Diversity and Distribution of Marine Synechococcus: Multiple Gene Phylogenies for Consensus Classification and Development of qPCR Assays for Sensitive Measurement of Clades in the Ocean

Temporal and Spatial Dynamics of Synechococcus Clade II and Other Microbes in the Eutrophic Subtropical San Diego Bay

The diversity of the marine cyanobacterium Synechococcus can be broadly separated into clades, with clade II typically present in warm oligotrophic water, and clades I and IV found in cooler coastal water. We found amplicon sequence variants (ASVs) belonging to clade II in the nutrient-replete waters of San Diego Bay (SDB). Using the 16S rRNA gene, 18S rRNA gene and internal transcribed spacer region sequencing, we analysed multiple locations in SDB monthly for over a year, with additional samples dating back to 2015. Synechococcus community composition differed from the nearby coast into SDB in terms of dominant clade and ASVs. Specific clade II ASVs became relatively more abundant towards the back of the bay and showed seasonality, with higher relative abundance in the warm months. Select ASVs group phylogenetically and show similar seasonal and spatial distribution patterns, indicating these ASVs have adapted to SDB. Isolates matching clade II ASVs from SDB show pigment composition that is better adapted to the green light available in SDB, further supporting our findings. Other microbial taxa also show SDB enrichment, providing evidence that SDB is a chemostat-like environment where circulation, temperature, light and other environmental conditions create a zone for microbial evolution and diversification.

Adaptive loss of tRNA gene expression leads to phage resistance in a marine Synechococcus cyanobacterium

Synechococcus is a significant primary producer in the oceans, coexisting with cyanophages, which are important agents of mortality. Bacterial resistance against phage infection is a topic of significant interest, yet little is known for ecologically relevant systems. Here we use exogenous gene expression and gene disruption to investigate mechanisms underlying intracellular resistance of marine Synechococcus WH5701 to the Syn9 cyanophage. The restriction-modification and Gabija defence systems possessed by Synechococcus WH5701 did not contribute to resistance. Instead, resistance was primarily driven by insufficient levels of LeuTAA tRNA, preventing translation of key phage genes in a passive, intracellular mode of resistance. Restoring cellular tRNA expression rendered the cyanobacterium sensitive to infection. We propose an evolutionary scenario whereby changes in cell codon usage, acquisition of tRNAs by the phage and loss of cell and phage tRNA expression resulted in an effective means of resistance, highlighting the dynamic interplay between bacteria and phages in shaping their co-evolutionary trajectories.

The rDNA Diversity, Interseasonal Dynamic, and Functional Role of Cyanobacteria Synechococcus in the Sub-Arctic White Sea

Planktonic unicellular cyanobacteria are the dominant biomass producers and carbon fixers in the global ocean ecosystem, but they are not abundant in polar seawater. The interseasonal dynamics of picocyanobacterial (PC) abundance, picophytoplankton primary production, and phylogenetic diversity of PC Synechococcus were studied in the sub-Arctic White Sea. The PC abundance varied from 0.2-0.3 × 106 cells/L in February to 5.2-16.7 × 106 cells/L in July. Picophytoplankton primary production ranged from 0.22 mg C/m3 per day in winter to 11.32 mg C/m3 per day in summer. Synechococcus abundance positively correlated with water temperature and river discharge that increased in recent years in the White Sea. Phylogenetic analysis of the 16S rRNA gene and ITS region clone libraries from the White Sea and Barents Sea eDNA revealed picocyanobacterial sequences related to marine Synechococcus subclusters 5.1-I, 5.I-IV, 5.2, and 5.3. All Synechococcus S5.1-I were common in the White and Barents seas and were consistently present in the picophytoplankton composition throughout the year. Synechococcus S5.2 and S5.3 appear in the PC community in summer, suggesting their river origin, and Synechococcus S5.1-IV inhabits only the Barents Sea and was not detected in the White Sea. A unique Synechococcus phylotype was revealed. It is expected that the increase in the abundance of PC and their increasing role in ecosystem functioning, as well as the enrichment of the species composition with new phylotypes in the semi-enclosed sub-Arctic White Sea, which is vulnerable to the effects of climate change, will be characteristic of all Arctic seas in general.

Ploidy levels in diverse picocyanobacteria from the Baltic Sea

In nature, the number of genome or chromosome copies within cells (ploidy) can vary between species and environmental conditions, potentially influencing how organisms adapt to changing environments. Although ploidy levels cannot be easily determined by standard genome sequencing, understanding ploidy is crucial for the quantitative interpretation of molecular data. Cyanobacteria are known to contain haploid, oligoploid, and polyploid species. The smallest cyanobacteria, picocyanobacteria (less than 2 μm in diameter), have a widespread distribution ranging from marine to freshwater environments, contributing significantly to global primary production. In this study, we determined the ploidy level of genetically and physiologically diverse brackish picocyanobacteria isolated from the Baltic Sea using a qPCR assay targeting the rbcL gene. The strains contained one to four genome copies per cell. The ploidy level was not linked with phylogeny based on the identity of the 16S rRNA gene. The variation of ploidy among the brackish strains was lower compared to what has been reported for freshwater strains and was more similar to what has been reported for marine strains. The potential ecological advantage of polyploidy among picocyanobacteria has yet to be described. Our study highlights the importance of considering ploidy to interpret the abundance and adaptation of brackish picocyanobacteria.

Production and utilization of pseudocobalamin in marine Synechococcus cultures and communities

Cobalamin influences marine microbial communities because an exogenous source is required by most eukaryotic phytoplankton, and demand can exceed supply. Pseudocobalamin is a cobalamin analogue produced and used by most cyanobacteria but is not directly available to eukaryotic phytoplankton. Some microbes can remodel pseudocobalamin into cobalamin, but a scarcity of pseudocobalamin measurements impedes our ability to evaluate its importance for marine cobalamin production. Here, we perform simultaneous measurements of pseudocobalamin and methionine synthase (MetH), the key protein that uses it as a co-factor, in Synechococcus cultures and communities. In Synechococcus sp. WH8102, pseudocobalamin quota decreases in low temperature (17°C) and low nitrogen to phosphorus ratio, while MetH did not. Pseudocobalamin and MetH quotas were influenced by culture methods and growth phase. Despite the variability present in cultures, we found a comparably consistent quota of 300 ± 100 pseudocobalamin molecules per cyanobacterial cell in the Northwest Atlantic Ocean, suggesting that cyanobacterial cell counts may be sufficient to estimate pseudocobalamin inventories in this region. This work offers insights into cellular pseudocobalamin metabolism, environmental and physiological conditions that may influence it, and provides environmental measurements to further our understanding of when and how pseudocobalamin can influence marine microbial communities.

Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates

The diversity of marine cyanobacteria has been extensively studied due to their vital roles in ocean primary production. However, little is understood about the diversity of cyanobacterial species involved in symbiotic relationships. In this study, we successfully sequenced the complete genome of a cyanobacterium in symbiosis with Citharistes regius, a dinoflagellate species thriving in the open ocean. A phylogenomic analysis revealed that the cyanobacterium (CregCyn) belongs to the marine picocyanobacterial lineage, akin to another cyanobacterial symbiont (OmCyn) of a different dinoflagellate closely related to Citharistes. Nevertheless, these two symbionts are representing distinct lineages, suggesting independent origins of their symbiotic lifestyles. Despite the distinct origins, the genome analyses of CregCyn revealed shared characteristics with OmCyn, including an obligate symbiotic relationship with the host dinoflagellates and a degree of genome reduction. In contrast, a detailed analysis of genome subregions unveiled that the CregCyn genome carries genomic islands that are not found in the OmCyn genome. The presence of the genomic islands implies that exogenous genes have been integrated into the CregCyn genome at some point in its evolution. This study contributes to our understanding of the complex history of the symbiosis between dinoflagellates and cyanobacteria, as well as the genomic diversity of marine picocyanobacteria.

