The Influence of Metabolic Inhibitors, Antibiotics, and Microgravity on Intact Cell MALDI-TOF Mass Spectra of the Cyanobacterium Synechococcus Sp. UPOC S4

The aim and novelty of this paper are found in assessing the influence of inhibitors and antibiotics on intact cell MALDI-TOF mass spectra of the cyanobacterium Synechococcus sp. UPOC S4 and to check the impact on reliability of identification. Defining the limits of this method is important for its use in biology and applied science. The compounds included inhibitors of respiration, glycolysis, citrate cycle, and proteosynthesis. They were used at 1–10 μM concentrations and different periods of up to 3 weeks. Cells were also grown without inhibitors in a microgravity because of expected strong effects. Mass spectra were evaluated using controls and interpreted in terms of differential peaks and their assignment to protein sequences by mass. Antibiotics, azide, and bromopyruvate had the greatest impact. The spectral patterns were markedly altered after a prolonged incubation at higher concentrations, which precluded identification in the database of reference spectra. The incubation in microgravity showed a similar effect. These differences were evident in dendrograms constructed from the spectral data. Enzyme inhibitors affected the spectra to a smaller extent. This study shows that only a long-term presence of antibiotics and strong metabolic inhibitors in the medium at 10⁻⁵ M concentrations hinders the correct identification of cyanobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF).

Persistent El Niño driven shifts in marine cyanobacteria populations

In the California Current Ecosystem, El Niño acts as a natural phenomenon that is partially representative of climate change impacts on marine bacteria at timescales relevant to microbial communities. Between 2014–2016, the North Pacific warm anomaly (a.k.a., the “blob”) and an El Niño event resulted in prolonged ocean warming in the Southern California Bight (SCB). To determine whether this “marine heatwave” resulted in shifts in microbial populations, we sequenced the rpoC1 gene from the biogeochemically important picocyanobacteria Prochlorococcus and Synechococcus at 434 time points from 2009–2018 in the MICRO time series at Newport Beach, CA. Across the time series, we observed an increase in the abundance of Prochlorococcus relative to Synechococcus as well as elevated frequencies of ecotypes commonly associated with low-nutrient and high-temperature conditions. The relationships between environmental and ecotype trends appeared to operate on differing temporal scales. In contrast to ecotype trends, most microdiverse populations were static and possibly reflect local habitat conditions. The only exceptions were microdiversity from Prochlorococcous HLI and Synechococcus Clade II that shifted in response to the 2015 El Niño event. Overall, Prochlorococcus and Synechococcus populations did not return to their pre-heatwave composition by the end of this study. This research demonstrates that extended warming in the SCB can result in persistent changes in key microbial populations.

A Novel Cyanobacterium Synechococcus elongatus PCC 11802 has Distinct Genomic and Metabolomic Characteristics Compared to its Neighbor PCC 11801

Cyanobacteria, a group of photosynthetic prokaryotes, are attractive hosts for biotechnological applications. It is envisaged that future biorefineries will deploy engineered cyanobacteria for the conversion of carbon dioxide to useful chemicals via light-driven, endergonic reactions. Fast-growing, genetically amenable, and stress-tolerant cyanobacteria are desirable as chassis for such applications. The recently reported strains such as Synechococcus elongatus UTEX 2973 and PCC 11801 hold promise, but additional strains may be needed for the ongoing efforts of metabolic engineering. Here, we report a novel, fast-growing, and naturally transformable cyanobacterium, S. elongatus PCC 11802, that shares 97% genome identity with its closest neighbor S. elongatus PCC 11801. The new isolate has a doubling time of 2.8 h at 1% CO2, 1000 µmole photons.m-2.s-1 and grows faster under high CO2 and temperature compared to PCC 11801 thus making it an attractive host for outdoor cultivations and eventual applications in the biorefinery. Furthermore, S. elongatus PCC 11802 shows higher levels of key intermediate metabolites suggesting that this strain might be better suited for achieving high metabolic flux in engineered pathways. Importantly, metabolite profiles suggest that the key enzymes of the Calvin cycle are not repressed under elevated CO2 in the new isolate, unlike its closest neighbor.

