurface Chl a maximum. In the mixed HNLC waters, the cell abundance and biomass of the three picophytoplankton groups were slightly lower than those in the warm pool. Due to a cyclonic eddy, the contours of the maximum subsurface Prochlorococcus abundance were uplifted, evidently with a lower value than the surrounding water. Synechococcus abundance varied greatly in patches, forming a weakly high subsurface peak when the isothermal layer rose to the near-surface (<50 m). The subsurface maximum picoeukaryote abundance was also highly consistent with that of the subsurface Chl a maximum. Correlation analysis and generalized additive models of environmental factors showed that nutrient availability had a two-faceted role in regulating the spatial patterns of picophytoplankton in diverse latitudinal and meridional environments. We concluded through regression that temperature and light irradiance were the key determinants of picophytoplankton variability in the tropical western Pacific. This study provides insights into the changing picophytoplankton community structure with potential future changing hydroclimatic force.

Seasonal development of a tidal mixing front drives shifts in community structure and diversity of bacterioplankton

Bacterioplankton underpin biogeochemical cycles and an improved understanding of the patterns and drivers of variability in their distribution is needed to determine their wider functioning and importance. Sharp environmental gradients and dispersal barriers associated with ocean fronts are emerging as key determinants of bacterioplankton biodiversity patterns. We examined how the development of the Celtic Sea Front (CF), a tidal mixing front on the Northwest European Shelf affects bacterioplankton communities. We performed 16S-rRNA metabarcoding on 60 seawater samples collected from three depths (surface, 20 m and seafloor), across two research cruises (May and September 2018), encompassing the intra-annual range of the CF intensity. Communities above the thermocline of stratified frontal waters were clearly differentiated and less diverse than those below the thermocline and communities in the well-mixed waters of the Irish Sea. This effect was much more pronounced in September, when the CF was at its peak intensity. The stratified zone likely represents a stressful environment for bacterioplankton due to a combination of high temperatures and low nutrients, which fewer taxa can tolerate. Much of the observed variation was driven by Synechococcus spp. (cyanobacteria), which were more abundant within the stratified zone and are known to thrive in warm oligotrophic waters. Synechococcus spp. are key contributors to global primary productivity and carbon cycling and, as such, variability driven by the CF is likely to influence regional biogeochemical processes. However, further studies are required to explicitly link shifts in community structure to function and quantify their wider importance to pelagic ecosystems.

Tolyporphins-Exotic Tetrapyrrole Pigments in a Cyanobacterium-A Review

Tolyporphins were discovered some 30 years ago as part of a global search for antineoplastic compounds from cyanobacteria. To date, the culture HT-58-2, comprised of a cyanobacterium-microbial consortium, is the sole known producer of tolyporphins. Eighteen tolyporphins are now known-each is a free base tetrapyrrole macrocycle with a dioxobacteriochlorin (14), oxochlorin (3), or porphyrin (1) chromophore. Each compound displays two, three, or four open β-pyrrole positions and two, one, or zero appended C-glycoside (or -OH or -OAc) groups, respectively; the appended groups form part of a geminal disubstitution motif flanking the oxo moiety in the pyrroline ring. The distinct structures and repertoire of tolyporphins stand alone in the large pigments-of-life family. Efforts to understand the cyanobacterial origin, biosynthetic pathways, structural diversity, physiological roles, and potential pharmacological properties of tolyporphins have attracted a broad spectrum of researchers from diverse scientific areas. The identification of putative biosynthetic gene clusters in the HT-58-2 cyanobacterial genome and accompanying studies suggest a new biosynthetic paradigm in the tetrapyrrole arena. The present review provides a comprehensive treatment of the rich science concerning tolyporphins.

Coexistence of Dominant Marine Phytoplankton Sustained by Nutrient Specialization

Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, but the basis for their coexistence has not been quantitatively demonstrated. Here, we combine in situ microcosm experiments and an ecological model to show that this coexistence can be sustained by specialization in the uptake of distinct nitrogen (N) substrates at low-level concentrations that prevail in subtropical environments. In field incubations, the response of both Prochlorococcus and Synechococcus to nanomolar N amendments demonstrates N limitation of growth in both populations. However, Prochlorococcus showed a higher affinity to ammonium, whereas Synechococcus was more adapted to nitrate uptake. A simple ecological model demonstrates that the differential nutrient preference inferred from field experiments with these genera may sustain their coexistence. It also predicts that as the supply of NO3- decreases, as expected under climate warming, the dominant genera should undergo a nonlinear shift from Synechococcus to Prochlorococcus, a pattern that is supported by subtropical field observations. Our study suggests that the evolution of differential nutrient affinities is an important mechanism for sustaining the coexistence of genera and that climate change is likely to shift the relative abundance of the dominant plankton genera in the largest biomes in the ocean. IMPORTANCE Our manuscript addresses the following fundamental question in microbial ecology: how do different plankton using the same essential nutrients coexist? Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, which support a significant amount of marine primary production. The geographical distributions of these two organisms are largely overlapping, but the basis for their coexistence in these biomes remains unclear. In this study, we combined in situ microcosm experiments and an ecosystem model to show that the coexistence of these two organisms can arise from specialization in the uptake of distinct nitrogen substrates; Prochlorococcus prefers ammonium, whereas Synechococcus prefers nitrate when these nutrients exist at low concentrations. Our framework can be used for simulating and predicting the coexistence in the future ocean and may provide hints toward understanding other similar types of coexistence.

A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments

In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.