Intraspecific trait variation modulates the temperature effect on elemental quotas and stoichiometry in marine Synechococcus

Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions, and we demonstrate contains extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in serially transferred cultures across a range of temperatures (16-25°C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We report differences in cell size (p<0.01) as a function of strain and clade (p<0.01). The carbon (QC), nitrogen (QN), and phosphorus (QP) cell quotas all increased with cell size. Furthermore, cell size has an inverse relationship to growth rate. Within our experimental design, temperature alone had a weak physiological effect on cell quota and elemental ratios. Instead, we find systemic intraspecific variance of C:N:P, with cell size and N:P having an inverse relationship. Our results suggest a key role for intraspecific life history traits in determining elemental quotas and stoichiometry. Thus, the extensive biodiversity harbored within many lineages may modulate the impact of environmental change on ocean biogeochemical cycles.

Proteomics analysis reveals differential acclimation of coastal and oceanic Synechococcus to climate warming and iron limitation

In many oceanic regions, anthropogenic warming will coincide with iron (Fe) limitation. Interactive effects between warming and Fe limitation on phytoplankton physiology and biochemical function are likely, as temperature and Fe availability affect many of the same essential cellular pathways. However, we lack a clear understanding of how globally significant phytoplankton such as the picocyanobacteria Synechococcus will respond to these co-occurring stressors, and what underlying molecular mechanisms will drive this response. Moreover, ecotype-specific adaptations can lead to nuanced differences in responses between strains. In this study, Synechococcus isolates YX04-1 (oceanic) and XM-24 (coastal) from the South China Sea were acclimated to Fe limitation at two temperatures, and their physiological and proteomic responses were compared. Both strains exhibited reduced growth due to warming and Fe limitation. However, coastal XM-24 maintained relatively higher growth rates in response to warming under replete Fe, while its growth was notably more compromised under Fe limitation at both temperatures compared with YX04-1. In response to concurrent heat and Fe stress, oceanic YX04-1 was better able to adjust its photosynthetic proteins and minimize the generation of reactive oxygen species while reducing proteome Fe demand. Its intricate proteomic response likely enabled oceanic YX04-1 to mitigate some of the negative impact of warming on its growth during Fe limitation. Our study highlights how ecologically-shaped adaptations in Synechococcus strains even from proximate oceanic regions can lead to differing physiological and proteomic responses to these climate stressors.

Molecular insights into nitrogen constraint for niche partitioning and physiological adaptation of coastal Synechococcus assemblages

Coastal nitrogen input has substantially increased due to human activity. However, much remains unknown about the nitrogen-driven patterns and the underlying genetic basis of coastal picoplankton. To investigate the response and mechanisms of picoplankton induced by nitrogen variation, we conducted in-situ investigations using high-throughput sequencing in the Bohai Sea and performed laboratory nitrogen simulation experiments accompanied by physiological, genomic, and transcriptomic analyses, with Synechococcus as a representative. The results of in-situ investigation revealed that Synechococcus clades I, III, WPC1, and VI of subcluster 5.1 (S5.1) are prevalent in strait areas characterized by robust water exchange with the North Yellow Sea, while clades II, VIII, and IX of S5.1, as well as subcluster 5.2 (S5.2) and subcluster 5.3 (S5.3) are more abundant in central and bay areas experiencing elevated nitrate and nitrite loads. The laboratory experiments further confirmed that inorganic nitrogen is a crucial determinant of diversity and niche partitioning of Synechococcus lineages. Besides, the raising inorganic nitrogen concentration within the current in-situ range (0.1-10 μmol L-1) enhances photosynthesis and carbon fixation of Synechococcus, however further escalation of inorganic nitrogen (100 μmol L-1) may hinder these processes instead. The phenomenon could be associated with the differential expression of genes in metabolic pathways regulating nitrogen metabolism, photosynthetic system II, and photosynthesis-antenna proteins in response to nitrogen concentration and type variation. These findings expand our understanding of the impact of macronutrient variation resulting from human activities on marine picoplankton and biogeochemical cycles.

Genomic insights into the adaptation of Synechococcus to the coastal environment on Xiamen

Synechococcus are widely distributed in the global ocean, from the pelagic zone to coastal waters. However, little is known about Synechococcus in coastal seawater due to limitations in isolation and culture conditions. In this study, a combination of metagenomic sequencing technology, flow cytometry sorting, and multiple displacement amplification was used to investigate Synechococcus in the coastal seawater of Xiamen Island. The results revealed 18 clades of Synechococcus and diverse metabolic genes that appear to contribute to their adaptation to the coastal environment. Intriguingly, some metabolic genes related to the metabolism of carbohydrates, energy, nucleotides, and amino acids were found in 89 prophage regions that were detected in 16,258 Synechococcus sequences. The detected metabolic genes can enable prophages to contribute to the adaptation of Synechococcus hosts to the coastal marine environment. The detection of prophages also suggests that the cyanophages have infected Synechococcus. On the other hand, the identification of 773 genes associated with antiviral defense systems indicates that Synechococcus in Xiamen have evolved genetic traits in response to cyanophage infection. Studying the community diversity and functional genes of Synechococcus provides insights into their role in environmental adaptation and marine ecosystems.

The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients

The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients-which have low temperature variation (27-29°C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 ± 4.4 × 104  cells ml-1 , predominantly HLII, whereas LLII and 'rare' ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 ± 2.3 × 104  cells ml-1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea-influenced high salinity (southerly; prasinophytes) to freshwater-influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 × 104  cells ml-1 , surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto 'rare' picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.

Synechococcus nitrogen gene loss in iron-limited ocean regions

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

Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria

Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcB and cpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10-30°C), light (10-190 μmol photons m-2  s-1 ), and salinity (2-14 PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.

Cobalamin producers and prokaryotic consumers in the Northwest Atlantic

Cobalamin availability can influence primary productivity and ecological interactions in marine microbial communities. The characterization of cobalamin sources and sinks is a first step in investigating cobalamin dynamics and its impact on productivity. Here, we identify potential cobalamin sources and sinks on the Scotian Shelf and Slope in the Northwest Atlantic Ocean. Functional and taxonomic annotation of bulk metagenomic reads, combined with analysis of genome bins, were used to identify potential cobalamin sources and sinks. Cobalamin synthesis potential was mainly attributed to Rhodobacteraceae, Thaumarchaeota, and cyanobacteria (Synechococcus and Prochlorococcus). Cobalamin remodelling potential was mainly attributed to Alteromonadales, Pseudomonadales, Rhizobiales, Oceanospirilalles, Rhodobacteraceae, and Verrucomicrobia, while potential cobalamin consumers include Flavobacteriaceae, Actinobacteria, Porticoccaceae, Methylophiliaceae, and Thermoplasmatota. These complementary approaches identified taxa with the potential to be involved in cobalamin cycling on the Scotian Shelf and revealed genomic information required for further characterization. The Cob operon of Rhodobacterales bacterium HTCC2255, a strain with known importance in cobalamin cycling, was similar to a major cobalamin producer bin, suggesting that a related strain may represent a critical cobalamin source in this region. These results enable future inquiries that will enhance our understanding of how cobalamin shapes microbial interdependencies and productivity in this region.