Gene Expression Measurement Module (GEMM) for space application: Design and validation

In order to facilitate studies on the impact of the space environment on biological systems, we have developed a prototype of GEMM (Gene Expression Measurement Module) - an automated, miniaturized, integrated fluidic system for in-situ measurements of gene expression in microbial samples. The GEMM instrument is capable of (1) lysing bacterial cell walls, (2) extracting and purifying RNA released from cells, (3) hybridizing the RNA to probes attached to a microarray and (4) providing electrochemical readout, all in a microfluidics cartridge. To function on small, uncrewed spacecraft, the conventional, laboratory protocols for both sample preparation and hybridization required significant modifications. Biological validation of the instrument was carried out on Synechococcus elongatus, a photosynthetic cyanobacterium known for its metabolic diversity and resilience to adverse conditions. It was demonstrated that GEMM yielded reliable, reproducible gene expression profiles. GEMM is the only high throughput instrument that can be deployed in near future on space platforms other than the ISS to advance biological research in space. It can also prove useful for numerous terrestrial applications in the field.

Ecological Divergence with Gene Flow in a Thermophilic Cyanobacterium

How ecological diversity is maintained and distributed within populations is a longstanding question in microbial ecology. In the thermophilic cyanobacterium Synechococcus B', high observed levels of recombination are predicted to maintain ecological variation despite the simultaneous action of diverse selective pressures on different regions of the genome. To investigate ecological diversity in these bacteria, we directly isolated laboratory strains of Synechococcus B' from samples collected along the thermal gradients of two geothermal environments in Yellowstone National Park. Extensive recombination was evident for a multi-locus sequence data set, and, consequently, our sample did not exhibit the sequence clustering expected for distinct ecotypes evolving by periodic clonal selection. Evidence for local selective sweeps at specific loci suggests that sweeps may be common but that recombination is effective for maintaining diversity of unlinked genomic regions. Thermal performance for strain growth was positively associated with the temperature of the environment, indicating that Synechococcus B' populations consist of locally adapted ecological specialists that occupy specific thermal niches. Because this ecological differentiation is observed despite the absence of dispersal barriers among sites, we conclude that these bacteria may freely exchange much of the genome but that barriers to gene flow exist for loci under direct temperature selection.

Latitudinal and Vertical Variation of Synechococcus Assemblage Composition Along 170° W Transect From the South Pacific to the Arctic Ocean

Synechococcus is one of the most widely distributed and abundant picocyanobacteria in the global oceans. Although latitudinal variation of Synechococcus assemblage in marine surface waters has been observed, few studies compared Synechococcus assemblage composition in surface and subsurface waters at the basin scale. Here, we report marine Synechococcus diversity in the surface and deep chlorophyll maximum (DCM) layers along 170° W from the South Pacific to the Arctic Ocean in summer. Along the transect, spatial niche partitioning of Synechococcus lineages in the surface waters was clearly observed. Species richness of surface Synechococcus assemblage was positively correlated with water temperature. Clade CRD1 was dominant in the areas (15° S-10° N and 35-40° N) associated with upwelling, and there were 3 different subclades with distinct distribution. CRD1-A was restricted in the North Equatorial Current (5-10° N), CRD1-B dominated in the equatorial upwelling region (15° S-0.17° N), and CRD1-C was only distributed in the North Pacific Current (35-40° N). Similarities between the Synechococcus assemblages in the surface and DCM layers were high at the upwelling regions and areas where the mixed layer was deep, while low in the Subtropical Gyres with strong stratification. Clade I, CRD1-B, and CRD1-C were major Synechococcus lineages in the DCM layer. In particular, clade I, which is composed of 7 subclades with distinct thermal niches, was widely distributed in the DCM layer. Overall, our results provide new insights into not only the latitudinal distribution of Synechococcus assemblages, but also their vertical variation in the central Pacific.