Water column stratification governs picophytoplankton community structure in the oligotrophic eastern Indian ocean

Under the background of global warming, the area extent of the oligotrophic tropical oceans has growing due to increased water-column stratification over the past decades. Picophytoplankton is usually the most dominant phytoplankton group in oligotrophic tropical oceans and substantially contribute to carbon biomass and primary production three. Understanding how vertical stratification governs the community structure of picophytoplankton communities in oligotrophic tropical oceans is important for comprehensively understanding the plankton ecology and biogeochemical cycle in these areas. In this study, the distribution of the picophytoplankton communities in the eastern Indian Ocean (EIO) was investigated during a period of thermal stratification in the spring of 2021. Prochlorococcus contributed most (54.9%) to picophytoplankton carbon biomass, followed by picoeukaryotes (38.5%) and Synechococcus (6.6%). Vertically, the three picophytoplankton groups showed quite different distribution pattern: the abundance of Synechococcus was highest in the surface layer, while Prochlorococcus and picoeukaryotes were usually located between 50 m and 100 m. The relationship between the abundance of picophytoplankton and environmental factors was analyzed, and the results revealed that picophytoplankton distribution was strongly correlated with the degree of vertical stratification of the water column. The density of Synechococcus was higher in strongly stratified waters, while Prochlorococcus was more abundant in regions of weaker stratification. This is mainly attributed to variation of physicochemical parameters such as nutrient structures and temperature resulted from water column stratification. Understanding the distribution patterns of these organisms and their relationship with stratification in the oligotrophic EIO is essential for comprehensive understanding on oligotrophic tropical ecosystem with increasing stratification in future.

Transcriptional Mechanisms of Thermal Acclimation in Prochlorococcus

Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30°C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17°C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones. IMPORTANCE Prochlorococcus is a major marine primary producer with a global impact on atmospheric CO₂ fixation. This cyanobacterium is widely distributed across the temperate ocean, but virtually absent at latitudes above 40° for yet unknown reasons. Temperature has been suggested as a major limiting factor, but the exact mechanisms behind Prochlorococcus thermal growth restriction remain unexplored. This study brings us closer to understanding how Prochlorococcus functions under challenging temperature conditions, by focusing on its transcriptional response after long-term acclimation from its optimum to its thermal thresholds. Our results show that the drop in Prochlorococcus growth rate under cold conditions was paralleled by a transcriptional suppression of the photosynthetic machinery during daytime and a loss in the organism's regulatory capacity to maintain circadian expression patterns. Notably, warm temperature induced a marked shrinkage of the organism's cellular transcript inventory, which may also induce regulatory imbalances in the future functioning of this cyanobacterium.

Control of light-dependent behaviour in cyanobacteria by the second messenger cyclic di-GMP

Nucleotide-derived signalling molecules control a wide range of cellular processes in all organisms. The bacteria-specific cyclic dinucleotide c-di-GMP plays a crucial role in regulating motility-to-sessility transitions, cell cycle progression, and virulence. Cyanobacteria are phototrophic prokaryotes that perform oxygenic photosynthesis and are widespread microorganisms that colonize almost all habitats on Earth. In contrast to photosynthetic processes that are well understood, the behavioural responses of cyanobacteria have rarely been studied in detail. Analyses of cyanobacterial genomes have revealed that they encode a large number of proteins that are potentially involved in the synthesis and degradation of c-di-GMP. Recent studies have demonstrated that c-di-GMP coordinates many different aspects of the cyanobacterial lifestyle, mostly in a light-dependent manner. In this review, we focus on the current knowledge of light-regulated c-di-GMP signalling systems in cyanobacteria. Specifically, we highlight the progress made in understanding the most prominent behavioural responses of the model cyanobacterial strains Thermosynechococcus vulcanus and Synechocystis sp. PCC 6803. We discuss why and how cyanobacteria extract crucial information from their light environment to regulate ecophysiologically important cellular responses. Finally, we emphasize the questions that remain to be addressed.

Production, homology modeling and mutagenesis studies on GlcH glucose transporter from Prochlorococcus sp. strain SS120

The marine cyanobacterium Prochlorococcus is one of the main primary producers on Earth, which can take up glucose by using the high affinity, multiphasic transporter GlcH. We report here the overexpression of glcH from Prochlorococcus marinus strain SS120 in Escherichia coli. Modeling studies of GlcH using the homologous MelB melibiose transporter from Salmonella enterica serovar Typhimurium showed high conservation at the overall fold. We observed that an important structural interaction, mediated by a strong hydrogen bond between D8 and R141, is conserved in Prochlorococcus, although the corresponding amino acids in MelB from Salmonella are different. Biased docking studies suggested that when glucose reaches the pocket of the transporter and interacts with D8 and R141, the hydrogen bond network in which these residues are involved could be disrupted, favoring a conformational change with the subsequent translocation of the glucose molecule towards the cytoplasmic region of the pmGlcH structure. Based on these theoretical predictions and on the conservation of N117 and W348 in other MelB structures, D8, N117, R141 and W348 were mutated to glycine residues. Their key role in glucose transport was evaluated by glucose uptake assays. N117G and W348G mutations led to 17 % decrease in glucose uptake, while D8G and R141G decreased the glucose transport by 66 % and 92 % respectively. Overall, our studies provide insights into the Prochlorococcus 3D-structure of GlcH, paving the way for further analysis to understand the features which are involved in the high affinity and multiphasic kinetics of this transporter.