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change.

Genomic and Transcriptomic Insights into Salinity Tolerance-Based Niche Differentiation of Synechococcus Clades in Estuarine and Coastal Waters

Cluster 5 Synechococcus is one of the most important primary producers on earth. However, ecotypes of this genus exhibit complex geographical distributions, and the genetic basis of niche partitioning is still not fully understood. Here, we report distinct distributions of subcluster 5.1 (SC5.1) and subcluster 5.2 (SC5.2) Synechococcus in estuarine waters, and we reveal that salinity is the main factor determining their distribution. Clade III (belonging to SC5.1) and CB4 (belonging to SC5.2) are dominant clades in the study region, with different ecological distributions. We further conducted physiological, genomic, and transcriptomic studies of Synechococcus strains YX04-3 and HK05, which are affiliated with clade III and CB4, respectively. Laboratory tests showed that HK05 could grow at low salinity (13 ppt), whereas the growth of YX04-3 was suppressed when salinity decreased to 13 ppt. Genomic and transcriptomic analysis suggested that euryhaline clade CB4 is capable of dealing with a sudden drop of salinity by releasing compatible solutes through mechanosensitive channels that are coded by the mscL gene, decreasing biosynthesis of organic osmolytes, and increasing expression of heat shock proteins and high light-inducible proteins to protect photosystem. Furthermore, CB4 strain HK05 exhibited a higher growth rate when growing at low salinity than at high salinity. This is likely achieved by reducing its biosynthesis of organic osmolyte activity and increasing its photosynthetic activity at low salinity, which allowed it to enhance the assimilation of inorganic carbon and nitrogen. Together, these results provide new insights regarding the ecological distribution of SC5.2 and SC5.1 ecotypes and their underlying molecular mechanisms. IMPORTANCE Synechococcus is a group of unicellular Cyanobacteria that are widely distributed in global aquatic ecosystems. Salinity is a factor that affects the distribution of microorganisms in estuarine and coastal environments. In this study, we studied the distribution pattern of Synechococcus community along the salinity gradient in a subtropical estuary. By using omic methods, we unveiled genetic traits that determine the niche partitioning of euryhaline and strictly marine Synechococcus. We also explored the strategies employed by euryhaline Synechococcus to cope with a sudden drop of salinity, and revealed possible mechanisms for the higher growth rate of euryhaline Synechococcus in low salinity conditions. This study provides new insight into the genetic basis of niche partitioning of Synechococcus clades.

Spatio-temporal patterns of Synechococcus oligotypes in Moroccan lagoonal environments

Synechococcus are unicellular cyanobacteria susceptible to environmental fluctuations and can be used as bioindicators of eutrophication in marine ecosystems. We examined their distribution in two Moroccan lagoons, Marchica on the Mediterranean coast and Oualidia on the Atlantic, in the summers of 2014 and 2015 using 16S rRNA amplicon oligotyping. Synechococcus representatives recruited a higher number of reads from the 16S rRNA in Marchica in comparison to Oualidia. We identified 31 Synechococcus oligotypes that clustered into 10 clades with different distribution patterns. The Synechococcus community was mainly represented by oligotype 1 (clade III) in Marchica. Cooccurring clades IV and I had an important relative abundance in Marchica in the summer of 2014, which is unusual, as these clades are widespread in cold waters. Moreover, Clades VII and subcluster "5.3" formed a sizeable percentage of the Synechococcus community in Marchica. Notably, we found low Synechococcus sequence counts in the Atlantic Lagoon. These results showed that the relative abundance of Synechococcus reads is not constant over space and time and that rare members of the Synechococcus community did not follow a consistent pattern. Further studies are required to decipher Synechococcus dynamics and the impact of environmental parameters on their spatial and temporal distributions.

Quantification of Marine Picocyanobacteria on Water Column Particles and in Sediments Using Real-Time PCR Reveals Their Role in Carbon Export

Picocyanobacteria are the most abundant primary producers in the ocean and play a fundamental role in marine carbon cycling. Quantification of picocyanobacteria on sinking particles and in sediments is essential to understanding their contribution to the biological carbon pump. We designed a primer set targeting the 16S-23S rRNA internal transcribed spacer (ITS) sequence of cyanobacteria and established a quantitative PCR (qPCR) method for quantifying the ITS sequence abundance. High-throughput sequencing confirmed that this primer set can cover broad diversities of marine picocyanobacteria and avoid amplification of other marine cyanobacteria such as Trichodesmium and Crocosphaera. Amplification efficiencies were slightly different when seven marine Synechococcus and Prochlorococcus strains were assayed. The qPCR results were comparable with flow cytometry for water samples. Using this method, we found that, in the dark ocean, picocyanobacterial ITS sequence abundances were 10 to 100 copies/mL in the size fraction of 0.2 to 3 μm, which were 1 to 3 orders of magnitude more abundant than on the >3-μm particles. We also found that picocyanobacterial ITS abundance in sediment ranged from 10⁵ to 10⁷ copies/g along two nearshore-to-offshore transects in the northern South China Sea. These results further explain the important role of picocyanobacteria in carbon export. Collectively, we provide a qPCR method quantifying the total abundance of marine picocyanobacteria on water column particles and in sediments. Moreover, this newly designed primer set can be also applied to investigate the community of picocyanobacteria via high-throughput sequencing. IMPORTANCE Picocyanobacteria are the most abundant primary producers in the ocean. However, quantification of picocyanobacteria on the sinking particles and in sediments remains challenging using flow cytometry or epifluorescence microscopy. Here, we developed a real-time PCR method to quantify picocyanobacteria using a newly designed primer set specifically targeting the 16S-23S rRNA ITS sequence of cyanobacteria. We showed that in the dark ocean, picocyanobacteria are 1 to 3 orders of magnitude more abundant in small particles (0.2 to 3 μm) than in larger particles (>3 μm). This result supports the important role of direct sinking free-living picocyanobacteria cells in the carbon export to deep ocean. We also found that the picocyanobacterial ITS sequence abundance were 10⁵ to 10⁷ copies per gram in sediments, suggesting significant accumulation of sinking picocyanobacteria in the benthic ecosystem. This qPCR method can be used to quantify the contribution of picocyanobacteria to the biological carbon pump.

Population structure of an Antarctic aquatic cyanobacterium

BACKGROUND

Ace Lake is a marine-derived, stratified lake in the Vestfold Hills of East Antarctica with an upper oxic and lower anoxic zone. Cyanobacteria are known to reside throughout the water column. A Synechococcus-like species becomes the most abundant member in the upper sunlit waters during summer while persisting annually even in the absence of sunlight and at depth in the anoxic zone. Here, we analysed ~ 300 Gb of Ace Lake metagenome data including 59 Synechococcus-like metagenome-assembled genomes (MAGs) to determine depth-related variation in cyanobacterial population structure. Metagenome data were also analysed to investigate viruses associated with this cyanobacterium and the host's capacity to defend against or evade viruses.