Bacterial communities of four adjacent fresh lakes at different trophic status

Knowing the microbial compositions in fresh lakes is significant to explore the mechanisms of eutrophication and algal blooms. This study reported on the bacterial communities of the four adjacent fresh lakes at different trophic status by Illumina MiSeq Platform, which were Tangxun Lake (J1), Qingling Lake (J2), Huangjia Lake (J3) and Niushan Lake (J4) in Wuhan, China. J1 had the highest salinity and phosphorus. J2 was abundant in TC (Total Carbon)/TOC (Total Organic Carbon.), calcium and magnesium. J3 had the highest content of nitrogen, iron and pollution of heavy metals. High-throughput sequencing analysis of the 16S rRNA gene revealed that the eutrophic lakes (J1, J2 and J3) were dominated by Cyanobacteria (46.1% for J1, 40.8% for J2, 33.4% for J3) and the oligotrophic lake (J4) was dominated by Actinobacteria (34.2%). An increase of Cyanobacteria could inhibit the growth of Proteobacteria, Actinobacteria and Bacteroidetes. Functional inferences from 16S rRNA sequences suggested that J4 had more abundant bacteria with regard to substrate metabolism than J1, J2, and J3. Burkholderia and Fluviicola might be a suggestion of good water quality. The results demonstrated that the bacterial community could well reflect the water quality of the four lakes.

Effect of temperature on the accumulation of marine biogenic gels in the surface microlayer near the outlet of nuclear power plants and adjacent areas in the Daya Bay, China

The surface microlayer (SML) in marine systems is often characterized by an enrichment of biogenic, gel-like particles, such as the polysaccharide-containing transparent exopolymer particles (TEP) and the protein-containing Coomassie stainable particles (CSP). This study investigated the distribution of TEP and CSP, in the SML and underlying water, as well as their bio-physical controlling factors in Daya Bay, an area impacted by warm discharge from two Nuclear power plants (Npp’s) and aquaculture during a research cruise in July 2014. The SML had higher proportions of cyanobacteria and of pico-size Chl a contrast to the underlayer water, particularly at the nearest outlet station characterized by higher temperature. Diatoms, dinoflagellates and chlorophyll a were depleted in the SML. Both CSP and TEP abundance and total area were enriched in the SML relative to the underlying water, with enrichment factors (EFs) of 1.5–3.4 for CSP numbers and 1.32–3.2 for TEP numbers. Although TEP and CSP showed highest concentration in the region where high productivity and high nutrient concertation were observed, EFs of gels and of dissolved organic carbon (DOC) and dissolved acidic polysaccharide (> 1 kDa), exhibited higher values near the outlet of the Npp’s than in the adjacent waters. The positive relation between EF’s of gels and temperature and the enrichment of cyanobacteria in the SML may be indicative of future conditions in a warmer ocean, suggesting potential effects on adjusting phytoplankton community, biogenic element cycling and air-sea exchange processes.

Variation of Synechococcus Pigment Genetic Diversity Along Two Turbidity Gradients in the China Seas

Synechococcus are important and widely distributed picocyanobacteria that encompass a high pigment diversity. In this study, we developed a primer set (peBF/peAR) for amplifying the cpeBA operon sequence from Synechococcus genomic DNA to study Synechococcus pigment diversity along two turbidity gradients in the China seas. Our data revealed that all previously reported pigment types occurred in the South (SCS) and East (ECS) China Seas. In addition, a novel pigment genetic type (type 3f), represented by the high phycourobilin Synechococcus sp. strain KORDI-100 (Exc495:545 = 2.35), was detected. This pigment genetic type differs from the 3c/3d types not only for a very high PUB/PEB ratio but also for a different intergenic spacer sequence and gene organization of the phycobilisome. Synechococcus of different pigment types exhibited clear niche differentiation. Type 2 dominated in the coastal waters, whereas type 3c/3d and 3f were predominant in oceanic waters of the SCS in summer. In the ECS, however, type 3a was the major pigment type throughout the transect. We suggest that in marine environment, various pigment types often co-occur but with one type dominant and PUB/PEB ratio is related to geographic distribution of Synechococcus pigment types. The two marginal seas of China have markedly different Synechococcus pigment compositions.