Understanding opposing predictions of Prochlorococcus in a changing climate

Statistically derived species distribution models (SDMs) are increasingly used to predict ecological changes on a warming planet. For Prochlorococcus, the most abundant phytoplankton, an established statistical prediction conflicts with dynamical models as they predict large, opposite, changes in abundance. We probe the SDM at various spatial-temporal scales, showing that light and temperature fail to explain both temporal fluctuations and sharp spatial transitions. Strong correlations between changes in temperature and population emerge only at very large spatial scales, as transects pass through transitions between regions of high and low abundance. Furthermore, a two-state model based on a temperature threshold matches the original SDM in the surface ocean. We conclude that the original SDM has little power to predict changes when Prochlorococcus is already abundant, which resolves the conflict with dynamical models. Our conclusion suggests that SDMs should prove efficacy across multiple spatial-temporal scales before being trusted in a changing ocean.

Structural Characterization of the Chlorophyllide a Oxygenase (CAO) Enzyme Through an In Silico Approach

Chlorophyllide a oxygenase (CAO) is responsible for converting chlorophyll a to chlorophyll b in a two-step oxygenation reaction. CAO belongs to the family of Rieske-mononuclear iron oxygenases. Although the structure and reaction mechanism of other Rieske monooxygenases have been described, a member of plant Rieske non-heme iron-dependent monooxygenase has not been structurally characterized. The enzymes in this family usually form a trimeric structure and electrons are transferred between the non-heme iron site and the Rieske center of the adjoining subunits. CAO is supposed to form a similar structural arrangement. However, in Mamiellales such as Micromonas and Ostreococcus, CAO is encoded by two genes where non-heme iron site and Rieske cluster localize on the distinct polypeptides. It is not clear if they can form a similar structural organization to achieve the enzymatic activity. In this study, the tertiary structures of CAO from the model plant Arabidopsis thaliana and the Prasinophyte Micromonas pusilla were predicted by deep learning-based methods, followed by energy minimization and subsequent stereochemical quality assessment of the predicted models. Furthermore, the chlorophyll a binding cavity and the interaction of ferredoxin, which is the electron donor, on the surface of Micromonas CAO were predicted. The electron transfer pathway was predicted in Micromonas CAO and the overall structure of the CAO active site was conserved even though it forms a heterodimeric complex. The structures presented in this study will serve as a basis for understanding the reaction mechanism and regulation of the plant monooxygenase family to which CAO belongs.

Draft genomes of three closely related low light-adapted Prochlorococcus

OBJECTIVES

The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here.

DATA DESCRIPTION

We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.

Single-amplified genomes reveal most streamlined free-living marine bacteria

Evolutionary adaptations of prokaryotes to the environment sometimes result in genome reduction. Our knowledge of this phenomenon among free-living bacteria remains scarce. We address the dynamics and limits of genome reduction by examining one of the most abundant bacteria in the ocean, the SAR86 clade. Despite its abundance, comparative genomics has been limited by the absence of pure cultures and the poor representation in metagenome-assembled genomes. We co-assembled multiple previously available single-amplified genomes to obtain the first complete genomes from members of the four families. All families showed a convergent evolutionary trajectory with characteristic features of streamlined genomes, most pronounced in the TMED112 family. This family has a genome size of ca. 1 Mb and only 1 bp as median intergenic distance, exceeding values found in other abundant microbes such as SAR11, OM43 and Prochlorococcus. This genomic simplification led to a reduction in the biosynthesis of essential molecules, DNA repair-related genes, and the ability to sense and respond to environmental factors, which could suggest an evolutionary dependence on other co-occurring microbes for survival (Black Queen hypothesis). Therefore, these reconstructed genomes within the SAR86 clade provide new insights into the limits of genome reduction in free-living marine bacteria.

Global scale phylogeography of functional traits and microdiversity in Prochlorococcus

Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenomically assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenomically assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype’s phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus .

Exploring the dynamics of marine picophytoplankton among the Yellow Sea, Indian Ocean and Pacific Ocean: The importance of temperature and nitrogen

Marine picophytoplankton (<2 μm) are the most abundant photosynthetic group and also important contributors to global primary production. However, it is still constrained to incorporate picophytoplankton into dynamic ecosystem models, as a result of our limited understanding of their global distribution and abundance. Here, we applied a large dataset consisted of 1817 in situ observations from the Yellow Sea, Indian Ocean, and Pacific Ocean to suggest that picophytoplankton abundance and distribution had a large variability among the three distinct regions. Based on the correlation analysis, aggregated boosted tree analysis, and generalized additive model, we proposed that water temperature and dissolved inorganic nitrogen (N) were key determinants in driving the large-scale variability of marine picophytoplankton. For example, we revealed that high temperature and low N would stimulate the growth of Prochlorococcus. Therefore, these results could provide some insights into the various environmental factors which affect the dynamics of picophytoplankton, as well as the dynamic ecosystem models.

Phytoplankton responses to changing temperature and nutrient availability are consistent across the tropical and subtropical Atlantic

Temperature and nutrient supply interactively control phytoplankton growth and productivity, yet the role of these drivers together still has not been determined experimentally over large spatial scales in the oligotrophic ocean. We conducted four microcosm experiments in the tropical and subtropical Atlantic (29°N-27°S) in which surface plankton assemblages were exposed to all combinations of three temperatures (in situ, 3 °C warming and 3 °C cooling) and two nutrient treatments (unamended and enrichment with nitrogen and phosphorus). We found that chlorophyll a concentration and the biomass of picophytoplankton consistently increase in response to nutrient addition, whereas changes in temperature have a smaller and more variable effect. Nutrient enrichment leads to increased picoeukaryote abundance, depressed Prochlorococcus abundance, and increased contribution of small nanophytoplankton to total biomass. Warming and nutrient addition synergistically stimulate light-harvesting capacity, and accordingly the largest biomass response is observed in the warmed, nutrient-enriched treatment at the warmest and least oligotrophic location (12.7°N). While moderate nutrient increases have a much larger impact than varying temperature upon the growth and community structure of tropical phytoplankton, ocean warming may increase their ability to exploit events of enhanced nutrient availability.