RESULTS

A single Synechococcus-like species was found to exist in Ace Lake, Candidatus Regnicoccus frigidus sp. nov., consisting of one phylotype more abundant in the oxic zone and a second phylotype prevalent in the oxic-anoxic interface and surrounding depths. An important aspect of genomic variation pertained to nitrogen utilisation, with the capacity to perform cyanide assimilation and asparagine synthesis reflecting the depth distribution of available sources of nitrogen. Both specialist (host specific) and generalist (broad host range) viruses were identified with a predicted ability to infect Ca. Regnicoccus frigidus. Host-virus interactions were characterised by a depth-dependent distribution of virus type (e.g. highest abundance of specialist viruses in the oxic zone) and host phylotype capacity to defend against (e.g. restriction-modification, retron and BREX systems) and evade viruses (cell surface proteins and cell wall biosynthesis and modification enzymes).

CONCLUSION

In Ace Lake, specific environmental factors such as the seasonal availability of sunlight affects microbial abundances and the associated processes that the microbial community performs. Here, we find that the population structure for Ca. Regnicoccus frigidus has evolved differently to the other dominant phototroph in the lake, Candidatus Chlorobium antarcticum. The geography (i.e. Antarctica), limnology (e.g. stratification) and abiotic (e.g. sunlight) and biotic (e.g. microbial interactions) factors determine the types of niches that develop in the lake. While the lake community has become increasingly well studied, metagenome-based studies are revealing that niche adaptation can take many paths; these paths need to be determined in order to make reasonable predictions about the consequences of future ecosystem perturbations. Video Abstract.

Interactive effects of CO2 , temperature, irradiance, and nutrient limitation on the growth and physiology of the marine cyanobacterium Synechococcus (Cyanophyceae)

The marine cyanobacterium Synechococcus elongatus was grown in a continuous culture system to study the interactive effects of temperature, irradiance, nutrient limitation, and the partial pressure of CO₂ (pCO2) on its growth and physiological characteristics. Cells were grown on a 14:10 h light:dark cycle at all combinations of low and high irradiance (50 and 300 μmol photons ⋅ m^-2 ⋅ s^-1 , respectively), low and high pCO₂ (400 and 1000 ppmv, respectively), nutrient limitation (nitrate-limited and nutrient-replete conditions), and temperatures of 20-45°C in 5°C increments. The maximum growth rate was ~4.5 · d^-1 at 30-35°C. Under nutrient-replete conditions, growth rates at most temperatures and irradiances were about 8% slower at a pCO₂ of 1000 ppmv versus 400 ppmv. The single exception was 45°C and high irradiance. Under those conditions, growth rates were ~45% higher at 1000 ppmv. Cellular carbon:nitrogen ratios were independent of temperature at a fixed relative growth rate but higher at high irradiance than at low irradiance. Initial slopes of photosynthesis-irradiance curves were higher at all temperatures under nutrient-replete versus nitrate-limited conditions; they were similar at all temperatures under high and low irradiance, except at 20°C, when they were suppressed at high irradiance. A model of phytoplankton growth in which cellular carbon was allocated to structure, storage, or the light or dark reactions of photosynthesis accounted for the general patterns of cell composition and growth rate. Allocation of carbon to the light reactions of photosynthesis was consistently higher at low versus high light and under nutrient-replete versus nitrate-limited conditions.

Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea

Picocyanobacteria (< 2 µm in diameter) are significant contributors to total phytoplankton biomass. Due to the high diversity within this group, their seasonal dynamics and relationship with environmental parameters, especially in brackish waters, are largely unknown. In this study, the abundance and community composition of phycoerythrin rich picocyanobacteria (PE-SYN) and phycocyanin rich picocyanobacteria (PC-SYN) were monitored at a coastal (K-station) and at an offshore station (LMO; ~ 10 km from land) in the Baltic Sea over three years (2018–2020). Cell abundances of picocyanobacteria correlated positively to temperature and negatively to nitrate (NO₃) concentration. While PE-SYN abundance correlated to the presence of nitrogen fixers, PC-SYN abundance was linked to stratification/shallow waters. The picocyanobacterial targeted amplicon sequencing revealed an unprecedented diversity of 2169 picocyanobacterial amplicons sequence variants (ASVs). A unique assemblage of distinct picocyanobacterial clades across seasons was identified. Clade A/B dominated the picocyanobacterial community, except during summer when low NO_3, high phosphate (PO₄) concentrations and warm temperatures promoted S5.2 dominance. This study, providing multiyear data, links picocyanobacterial populations to environmental parameters. The difference in the response of the two functional groups and clades underscore the need for further high-resolution studies to understand their role in the ecosystem.

Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas

Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters.

Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak

The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3–V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 × 104 cells ml–1. This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.

Picocyanobacterial Synechococcus in marine ecosystem: Insights from genetic diversity, global distribution, and potential function

Marine Synechococcus, a main group of picocyanobacteria, has been ubiquitously observed across the global oceans. Synechococcus exhibits high phylogenetical and phenotypical diversity, and horizontal gene transfer makes its genetic evolution much more intricate. With the development of measurement technologies and analysis methods, the genomic information and niche partition of each Synechococcus lineage tend to be precisely described, but the global analysis is still lacking. Therefore, it is necessary to summarize existing studies and integrate published data to gain a comprehensive understanding of Synechococcus on genetic variation, niche division, and potential functions. In this review, the maximum likelihood trees are constructed based on existing sequence data, including both phylogenetic and pigmentary gene markers. The global distribution characteristics of abundance, lineages, and pigment types are concluded through pooled analysis of more than 700 samples obtained from approximately 50 scientific research cruises. The potential functions of Synechococcus are explored in element cycles and biological interactions. Future work on Synechococcus is suggested to focus on not only elucidating the nature of Synechococcus biodiversity but also demonstrating its interactions with the ecosystem by combining bioinformatics and macroscopic isotope-labeled environmental parameters.

Phylogenetic Structure of Synechococcus Assemblages and Its Environmental Determinants in the Bay and Strait Areas of a Continental Sea

Marine Synechococcus, a significant contributor to primary production, shows high phylogenetic diversity. However, studies on its phylogenetic composition in the Bohai Sea, the largest continental sea in China, are lacking. We sequenced rpoC1 (encodes the RNA polymerase β’ subunit protein) in samples from the Laizhou Bay (LZB) and Bohai Strait (BS) in June and November using high-throughput sequencing to reveal the phylogenetic composition of Synechococcus assemblages in the bay and strait areas of the Bohai Sea. In total, 12 lineages representing Synechococcus subclusters S5.1, S5.2, and S5.3 were identified. Spatially, clade I was obligately dominant in BS. In contrast, the Synechococcus assemblage in LZB was more diverse, with clades VI and III being highly abundant. In addition, we detected strong variation in Synechococcus structure between June and November in the Bohai Sea. Clades II, III, XX, and miyav were only detected in November. Vertically, variation in Synechococcus assemblage was not apparent among the water layers probably due to the shallow water depth with intense water mixing. Results of redundancy analysis (RDA) and random forest (RF) analysis together highlighted the key role of silicate in the Synechococcus assemblage. Our results suggested that the Bohai Sea provides various niches for different Synechococcus clades, resulting in a special phylogenetic composition of the Synechococcus assemblage, compared with that in the adjacent shelf sea and other continental seas in the world.