Distribution of picoplankton in the northeastern South China Sea with special reference to the effects of the Kuroshio intrusion and the associated mesoscale eddies

We investigated picoplankton distribution patterns and environmental variables along an east-to-west transect in the northeastern South China Sea (SCS) during late winter 2016, giving us the opportunity to examine the impacts of the Kuroshio intrusion and the associated eddies. The results indicated that the subsurface (50-75m) phytoplankton biomass chlorophyll (Chl a) maximum (SCM) disappeared and was replaced by higher Chl a in the middle part of the transect due to the impacts of the Kuroshio intrusion and mesoscale eddies. Both flow cytometry and pyrosequencing data revealed that picoplankton abundance and community structure were significantly influenced by perturbations in complex physical processes. Picoeukaryotes represented most of the total phytoplankton biomass, and their maximum abundance (>10⁴cellsmL^-1) occurred within cyclonic eddy-affected regions (Stations 11 and 12), whereas the abundance of Prochlorococcus was the lowest in these regions. Prochlorococcus showed a higher abundance in the Kuroshio-affected area, while Synechococcus was mostly distributed at the upper well-lit depths, with its maximum abundance observed in surface waters (0-30m) adjacent to the cyclonic eddy center. Heterotrophic bacteria (HBA) displayed high abundance along the transect, consistent with the total phytoplankton biomass. Phylogenetic analysis revealed 26 bacterial phyla, with major components belonging to Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, as well as SAR406. Notably, relatively more Rhodobacterales, Flavobacteriales, Alteromonadales, and Vibrionales that were distributed in surface waters of the cyclonic eddy center were specifically associated with the phytoplankton (mainly picoeukaryotes) bloom. Our study highlights the impacts of the Kuroshio intrusion in regulating the microbial ecology of the northeastern SCS and the potential coupling between phytoplankton and bacteria.

Characteristics of picoplankton abundances during a Thalassiosira diporocyclus bloom in the Taiwan Bank in late winter

To understand the variations of picoplankton (Prochlorococcus, Synechococcus, picoeukaryotes, and heterotrophic bacteria) abundances during diatom bloom, the distribution of picoplankton in the Taiwan Bank, South China Sea was investigated using flow cytometry during a Thalassiosira diporocyclus bloom in March 2016. The results indicated an abrupt abundance decrease for Prochlorococcus, Synechococcus, and picoeukaryotes within the bloom area while the abundance of heterotrophic bacteria showed no significant difference between the bloom and non-bloom areas. We found two sub-groups of heterotrophic bacteria: high- and low-nucleic acid content (HNA and LNA) bacteria with HNA dominated in the bloom area whereas LNA dominated in the non-bloom area. Among the picoplankton components, HNA represented the highest (61.1%) carbon biomass in the bloom area while picoeukaryotes represented the highest (37.6%) in the non-bloom area. Our findings implied that heterotrophic bacteria, especially HNA, played an essential role during the diatom bloom.

Overexpression of halophilic serine hydroxymethyltransferase in fresh water cyanobacterium Synechococcus elongatus PCC7942 results in increased enzyme activities of serine biosynthetic pathways and enhanced salinity tolerance

Serine hydroxymethyltransferase (SHMT) catalyzes the conversion of serine to glycine and provides activated one-carbon units required for synthesis of nucleic acids, proteins and numerous biological compounds. SHMT is involved in photorespiratory pathway of oxygenic photosynthetic organisms. Accumulating evidence revealed that SHMT plays vital role for abiotic stresses such as low CO₂ and high salinity in plants, but its role in cyanobacteria remains to be clarified. In this study, we examined to overexpress the SHMT from halotolerant cyanobacterium Aphanothece halophytica in freshwater cyanobacterium, Synechococcus elongatus PCC7942. The transformed cells did not show an obvious phenotype under non-stress condition, but exhibited more tolerance to salinity than the control cells harboring vector only under high salinity. Elevated levels of enzymes in phosphorylated serine biosynthetic pathway and photorespiration pathway were observed in the transformed cells. Glycine level was also increased in the transformed cells. Physiological roles of SHMT for salt tolerance were discussed.