Microcosm experiments in the tropical and subtropical Atlantic reveal consistent responses of phytoplankton to changing temperature and nutrient availability, with implications for the impacts of ocean warming in oligotrophic ecosystems.

Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation

Marine cyanobacteria depend on light for photosynthesis, restricting their growth to the photic zone. The upper part of this layer is exposed to strong UV radiation (UVR), a DNA mutagen that can harm these microorganisms. To thrive in UVR-rich waters, marine cyanobacteria employ photoprotection strategies that are still not well defined. Among these are photolyases, light-activated enzymes that repair DNA dimers generated by UVR. Our analysis of genomes of 81 strains of Synechococcus, Cyanobium, and Prochlorococcus isolated from the world’s oceans shows that they possess up to five genes encoding different members of the photolyase/cryptochrome family, including a photolyase with a novel domain arrangement encoded by either one or two separate genes. We disrupted the putative photolyase-encoding genes in Synechococcus sp. strain RS9916 and discovered that each gene contributes to the overall capacity of this organism to survive UVR. Additionally, each conferred increased survival after UVR exposure when transformed into Escherichia coli lacking its photolyase and SOS response. Our results provide the first evidence that this large set of photolyases endows Synechococcus with UVR resistance that is far superior to that of E. coli, but that, unlike for E. coli, these photolyases provide Synechococcus with the vast majority of its UVR tolerance.

Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean

Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in the oceans. Gene content variation among picocyanobacterial populations in separate ocean basins often mirrors the selective pressures imposed by the region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in Synechococcus and low-light adapted Prochlorococcus populations from deep chlorophyll maximum layers of iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher new iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower new iron flux). Picocyanobacterial siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, especially at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of marine picocyanobacteria.

Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales

The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel’s lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.

The evolutionary forces driving genome size in bacteria and archaea have been subject to debate during the last decades. Typically, independent comparative analyses have suggested that unique variables, such as the strength of selection, environmental complexity, and mutation rate, are the main drivers of this trait, without considering for potential biases derived from shared ancestry. Here, we applied a phylogeny-based statistical approach to assess how tightly genome size in bacteria and archaea is linked to evolutionary history. Moreover, we also evaluated the predictability of genome size from the strength of purifying selection and ecological strategy on a broad diversity of bacteria and archaea genomes under a phylogenetic comparative framework. Our approach indicates that despite the ability of bacteria and archaea to rapidly exchange genes, a strong phylogenetic signal to genome size distributions can be recovered at broad phylogenetic scales.

Picophytoplankton in the West Pacific Ocean: A Snapshot

Marine picophytoplankton have crucial ecological value and make an important contribution to marine primary productivity. While biomass of phytoplankton in general is projected to decline as a result of global warming, picophytoplankton will likely dominate in the future oceans due to their growth advantages in an oligotrophic environment. To better understand the biography of picophytoplankton, we undertook a comprehensive study of the distribution patterns of picophytoplankton, carbon biomass, and Chl a concentrations, etc. based on large-scale sampling in the tropical Western Pacific Ocean. In terms of cellular abundance, Prochlorococcus was the most abundant group (averaging [1.03 ± 0.40] × 10⁴ cells/mL), followed by Synechococcus (averaging [1.31 ± 1.22] × 10³ cells/mL) and then picoeucaryote (averaging [4.83 ± 2.84] × 10² cells/mL). The picophytoplankton size-fractionated chlorophyll a (Pico-Chl a) accounted for about 30% of the total Chl a, with Prochlorococcus and picoeukaryotes contributing 41 and 35%, respectively, of the Pico-Chl a-normalized carbon biomass, indicating the ecological importance of picophytoplankton as the primary producers. In terms of biogeographic distribution, the picophytoplankton communities exhibited contrasting patterns. The surface distribution of Prochlorococcus and Synechococcus was concentrated in the low latitude of the 142°E section, while picoeucaryote was more abundant near the 130°E and equator sections. Synechococcus was higher in the shallow layer at 25 m, and it was extremely tolerant of high-light irradiation, while Prochlorococcus and picoeucaryote were distributed in the deep Chlorophyll maximum layer (DCM) (about 100 m). From the carbon-to-Chlorophyll a ratios, which was derived from Prochlorococcus and picoeucaryote population groups, we found that the ratio varied widely, from 0.19 to 75.56, and was highest at the depth of 200 m. Of these, Prochlorococcus had an important contribution. The correlation analysis of environmental factors showed that Prochlorococcus, Synechococcus, and picoeucaryote were negatively correlated with nutrient concentration. We concluded that Prochlorococcus group was dominant in the WPO, both in abundance and biomass, and the various abiotic factors such as temperature, salinity, and nutrient concentrations were closely correlated with the spatial variation in the picophytoplankton community. These findings aid our understanding of how contrasting environmental conditions influence picophytoplankton community and the importance of picophytoplankton in contributing the carbon pool in the oligotrophic ocean.