Highly-resolved interannual phytoplankton community dynamics of the coastal Northwest Atlantic

Microbial observatories can track phytoplankton at frequencies that resolve monthly, seasonal, and multiyear trends in environmental change from short-lived events. Using 4-years of weekly flow cytometry along with chloroplast and cyanobacterial 16S rRNA gene sequence data from a time-series station in the coastal Northwest Atlantic (Bedford Basin, Nova Scotia, Canada), we analyzed temporal observations for globally-relevant genera (e.g., Bolidomonas, Teleaulax, Minidiscus, Chaetoceros, Synechococcus, and Phaeocystis) in an oceanic region that has been recognized as a likely hotspot for phytoplankton diversity. Contemporaneous Scotian Shelf data also collected during our study established that the major phytoplankton within the Bedford Basin were important in the Scotian Shelf during spring and fall, therefore pointing to their broader significance within the coastal Northwest Atlantic (NWA). Temporal trends revealed a subset of indicator taxa along with their DNA signatures (e.g., Eutreptiella and Synechococcus), whose distribution patterns make them essential for timely detection of environmentally-driven shifts in the NWA. High-resolution sampling was key to identifying important community shifts towards smaller phytoplankton under anomalous environmental conditions, while further providing a detailed molecular view of community compositions underpinning general phytoplankton succession within the coastal NWA. Our study demonstrates the importance of accessible coastal time-series sites where high-frequency DNA sampling allows for the detection of shifting baselines in phytoplankton communities.

Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria

Synechococcus cyanobacteria are ubiquitous and abundant in the marine environment and contribute to an estimated 16% of the ocean net primary productivity. Their light-harvesting complexes, called phycobilisomes (PBS), are composed of a conserved allophycocyanin core, from which radiates six to eight rods with variable phycobiliprotein and chromophore content. This variability allows Synechococcus cells to optimally exploit the wide variety of spectral niches existing in marine ecosystems. Seven distinct pigment types or subtypes have been identified so far in this taxon based on the phycobiliprotein composition and/or the proportion of the different chromophores in PBS rods. Most genes involved in their biosynthesis and regulation are located in a dedicated genomic region called the PBS rod region. Here, we examine the variability of gene content and organization of this genomic region in a large set of sequenced isolates and natural populations of Synechococcus representative of all known pigment types. All regions start with a tRNA-PheGAA and some possess mobile elements for DNA integration and site-specific recombination, suggesting that their genomic variability relies in part on a "tycheposon"-like mechanism. Comparison of the phylogenies obtained for PBS and core genes revealed that the evolutionary history of PBS rod genes differs from the core genome and is characterized by the co-existence of different alleles and frequent allelic exchange. We propose a scenario for the evolution of the different pigment types and highlight the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in different Synechococcus lineages despite multiple speciation events.

Spatio-Temporal Variation of Synechococcus Assemblages at DNA and cDNA Levels in the Tropical Estuarine and Coastal Waters

Synechococcus is a major contributor to global marine primary production. Here, its spatio-temporal variations in abundance and phylogenetic structure were studied at three stations of the South China Sea at both DNA and cDNA levels. Synechococcus cell abundance was lowest in March, but highest in October at two coastal stations. Its abundance was higher at the estuarine station, which reached a peak value of 1.36 × 105 cells/ml in April, owing to the nitrogen nutrients discharged from the Sanya River. Gene and gene transcript abundances of four Synechococcus lineages, clades II, III, VIII, and S5.3, were studied by quantitative PCR, which showed that clade II was the most abundant lineage at both DNA and cDNA levels. High-throughput sequencing revealed that, at the DNA level, Synechococcus assemblage was dominated by clade SY4 (a novel clade defined in this study), S5.2, and clade II in the coastal waters and was dominated by freshwater/S5.2 Synechococcus, reaching a value up to 88.61% in June, in estuarine waters. Changes in salinity and nutrient concentration caused by seasonal monsoonal forcing and river discharge were the key determinants of the spatio-temporal variation in Synechococcus assemblages at the DNA level. In comparison, high dissimilation among samples at the same stations and in the same seasons leads to the imperceptible spatio-temporal variation pattern of Synechococcus assemblages at the cDNA level. Furthermore, co-occurrence networks disclosed that Synechococcus community had closer and more complex internal interactions at the cDNA level. These discrepancies highlighted the necessity to study Synechococcus assemblages at both DNA and cDNA levels.

Highly Diverse Synechococcus Pigment Types in the Eastern Indian Ocean

Marine picocyanobacteria Synechococcus exhibit highly diverse pigment types (PTs) and hence possess great advantage to utilize different spectrum of light effectively and to occupy a wide range of light niches. In this study, we explored the diversity of Synechococcus PTs in the eastern Indian Ocean (EIO), surface water of Strait of Malacca (SSM), and coastal waters of Sri Lanka (SSL). All the detected PTs were phycourobilin (PUB) containing PT 3 and showed distinct distribution patterns. Low PUB PT 3a and partial chromatic acclimater PT 3eA dominated in coastal and shallow waters (SSM and SSL). In contrast, high PUB and chromatic acclimaters PT 3dA and PT 3c/3dB were mainly distributed in open ocean (EIO). PT 3dA and PT 3c/3dB occurred at similar depths of the lower euphotic layers but showed distinct distribution pattern that are partially exclusive, indicating that they compete with each other for the same light niche. Interestingly, the newly described PT 3f was detected with high relative abundances at all stations and particularly dominated in the upper euphotic layer in EIO, which was confirmed with PT-specific quantitative polymerase chain reaction (qPCR). The relative abundance of PT 3f was negatively correlated with nutrient level, implying that PT 3f is adapted to oligotrophic waters. Pronounced niche partition of different PTs was observed in the upper and lower layers of euphotic zone in EIO and SSM/SSL. Light, nutrients, and strong stratification may play important roles in the niche partition of different PTs. Further analysis about ecologically significant taxonomic units revealed high diversity within each PT at different locations, which provided insights for understanding specific PT with wide range of niches.

Genomic and transcriptomic evidence for the diverse adaptations of Synechococcus subclusters 5.2 and 5.3 to mesoscale eddies

Mesoscale eddies are ubiquitous oceanographic features that influence the metabolism and community structure of Synechococcus. However, the metabolic adaptations of this genus to eddy-associated environmental changes have rarely been studied. We recovered two high-quality Synechococcus metagenome-assembled genomes (MAGs) from eddies in the South China Sea and compared their metabolic variations using metatranscriptomic samples obtained at the same time. The two MAGs (syn-bin1 and syn-bin2) are affiliated with marine Synechococcus subclusters 5.2 (S5.2) and 5.3 (S5.3), respectively. The former exhibited a higher abundance at the surface layer, whereas the latter was more abundant in the deep euphotic layer. Further analysis indicated that syn-bin1 had a strong ability to utilize organic nutrients, which could help it to thrive in the nutrient-deprived surface water. By contrast, syn-bin2 had the genetic potential to perform chromatic acclimation, which could allow it to capture green or blue light at different depths. Additionally, transcriptomic analysis showed that syn-bin2 upregulated genes involved in the synthesis of C4 acids, photosystem II proteins, and HCO3- transporters in the deep euphotic layer, which might contribute to its predominance in low-light environments. Overall, this study expands our understanding of oceanic S5.2 and S5.3 Synechococcus by revealing their metabolic adaptations to mesoscale eddies.

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.