Diverse Subclade Differentiation Attributed to the Ubiquity of Prochlorococcus High-Light-Adapted Clade II

Prochlorococcus is the key primary producer in marine ecosystems, and the high-light-adapted clade II (HLII) is the most abundant ecotype. However, the genomic and ecological basis of Prochlorococcus HLII in the marine environment has remained elusive. Here, we show that the ecologically coherent subclade differentiation of HLII corresponds to genomic and ecological characteristics on the basis of analyses of 31 different strains of HLII, including 12 novel isolates. Different subclades of HLII with different core and accessory genes were identified, and their distribution in the marine environment was explored using the TARA Oceans metagenome database. Three major subclade groups were identified, viz., the surface group (HLII-SG), the transition group (HLII-TG), and the deep group (HLII-DG). These subclade groups showed different temperature ranges and optima for distribution. In regression analyses, temperature and nutrient availability were identified as key factors affecting the distribution of HLII subclades. A 35% increase in the relative abundance of HLII-SG by the end of the 21st century was predicted under the Representative Concentration Pathway 8.5 scenario. Our results show that the ubiquity and distribution of Prochlorococcus HLII in the marine environment are associated with the differentiation of diverse subclades. These findings provide insights into the large-scale shifts in the Prochlorococcus community in response to future climate change.

Basin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiology

Extensive microdiversity within Prochlorococcus, the most abundant marine cyanobacterium, occurs at scales from a single droplet of seawater to ocean basins. To interpret the structuring role of variations in genetic potential, as well as metabolic and physiological acclimation, we developed a mechanistic constraint-based modeling framework that incorporates the full suite of genes, proteins, metabolic reactions, pigments, and biochemical compositions of 69 sequenced isolates spanning the Prochlorococcus pangenome. Optimizing each strain to the local, observed physical and chemical environment along an Atlantic Ocean transect, we predicted variations in strain-specific patterns of growth rate, metabolic configuration, and physiological state, defining subtle niche subspaces directly attributable to differences in their encoded metabolic potential. Predicted growth rates covaried with observed ecotype abundances, affirming their significance as a measure of fitness and inferring a nonlinear density dependence of mortality. Our study demonstrates the potential to interpret global-scale ecosystem organization in terms of cellular-scale processes.

Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus

Prochlorococcus is both the smallest and numerically most abundant photosynthesizing organism on the planet. While thriving in the warm oligotrophic gyres, Prochlorococcus concentrations drop rapidly in higher-latitude regions. Transect data from the North Pacific show the collapse occurring at a wide range of temperatures and latitudes (temperature is often hypothesized to cause this shift), suggesting an ecological mechanism may be at play. An often used size-based theory of phytoplankton community structure that has been incorporated into computational models correctly predicts the dominance of Prochlorococcus in the gyres, and the relative dominance of larger cells at high latitudes. However, both theory and computational models fail to explain the poleward collapse. When heterotrophic bacteria and predators that prey nonspecifically on both Prochlorococcus and bacteria are included in the theoretical framework, the collapse of Prochlorococcus occurs with increasing nutrient supplies. The poleward collapse of Prochlorococcus populations then naturally emerges when this mechanism of "shared predation" is implemented in a complex global ecosystem model. Additionally, the theory correctly predicts trends in both the abundance and mean size of the heterotrophic bacteria. These results suggest that ecological controls need to be considered to understand the biogeography of Prochlorococcus and predict its changes under future ocean conditions. Indirect interactions within a microbial network can be essential in setting community structure.

A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series

The rates of cell growth, division, and carbon loss of microbial populations are key parameters for understanding how organisms interact with their environment and how they contribute to the carbon cycle. However, the invasive nature of current analytical methods has hindered efforts to reliably quantify these parameters. In recent years, size-structured matrix population models (MPMs) have gained popularity for estimating division rates of microbial populations by mechanistically describing changes in microbial cell size distributions over time. Motivated by the mechanistic structure of these models, we employ a Bayesian approach to extend size-structured MPMs to capture additional biological processes describing the dynamics of a marine phytoplankton population over the day-night cycle. Our Bayesian framework is able to take prior scientific knowledge into account and generate biologically interpretable results. Using data from an exponentially growing laboratory culture of the cyanobacterium Prochlorococcus, we isolate respiratory and exudative carbon losses as critical parameters for the modeling of their population dynamics. The results suggest that this modeling framework can provide deeper insights into microbial population dynamics provided by size distribution time-series data.

Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria

Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.

Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas

Nordic Seas are the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean with complex water masses, experiencing an abrupt climate change. Though knowledge of the marine virosphere has expanded rapidly, the diversity of viruses and their relationships with host cells and water masses in the Nordic Seas remain to be fully revealed. Here, we establish the Nordic Sea DNA virome (NSV) data set of 55,315 viral contigs including 1,478 unique viral populations from seven stations influenced by both the warm Atlantic and cold Arctic water masses. Caudovirales dominated in the seven NSVs, especially in the warm Atlantic waters. The major giant nucleocytoplasmic large DNA viruses (NCLDVs) contributed a significant proportion of the classified viral contigs in the NSVs (32.2%), especially in the cold Arctic waters (44.9%). The distribution patterns of Caudovirales and NCLDVs were a reflection of the community structure of their hosts in the corresponding water masses and currents. Latitude, pH, and flow speed were found to be key factors influencing the microbial communities and coinfluencing the variation of viral communities. Network analysis illustrated the tight coupling between the variation of viral communities and microbial communities in the Nordic Seas. This study suggests a probable linkage between viromes, host cells, and surface water masses from both the cool Arctic and warm Atlantic Oceans. IMPORTANCE This is a systematic study of Nordic Sea viromes using metagenomic analysis. The viral diversity, community structure, and their relationships with host cells and the complex water masses from both the cool Arctic and the warm Atlantic oceans were illustrated. The NCLDVs and Caudovirales are proposed as the viral characteristics of the cold Arctic and warm Atlantic waters, respectively. This study provides an important background for the viromes in the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean and sheds light on their responses to abrupt climate change in the future.