Phylogenetic and Phenogenetic Diversity of Synechococcus along a Yellow Sea Section Reveal Its Environmental Dependent Distribution and Co-Occurrence Microbial Pattern

Synechococcus is a dominant genus of the coastal phytoplankton with an effective contribution to primary productivity. Here, the phylogenetic and phenogenetic composition of Synechococcus in the coastal Yellow Sea was addressed by sequencing marker gene methods. Meanwhile, its co-occurrence pattern with bacterial and eukaryotic microbes was further investigated based on the construction of networks. The result revealed that Synechococcus abundance ranged from 9.8 × 102 cells mL−1 to 1.6 × 105 cells mL−1, which was significantly correlated to sampling depth and nutrient contents of nitrite, ammonia, and dissolved silicon. A total of eight Synechococcus phylogenetic lineages were detected, of which clade III was dominant in most of the samples. Meanwhile, clade I increased along the water column and even reached a maximum value of 76.13% at 20 m of station B. Phenogenetically, Synechococcus PT3 was always the predominant pigment type across the whole study zone. Only salinity was significantly correlated to the phenogenetic constitution. The networks revealed that Synechococcus co-occurred with 159 prokaryotes, as well as 102 eukaryotes including such possible grazers as Gymnodinium clades and Alveolata. Potential function prediction further showed that microbes co-occurring with Synechococcus were associated with diverse element cycles, but the exact mechanism needed further experimentation to verify. This research promotes exploring regularity in the genomic composition and niche position of Synechococcus in the coastal ecosystem and is significant to further discuss its potential participation in materials circulation and bottom-up effects in microbial food webs.

Seasonal environmental variability drives microdiversity within a coastal Synechococcus population

Marine microbes often show a high degree of physiological or ecological diversity below the species level. This microdiversity raises questions about the processes that drive diversification and permit coexistence of diverse yet closely related marine microbes, especially given the theoretical efficiency of competitive exclusion. Here, we provide insight with an 8‐year time series of diversity within Synechococcus, a widespread and important marine picophytoplankter. The population of Synechococcus on the Northeast U.S. Shelf is comprised of six main types, each of which displays a distinct and consistent seasonal pattern. With compositional data analysis, we show that these patterns can be reproduced with a simple model that couples differential responses to temperature and light with the seasonal cycle of the physical environment. These observations support the hypothesis that temporal variability in environmental factors can maintain microdiversity in marine microbial populations. We also identify how seasonal diversity patterns directly determine overarching Synechococcus population abundance features.

Amino Acid Analog Induces Stress Response in Marine Synechococcus

Characterizing the cell-level metabolic trade-offs that phytoplankton exhibit in response to changing environmental conditions is important for predicting the impact of these changes on marine food web dynamics and biogeochemical cycling. The time-selective proteome-labeling approach, bioorthogonal noncanonical amino acid tagging (BONCAT), has potential to provide insight into differential allocation of resources at the cellular level, especially when coupled with proteomics. However, the application of this technique in marine phytoplankton remains limited. We demonstrate that the marine cyanobacteria Synechococcus sp. and two groups of eukaryotic algae take up the modified amino acid l-homopropargylglycine (HPG), suggesting that BONCAT can be used to detect translationally active phytoplankton. However, the impact of HPG addition on growth dynamics varied between groups of phytoplankton. In addition, proteomic analysis of Synechococcus cells grown with HPG revealed a physiological shift in nitrogen metabolism, general protein stress, and energy production, indicating a potential limitation for the use of BONCAT in understanding the cell-level response of Synechococcus sp. to environmental change. Variability in HPG sensitivity between algal groups and the impact of HPG on Synechococcus physiology indicates that particular considerations should be taken when applying this technique to other marine taxa or mixed marine microbial communities. IMPORTANCE Phytoplankton form the base of the marine food web and substantially impact global energy and nutrient flow. Marine picocyanobacteria of the genus Synechococcus comprise a large portion of phytoplankton biomass in the ocean and therefore are important model organisms. The technical challenges of environmental proteomics in mixed microbial communities have limited our ability to detect the cell-level adaptations of phytoplankton communities to a changing environment. The proteome labeling technique, bioorthogonal noncanonical amino acid tagging (BONCAT), has potential to address some of these challenges by simplifying proteomic analyses. This study explores the ability of marine phytoplankton to take up the modified amino acid, l-homopropargylglycine (HPG), required for BONCAT, and investigates the proteomic response of Synechococcus to HPG. We not only demonstrate that cyanobacteria can take up HPG but also highlight the physiological impact of HPG on Synechococcus, which has implications for future applications of this technique in the marine environment.

Selective Uptake of Pelagic Microbial Community Members by Caribbean Reef Corals

We identify interactions between coral grazing behavior and the growth rates and cell abundances of pelagic microbial groups found surrounding a Caribbean reef. During incubation experiments with three reef corals, reductions in microbial cell abundance differed according to coral species and suggest specific coral or microbial mechanisms are at play.

Coral reefs are possible sinks for microbes; however, the removal mechanisms at play are not well understood. Here, we characterize pelagic microbial groups at the CARMABI reef (Curaçao) and examine microbial consumption by three coral species: Madracis mirabilis, Porites astreoides, and Stephanocoenia intersepta. Flow cytometry analyses of water samples collected from a depth of 10 m identified 6 microbial groups: Prochlorococcus, three groups of Synechococcus, photosynthetic eukaryotes, and heterotrophic bacteria. Minimum growth rates (μ) for Prochlorococcus, all Synechococcus groups, and photosynthetic eukaryotes were 0.55, 0.29, and 0.45 μ day⁻¹, respectively, and suggest relatively high rates of productivity despite low nutrient conditions on the reef. During a series of 5-h incubations with reef corals performed just after sunset or prior to sunrise, reductions in the abundance of photosynthetic picoeukaryotes, Prochlorococcus and Synechococcus cells, were observed. Of the three Synechococcus groups, one decreased significantly during incubations with each coral and the other two only with M. mirabilis. Removal of carbon from the water column is based on coral consumption rates of phytoplankton and averaged between 138 ng h⁻¹ and 387 ng h⁻¹, depending on the coral species. A lack of coral-dependent reduction in heterotrophic bacteria, differences in Synechococcus reductions, and diurnal variation in reductions of Synechococcus and Prochlorococcus, coinciding with peak cell division, point to selective feeding by corals. Our study indicates that bentho-pelagic coupling via selective grazing of microbial groups influences carbon flow and supports heterogeneity of microbial communities overlying coral reefs.

IMPORTANCE We identify interactions between coral grazing behavior and the growth rates and cell abundances of pelagic microbial groups found surrounding a Caribbean reef. During incubation experiments with three reef corals, reductions in microbial cell abundance differed according to coral species and suggest specific coral or microbial mechanisms are at play. Peaks in removal rates of Prochlorococcus and Synechococcus cyanobacteria appear highest during postsunset incubations and coincide with microbial cell division. Grazing rates and effort vary across coral species and picoplankton groups, possibly influencing overall microbial composition and abundance over coral reefs. For reef corals, use of such a numerically abundant source of nutrition may be advantageous, especially under environmentally stressful conditions when symbioses with dinoflagellate algae break down.

In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay

Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.

Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems

Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell's hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

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.

Microbial diversity of co-occurring heterotrophs in cultures of marine picocyanobacteria

BACKGROUND

The cyanobacteria Prochlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; heterotrophs grow on organic carbon supplied by the photolithoautotrophs. For examining the selective pressures shaping autotroph/heterotroph interactions, we have made use of unialgal enrichment cultures of Prochlorococcus and Synechococcus maintained for hundreds to thousands of generations in the lab. We examine the diversity of heterotrophs in 74 enrichment cultures of these picocyanobacteria obtained from diverse areas of the global oceans.

RESULTS

Heterotroph community composition differed between clades and ecotypes of the autotrophic 'hosts' but there was significant overlap in heterotroph community composition across these cultures. Collectively, the cultures were comprised of many shared taxa, even at the genus level. Yet, observed differences in community composition were associated with time since isolation, location, depth, and methods of isolation. The majority of heterotrophs in the cultures are rare in the global ocean, but enrichment conditions favor the opportunistic outgrowth of these rare bacteria. However, we found a few examples, such as bacteria in the family Rhodobacteraceae, of heterotrophs that were ubiquitous and abundant in cultures and in the global oceans. We found their abundance in the wild is also positively correlated with that of picocyanobacteria.

CONCLUSIONS

Particular conditions surrounding isolation have a persistent effect on long-term culture composition, likely from bottlenecking and selection that happen during the early stages of enrichment for the picocyanobacteria. We highlight the potential for examining ecologically relevant relationships by identifying patterns of distribution of culture-enriched organisms in the global oceans.

Discovery of Euryhaline Phycoerythrobilin-Containing Synechococcus and Its Mechanisms for Adaptation to Estuarine Environments

Understanding the strategies developed by different microbial groups to adapt to specific niches is critical. Through genome and transcriptome analyses of two newly isolated novel euryhaline Synechococcus strains, this study revealed that cluster 5 phycoerythrobilin-containing Synechococcus, which are thought to be strictly marine strains, could be abundant in low-salinity waters of the Pearl River estuary (salinity <15 ppt) and explained the molecular mechanisms that enabled them to adapt the low and fluctuating salinity in the estuarine environment.

Synechococcus are among the most abundant and widely distributed picocyanobacteria on earth. Cluster 5 phycoerythrobilin-containing (PEB-containing) Synechococcus, the major marine Synechococcus, were considered to prefer high salinity, and they are absent in estuarine ecosystems. However, we have detected PEB-containing Synechococcus in some low-salinity (<15-ppt) areas of the Pearl River estuary at an abundance up to 1.0 × 10⁵ cells ml⁻¹. Two PEB-containing Synechococcus strains (HK01 and LTW-R) were isolated, and tests on them revealed their ability to cope with variations in the salinity (from 14 to 44 ppt). Phylogenetic analysis showed that HK01 belonged to a novel Synechococcus clade (HK1), whereas LTW-R was clustered with S5.2 strains. Whole-genome analysis revealed that a membrane channel protein with glycine zipper motifs is unique to euryhaline Synechococcus. The upregulation of this protein, the osmotic sensors, and the heat shock protein HSP20 and the downregulation of the osmolyte biosynthesis enable euryhaline Synechococcus to well adapt to the low and fluctuating salinity in the estuarine environment. In addition, decreasing the salinity in LTW-R strongly downregulated several important metabolic pathways, including photosynthesis, and the Calvin-Benson cycle, whereas its growth was not significantly affected. Moreover, obtaining PEB genes from horizontal gene transfer expands the light niche significantly for euryhaline Synechococcus. These results provided new insights into the life strategies and ecological function of marine PEB-containing Synechococcus under the unique environmental condition of estuarine waters, particularly in response to salinity variations.

IMPORTANCE Understanding the strategies developed by different microbial groups to adapt to specific niches is critical. Through genome and transcriptome analyses of two newly isolated novel euryhaline Synechococcus strains, this study revealed that cluster 5 phycoerythrobilin-containing Synechococcus, which are thought to be strictly marine strains, could be abundant in low-salinity waters of the Pearl River estuary (salinity <15 ppt) and explained the molecular mechanisms that enabled them to adapt the low and fluctuating salinity in the estuarine environment. This study expands current understanding on mechanisms involved in niche separation of marine Synechococcus lineages.

Spatial and temporal variations in Synechococcus microdiversity in the Southern California coastal ecosystem

The Synechococcus cyanobacterial population at the Scripps Institution of Oceanography pier in La Jolla, CA, shows large increases in abundance, typically in the spring and summer followed, by rapid declines within weeks. Here we used amplicon sequencing of the ribosomal RNA internal transcribed spacer region to examine the microdiversity within this cyanobacterial genus during these blooms as well as further offshore in the Southern California coastal ecosystem (CCE). These analyses revealed numerous Synechococcus amplicon sequence variants (ASVs) and that clade and ASV composition can change over the course of blooms. We also found that a large bloom in August 2016 was highly anomalous both in its overall Synechococcus abundance and in terms of the presence of normally oligotrophic Synechococcus clade II. The dominant ASVs at the pier were found further offshore and in the California Current, but we did observe more oligotrophic ASVs and clades along with depth variation in Synechococcus diversity. We also observed that the dominant sequence variant switched during the peak of multiple Synechococcus blooms, with this switch occurring in multiple clades, but we present initial evidence that this apparent ASV switch is a physiological response rather than a change in the dominant population.

Revealing new sponge-associated cyanobacterial diversity: Novel genera and species

Cyanobacteria are often reported as abundant components of the sponge microbiome; however their diversity below the phylum level is still underestimated. Aiming to broaden our knowledge of sponge-cyanobacteria association, we isolated cyanobacterial strains from Aegean Sea sponges in previous research, which revealed high degree of novel cyanobacterial diversity. Herein, we aim to further characterize sponge-associated cyanobacteria and re-evaluate their classification based on an extensive polyphasic approach, i.e. a combination of molecular, morphological and ecological data. This approach resulted in the description of five new genera (Rhodoploca, Cymatolege, Metis, Aegeococcus, and Thalassoporum) and seven new species (R. sivonenia, C. spiroidea, C. isodiametrica, M. fasciculata, A. anagnostidisi, A. thureti, T. komareki) inside the order Synechococcales, and a new pleurocapsalean species (Xenococcus spongiosum). X. spongiosum is a baeocyte-producing species that shares some morphological features with other Xenococcus species, but has distinct phylogenetic and ecological identity. Rhodoploca, Cymatolege, Metis and Thalassoporum are novel well supported linages of filamentous cyanobacteria that possess distinct characters compared to their sister taxa. Aegeococcus is a novel monophyletic linage of Synechococcus-like cyanobacteria exhibiting a unique ecology, as sponge-dweller. The considerable number of novel taxa characterized in this study highlights the importance of employing polyphasic culture-dependent approaches in order to reveal the true cyanobacterial diversity associated with sponges.

Spatial Distribution Patterns of Bacterioplankton in the Oxygen Minimum Zone of the Tropical Mexican Pacific

Microbial communities within oxygen minimum zones (OMZs) are crucial drivers of marine biogeochemical cycles; however, we still lack an understanding of how these communities are distributed across an OMZ. We explored vertical (from 5 to 500 m depth) and horizontal (coast to open ocean) distribution of bacterioplankton and its relationships with the main oceanographic conditions in three transects of the tropical Mexican Pacific OMZ. The distribution of the microbial diversity and the main clades changed along the transition from oxygen-rich surface water to the OMZ core, demonstrating the sensitivity of key bacterial groups to deoxygenation. The euphotic zone was dominated by Synechococcales, followed by Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales, whereas the OMZ core was dominated by SAR11, followed by SAR406, SAR324, SAR202, UBA10353 marine group, Thiomicrospirales and Nitrospinales. The marked environmental gradients along the water column also supported a high potential for niche partitioning among OMZ microorganisms. Additionally, in the OMZ core, bacterial assemblages from the same water mass were more similar to each other than those from another water mass. There were also important differences between coastal and open-ocean communities: Flavobacteriales, Verrucomicrobiales, Rhodobacterales, SAR86, and Cellvibrionales were more abundant in coastal areas, while Synechococcales, SAR406, SAR324, SAR202, UBA10353 marine group, and Thiomicrospirales were more abundant in the open ocean. Our results suggest a biogeographic structure of the bacterioplankton in this OMZ region, with limited community mixing across water masses, except in upwelling events, and little dispersion of the community by currents in the euphotic zone.