Phytoplankton biodiversity and the inverted paradox

Earth's aquatic food webs are overwhelmingly supported by planktonic microalgae that live in the sunlit water column where only a minimum number of physical niches are readily identifiable. Despite this paucity of environmental differentiation, these "phytoplankton" populations exhibit a rich biodiversity, an observation not easily reconciled with broadly accepted rules of resource-based competitive exclusion. This conundrum is referred to as the "Paradox of the Plankton". Consideration of physical distancing between nutrient depletion zones around individual phytoplankton, however, suggests a competition-neutral resource landscape. Application of neutral theory to the sheer number of phytoplankton in physically-mixed water masses yields a prediction of astronomical biodiversity, suggesting the inverted paradox: Why are there so few phytoplankton species? Here, we introduce a trophic constraint on phytoplankton that, when combined with stochastic principals of ecological drift, predicts only modest levels of diversity in an otherwise competition-neutral landscape. Our "trophic exclusion" principle predicts diversity to be independent of population size and yields a species richness across cell-size classes that is consistent with broad oceanographic survey observations.

Microbial helpers allow cyanobacteria to thrive in ferruginous waters

The Great Oxidation Event (GOE) was a rapid accumulation of oxygen in the atmosphere as a result of the photosynthetic activity of cyanobacteria. This accumulation reflected the pervasiveness of O₂ on the planet's surface, indicating that cyanobacteria had become ecologically successful in Archean oceans. Micromolar concentrations of Fe²⁺ in Archean oceans would have reacted with hydrogen peroxide, a byproduct of oxygenic photosynthesis, to produce hydroxyl radicals, which cause cellular damage. Yet, cyanobacteria colonized Archean oceans extensively enough to oxygenate the atmosphere, which likely required protection mechanisms against the negative impacts of hydroxyl radical production in Fe²⁺ -rich seas. We identify several factors that could have acted to protect early cyanobacteria from the impacts of hydroxyl radical production and hypothesize that microbial cooperation may have played an important role in protecting cyanobacteria from Fe²⁺ toxicity before the GOE. We found that several strains of facultative anaerobic heterotrophic bacteria (Shewanella) with ROS defence mechanisms increase the fitness of cyanobacteria (Synechococcus) in ferruginous waters. Shewanella species with manganese transporters provided the most protection. Our results suggest that a tightly regulated response to prevent Fe²⁺ toxicity could have been important for the colonization of ancient ferruginous oceans, particularly in the presence of high manganese concentrations and may expand the upper bound for tolerable Fe²⁺ concentrations for cyanobacteria.

Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes

Despite intense research on genome architecture since the 2000s, genome-size evolution in prokaryotes has remained puzzling. Using a phylogenetic approach, a new study found that increased mutation rate is associated with gene loss and reduced genome size in prokaryotes.

Distribution and functional analysis of the two types of 8-vinyl reductase involved in chlorophyll biosynthesis in marine cyanobacteria

In the chlorophyll biosynthesis pathway, the 8-vinyl group of the chlorophyll precursor is reduced to an ethyl group by 8-vinyl reductase. Two isozymes of 8-vinyl reductase have been described in oxygenic photosynthetic organisms: one encoded by BciA and another by BciB. Only BciB contains an [Fe-S] cluster and most cyanobacteria harbor this form; whereas a few contain BciA. Given this disparity in distribution, cyanobacterial BciA has remained largely overlooked, which has limited understanding of chlorophyll biosynthesis in these microorganisms. Here, we reveal that cyanobacterial BciA encodes a functional 8-vinyl reductase, as evidenced by measuring the in vitro activity of recombinant Synechococcus and Acaryochloris BciA. Genomic comparison revealed that BciB had been replaced by BciA during evolution of the marine cyanobacterium Synechococcus, and coincided with replacement of Fe-superoxide dismutase (SOD) with Ni-SOD. These findings imply that the acquisition of BciA confers an adaptive advantage to cyanobacteria living in low-iron oceanic environments.

Metagenomic analysis reveals global-scale patterns of ocean nutrient limitation

Nutrient supply regulates the activity of phytoplankton, but the global biogeography of nutrient limitation and co-limitation is poorly understood. Prochlorococcus adapt to local environments by gene gains and losses, and we used genomic changes as an indicator of adaptation to nutrient stress. We collected metagenomes from all major ocean regions as part of the Global Ocean Ship-based Hydrographic Investigations Program (Bio-GO-SHIP) and quantified shifts in genes involved in nitrogen, phosphorus, and iron assimilation. We found regional transitions in stress type and severity as well as widespread co-stress. Prochlorococcus stress genes, bottle experiments, and Earth system model predictions were correlated. We propose that the biogeography of multinutrient stress is stoichiometrically linked by controls on nitrogen fixation. Our omics-based description of phytoplankton resource use provides a nuanced and highly resolved description of nutrient stress in the global ocean.