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.

A new genomic taxonomy system for the Synechococcus collective

Cyanobacteria of the genus Synechococcus are major contributors to global primary productivity and are found in a wide range of aquatic ecosystems. This Synechococcus collective (SC) is metabolically diverse, with some lineages thriving in polar and nutrient-rich locations and others in tropical or riverine waters. Although many studies have discussed the ecology and evolution of the SC, there is a paucity of knowledge on its taxonomic structure. Thus, we present a new taxonomic classification framework for the SC based on recent advances in microbial genomic taxonomy. Phylogenomic analyses of 1085 cyanobacterial genomes demonstrate that organisms classified as Synechococcus are polyphyletic at the order rank. The SC is classified into 15 genera, which are placed into five distinct orders within the phylum Cyanobacteria: (i) Synechococcales (Cyanobium, Inmanicoccus, Lacustricoccus gen. Nov., Parasynechococcus, Pseudosynechococcus, Regnicoccus, Synechospongium gen. nov., Synechococcus and Vulcanococcus); (ii) Cyanobacteriales (Limnothrix); (iii) Leptococcales (Brevicoccus and Leptococcus); (iv) Thermosynechococcales (Stenotopis and Thermosynechococcus) and (v) Neosynechococcales (Neosynechococcus). The newly proposed classification is consistent with habitat distribution patterns (seawater, freshwater, brackish and thermal environments) and reflects the ecological and evolutionary relationships of the SC.

Picocyanobacteria Community and Cyanophage Infection Responses to Nutrient Enrichment in a Mesocosms Experiment in Oligotrophic Waters

Prochlorococcus and Synechococcus are pico-sized cyanobacteria that play a fundamental role in oceanic primary production, being particularly important in warm, nutrient-poor waters. Their potential response to nutrient enrichment is expected to be contrasting and to differ from larger phytoplankton species. Here, we used a metagenomic approach to characterize the responses to nutrient enrichment in the community of picocyanobacteria and to analyze the cyanophage response during a mesocosms experiment in the oligotrophic Red Sea. Natural picoplankton community was dominated by Synechococcus clade II, with marginal presence of Prochlorococcus (0.3% bacterial reads). Increased nutrient input triggered a fast Synechococcus bloom, with clade II being the dominant, with no response of Prochlorococcus growth. The largest bloom developed in the mesocosms receiving a single initial input of nutrients, instead of daily additions. The relative abundances of cyanophage sequences in cellular metagenomes increased during the experiment from 12.6% of total virus reads up to 40% in the treatment with the largest Synechococcus bloom. The subsequent collapse of the bloom pointed to a cyanophage infection on Synechococcus that reduced its competitive capacity, and was then followed by a diatom bloom. The cyanophage attack appears to have preferentially affected the most abundant Synechococcus clade II, increasing the evenness within the host population. Our results highlight the relevance of host-phage interactions on determining population dynamics and diversity of Synechococcus populations.

Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system

Marine phytoplankton are responsible for approximately half of photosynthesis on Earth. However, their ability to drive ocean productivity depends on critical nutrients, especially bioavailable nitrogen (N) which is scarce over vast areas of the ocean. Phytoplankton differ in their preferences for N substrates as well as uptake efficiencies and minimal N requirements relative to other critical nutrients, including iron (Fe) and phosphorus. In this study, we used the MicroTOOLs high-resolution environmental microarray to examine transcriptomic responses of phytoplankton communities in the California Current System (CCS) transition zone to added urea, ammonium, nitrate, and also Fe in the late summer when N depletion is common. Transcript level changes of photosynthetic, carbon fixation, and nutrient stress genes indicated relief of N limitation in many strains of Prochlorococcus, Synechococcus, and eukaryotic phytoplankton. The transcriptomic responses helped explain shifts in physiological and growth responses observed later. All three phytoplankton groups had increased transcript levels of photosynthesis and/or carbon fixation genes in response to all N substrates. However, only Prochlorococcus had decreased transcript levels of N stress genes and grew substantially, specifically after urea and ammonium additions, suggesting that Prochlorococcus outcompeted other community members in these treatments. Diatom transcript levels of carbon fixation genes increased in response to Fe but not to Fe with N which might have favored phytoplankton that were co-limited by N and Fe. Moreover, transcription patterns of closely related strains indicated variability in N utilization, including nitrate utilization by some high-light adapted Prochlorococcus. Finally, up-regulation of urea transporter genes by both Prochlorococcus and Synechococcus in response to filtered deep water suggested a regulatory mechanism other than classic control via the global N regulator NtcA. This study indicated that co-existing phytoplankton strains experience distinct nutrient stresses in the transition zone of the CCS, an understudied region where oligotrophic and coastal communities naturally mix.

Whole-Genome Sequence of the Cyanobacterium Synechococcus sp. Strain WH 8101

Synechococcus spp. are unicellular cyanobacteria that are globally distributed and are important primary producers in marine coastal environments. Here, we report the complete genome sequence of Synechococcus sp. strain WH 8101 and identify genomic islands that may play a role in virus-host interactions.

Synechococcus spp. are unicellular cyanobacteria that are globally distributed and are important primary producers in marine coastal environments. Here, we report the complete genome sequence of Synechococcus sp. strain WH 8101 and identify genomic islands that may play a role in virus-host interactions.

Heterotrophic Bacteria Enhance the Aggregation of the Marine Picocyanobacteria Prochlorococcus and Synechococcus

Marine picocyanobacteria are ubiquitous primary producers across the world’s oceans, and play a key role in the global carbon cycle. Recent evidence stemming from in situ investigations have shown that picocyanobacteria are able to sink out of the euphotic zone to depth, which has traditionally been associated with larger, mineral ballasted cells. The mechanisms behind the sinking of picocyanobacteria remain a point of contention, given that they are too small to sink on their own. To gain a mechanistic understanding of the potential role of picocyanobacteria in carbon export, we tested their ability to form “suspended” (5–60 μm) and “visible” (ca. > 0.1 mm) aggregates, as well as their production of transparent exopolymer particles (TEP)—which are a key component in the formation of marine aggregates. Additionally, we investigated if interactions with heterotrophic bacteria play a role in TEP production and aggregation in Prochlorococcus and Synechococcus by comparing xenic and axenic cultures. We observed TEP production and aggregation in batch cultures of axenic Synechococcus, but not in axenic Prochlorococcus. Heterotrophic bacteria enhanced TEP production as well as suspended and visible aggregate formation in Prochlorococcus, while in Synechococcus, aggregation was enhanced with no changes in TEP. Aggregation experiments using a natural plankton community dominated by picocyanobacteria resulted in aggregation only in the presence of the ballasting mineral kaolinite, and only when Synechococcus were in their highest seasonal abundance. Our results point to a different export potential between the two picocyanobacteria, which may be mediated by interactions with heterotrophic bacteria and presence of ballasting minerals. Further studies are needed to clarify the mechanistic role of bacteria in TEP production and aggregation of these picocyanobacteria.