Eco-evolutionary feedbacks mediated by bacterial membrane vesicles

Bacterial membrane vesicles (BMVs) are spherical extracellular organelles whose cargo is enclosed by a biological membrane. The cargo can be delivered to distant parts of a given habitat in a protected and concentrated manner. This review presents current knowledge about BMVs in the context of bacterial eco-evolutionary dynamics among different environments and hosts. BMVs may play an important role in establishing and stabilizing bacterial communities in such environments; for example, bacterial populations may benefit from BMVs to delay the negative effect of certain evolutionary trade-offs that can result in deleterious phenotypes. BMVs can also perform ecosystem engineering by serving as detergents, mediators in biochemical cycles, components of different biofilms, substrates for cross-feeding, defense systems against different dangers and enzyme-delivery mechanisms that can change substrate availability. BMVs further contribute to bacteria as mediators in different interactions, with either other bacterial species or their hosts. In short, BMVs extend and deliver phenotypic traits that can have ecological and evolutionary value to both their producers and the ecosystem as a whole.

The cyanobacterium Prochlorococcus has divergent light-harvesting antennae and may have evolved in a low-oxygen ocean

The marine unicellular cyanobacterium Prochlorococcus is the most abundant photosynthetic organism on Earth. Members of this genus are classically thought to be adapted to high-oxygen and nutrient-poor ocean conditions, with a principle divergence between high-light and low-light ecotypes. We show that the most basal Prochlorococcus lineages are adapted to the low-oxygen, low-light, and high-nutrient conditions found in the dimly illuminated waters of anoxic marine zones. The most basal lineages have retained phycobilisomes as light-harvesting antennae—a characteristic of most other cyanobacteria—whose loss was thought to define all Prochlorococcus. As oxygenic photosynthesis drove ocean oxidation in the ancient Earth, oxygen appears to have played as much a role as light and nutrients in driving Prochlorococcus evolution.

Marine picocyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic organisms in the modern ocean, where they exert a profound influence on elemental cycling and energy flow. The use of transmembrane chlorophyll complexes instead of phycobilisomes as light-harvesting antennae is considered a defining attribute of Prochlorococcus. Its ecology and evolution are understood in terms of light, temperature, and nutrients. Here, we report single-cell genomic information on previously uncharacterized phylogenetic lineages of this genus from nutrient-rich anoxic waters of the eastern tropical North and South Pacific Ocean. The most basal lineages exhibit optical and genotypic properties of phycobilisome-containing cyanobacteria, indicating that the characteristic light-harvesting antenna of the group is not an ancestral attribute. Additionally, we found that all the indigenous lineages analyzed encode genes for pigment biosynthesis under oxygen-limited conditions, a trait shared with other freshwater and coastal marine cyanobacteria. Our findings thus suggest that Prochlorococcus diverged from other cyanobacteria under low-oxygen conditions before transitioning from phycobilisomes to transmembrane chlorophyll complexes and may have contributed to the oxidation of the ancient ocean.

Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii (“Iraqibacter”) was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment.

IMPORTANCE This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples. Our results indicate that there exists a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, their genomes only available thanks to single-cell genomics or single-molecule sequencing, demonstrating the importance of these methods for viral discovery. The spatiotemporal pattern of these abundant uncultivated viruses is more variable than that of cultured viruses. Despite strong environmental gradients, season and location had surprisingly little impact on the viral community within an estuary, but we saw a significant distinction between the two estuaries and also between estuarine and open ocean viromes.

Evolution of Ycf54-independent chlorophyll biosynthesis in cyanobacteria

Chlorophylls (Chls) are essential cofactors for photosynthesis. One of the least understood steps of Chl biosynthesis is formation of the fifth (E) ring, where the red substrate, magnesium protoporphyrin IX monomethyl ester, is converted to the green product, 3,8-divinyl protochlorophyllide a In oxygenic phototrophs, this reaction is catalyzed by an oxygen-dependent cyclase, consisting of a catalytic subunit (AcsF/CycI) and an auxiliary protein, Ycf54. Deletion of Ycf54 impairs cyclase activity and results in severe Chl deficiency, but its exact role is not clear. Here, we used a Δycf54 mutant of the model cyanobacterium Synechocystis sp. PCC 6803 to generate suppressor mutations that restore normal levels of Chl. Sequencing Δycf54 revertants identified a single D219G amino acid substitution in CycI and frameshifts in slr1916, which encodes a putative esterase. Introduction of these mutations to the original Δycf54 mutant validated the suppressor effect, especially in combination. However, comprehensive analysis of the Δycf54 suppressor strains revealed that the D219G-substituted CycI is only partially active and its accumulation is misregulated, suggesting that Ycf54 controls both the level and activity of CycI. We also show that Slr1916 has Chl dephytylase activity in vitro and its inactivation up-regulates the entire Chl biosynthetic pathway, resulting in improved cyclase activity. Finally, large-scale bioinformatic analysis indicates that our laboratory evolution of Ycf54-independent CycI mimics natural evolution of AcsF in low-light-adapted ecotypes of the oceanic cyanobacteria Prochlorococcus, which lack Ycf54, providing insight into the evolutionary history of the cyclase enzyme.

Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus

Microbial life in the oceans impacts the entire marine ecosystem, global biogeochemistry and climate. The marine cyanobacterium Prochlorococcus, an abundant component of this ecosystem, releases a significant fraction of the carbon fixed through photosynthesis, but the amount, timing and molecular composition of released carbon are still poorly understood. These depend on several factors, including nutrient availability, light intensity and glycogen storage. Here we combine multiple computational approaches to provide insight into carbon storage and exudation in Prochlorococcus. First, with the aid of a new algorithm for recursive filling of metabolic gaps (ReFill), and through substantial manual curation, we extended an existing genome-scale metabolic model of Prochlorococcus MED4. In this revised model (iSO595), we decoupled glycogen biosynthesis/degradation from growth, thus enabling dynamic allocation of carbon storage. In contrast to standard implementations of flux balance modeling, we made use of forced influx of carbon and light into the cell, to recapitulate overflow metabolism due to the decoupling of photosynthesis and carbon fixation from growth during nutrient limitation. By using random sampling in the ensuing flux space, we found that storage of glycogen or exudation of organic acids are favored when the growth is nitrogen limited, while exudation of amino acids becomes more likely when phosphate is the limiting resource. We next used COMETS to simulate day-night cycles and found that the model displays dynamic glycogen allocation and exudation of organic acids. The switch from photosynthesis and glycogen storage to glycogen depletion is associated with a redistribution of fluxes from the Entner–Doudoroff to the Pentose Phosphate pathway. Finally, we show that specific gene knockouts in iSO595 exhibit dynamic anomalies compatible with experimental observations, further demonstrating the value of this model as a tool to probe the metabolic dynamic of Prochlorococcus.

Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands

Physicochemical variables limit and control the distribution of microbial communities in all environments. In the oceans, this may significantly influence functional processes such the consumption of dissolved organic material and nutrient sequestration. Yet, the relative contributions of physical factors, such as water mass variability and depth, on functional processes are underexplored. We assessed microbial community structure and functionality in the Prince Edward Islands (PEIs) using 16S rRNA gene amplicon analysis and extracellular enzymatic activity assays, respectively. We found that depth and nutrients substantially drive the structural patterns of bacteria and archaea in this region. Shifts from epipelagic to bathypelagic zones were linked to decreases in the activities of several extracellular enzymes. These extracellular enzymatic activities were positively correlated with several phyla including several Alphaproteobacteria (including members of the SAR 11 clade and order Rhodospirillales) and Cyanobacteria. We show that depth-dependent variables may be essential drivers of community structure and functionality in the PEIs.

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.

Viral Lysis Alters the Optical Properties and Biological Availability of Dissolved Organic Matter Derived from Prochlorococcus Picocyanobacteria

Phytoplankton contribute almost half of the world's total primary production. The exudates and viral lysates of phytoplankton are two important forms of dissolved organic matter (DOM) in aquatic environments and fuel heterotrophic prokaryotic metabolism. However, the effect of viral infection on the composition and biological availability of phytoplankton-released DOM is poorly understood. Here, we investigated the optical characteristics and microbial utilization of the exudates and viral lysates of the ecologically important unicellular picophytoplankton Prochlorococcus Our results showed that Prochlorococcus DOM produced by viral lysis (Pro-vDOM) with phages of three different morphotypes (myovirus P-HM2, siphovirus P-HS2, and podovirus P-SSP7) had higher humic-like fluorescence intensities, lower absorption coefficients, and higher spectral slopes than DOM exuded by Prochlorococcus (Pro-exudate). The results indicate that viral infection altered the composition of Prochlorococcus-derived DOM and might contribute to the pool of oceanic humic-like DOM. Incubation with Pro-vDOM resulted in a greater dissolved organic carbon (DOC) degradation rate and lower absorption spectral slope and heterotrophic bacterial growth rate than incubation with Pro-exudate, suggesting that Pro-vDOM was more bioavailable than Pro-exudate. In addition, the stimulated microbial community succession trajectories were significantly different between the Pro-exudate and Pro-vDOM treatments, indicating that viral lysates play an important role in shaping the heterotrophic bacterial community. Our study demonstrated that viral lysis altered the chemical composition and biological availability of DOM derived from Prochlorococcus, which is the numerically dominant phytoplankton in the oligotrophic ocean.IMPORTANCE The unicellular picocyanobacterium Prochlorococcus is the numerically dominant phytoplankton in the oligotrophic ocean, contributing to the vast majority of marine primary production. Prochlorococcus releases a significant fraction of fixed organic matter into the surrounding environment and supports a vital portion of heterotrophic bacterial activity. Viral lysis is an important biomass loss process of Prochlorococcus However, little is known about whether and how viral lysis affects Prochlorococcus-released dissolved organic matter (DOM). Our paper shows that viral infection alters the optical properties (such as the absorption coefficients, spectral slopes, and fluorescence intensities) of released DOM and might contribute to a humic-like DOM pool and carbon sequestration in the ocean. Meanwhile, viral lysis also releases various intracellular labile DOM, including amino acids, protein-like DOM, and lower-molecular-weight DOM, increases the bioavailability of DOM, and shapes the successive trajectory of the heterotrophic bacterial community. Our study highlights the importance of viruses in impacting the DOM quality in the ocean.

Function and Benefits of Natural Competence in Cyanobacteria: From Ecology to Targeted Manipulation

Natural competence is the ability of a cell to actively take up and incorporate foreign DNA in its own genome. This trait is widespread and ecologically significant within the prokaryotic kingdom. Here we look at natural competence in cyanobacteria, a group of globally distributed oxygenic photosynthetic bacteria. Many cyanobacterial species appear to have the genetic potential to be naturally competent, however, this ability has only been demonstrated in a few species. Reasons for this might be due to a high variety of largely uncharacterised competence inducers and a lack of understanding the ecological context of natural competence in cyanobacteria. To shed light on these questions, we describe what is known about the molecular mechanisms of natural competence in cyanobacteria and analyse how widespread this trait might be based on available genomic datasets. Potential regulators of natural competence and what benefits or drawbacks may derive from taking up foreign DNA are discussed. Overall, many unknowns about natural competence in cyanobacteria remain to be unravelled. A better understanding of underlying mechanisms and how to manipulate these, can aid the implementation of cyanobacteria as sustainable production chassis.