Global genetic capacity for mixotrophy in marine picocyanobacteria

The assimilation of organic nutrients by autotrophs, a form of mixotrophy, has been demonstrated in the globally abundant marine picocyanobacterial genera Prochlorococcus and Synechococcus. However, the range of compounds used and the distribution of organic compound uptake genes within picocyanobacteria are unknown. Here we analyze genomic and metagenomic data from around the world to determine the extent and distribution of mixotrophy in these phototrophs. Analysis of 49 Prochlorococcus and 18 Synechococcus isolate genomes reveals that all have the transporters necessary to take up amino acids, peptides and sugars. However, the number and type of transporters and associated catabolic genes differ between different phylogenetic groups, with low-light IV Prochlorococcus, and 5.1B, 5.2 and 5.3 Synechococcus strains having the largest number. Metagenomic data from 68 stations from the Tara Oceans expedition indicate that the genetic potential for mixotrophy in picocyanobacteria is globally distributed and differs between clades. Phylogenetic analyses indicate gradual organic nutrient transporter gene loss from the low-light IV to the high-light II Prochlorococcus. The phylogenetic differences in genetic capacity for mixotrophy, combined with the ubiquity of picocyanobacterial organic compound uptake genes suggests that mixotrophy has a more central role in picocyanobacterial ecology than was previously thought.

Overexpression of halophilic serine hydroxymethyltransferase in fresh water cyanobacterium Synechococcus elongatus PCC7942 results in increased enzyme activities of serine biosynthetic pathways and enhanced salinity tolerance

Serine hydroxymethyltransferase (SHMT) catalyzes the conversion of serine to glycine and provides activated one-carbon units required for synthesis of nucleic acids, proteins and numerous biological compounds. SHMT is involved in photorespiratory pathway of oxygenic photosynthetic organisms. Accumulating evidence revealed that SHMT plays vital role for abiotic stresses such as low CO₂ and high salinity in plants, but its role in cyanobacteria remains to be clarified. In this study, we examined to overexpress the SHMT from halotolerant cyanobacterium Aphanothece halophytica in freshwater cyanobacterium, Synechococcus elongatus PCC7942. The transformed cells did not show an obvious phenotype under non-stress condition, but exhibited more tolerance to salinity than the control cells harboring vector only under high salinity. Elevated levels of enzymes in phosphorylated serine biosynthetic pathway and photorespiration pathway were observed in the transformed cells. Glycine level was also increased in the transformed cells. Physiological roles of SHMT for salt tolerance were discussed.

Diversity of Synechococcus at the Martha's Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry

The cyanobacterium Synechococcus is a ubiquitous, important phytoplankter across the world's oceans. A high degree of genetic diversity exists within the marine group, which likely contributes to its global success. Over 20 clades with different distribution patterns have been identified. However, we do not fully understand the environmental factors that control clade distributions. These factors are likely to change seasonally, especially in dynamic coastal systems. To investigate how coastal Synechococcus assemblages change temporally, we assessed the diversity of Synechococcus at the Martha's Vineyard Coastal Observatory (MVCO) over three annual cycles with culture-dependent and independent approaches. We further investigated the abundance of both phycoerythrin (PE)-containing and phycocyanin (PC)-only Synechococcus with a flow cytometric setup that distinguishes PC-only Synechococcus from picoeukaryotes. We found that the Synechococcus assemblage at MVCO is diverse (13 different clades identified), but dominated by clade I representatives. Many clades were only isolated during late summer and fall, suggesting more favorable conditions for isolation at this time. PC-only strains from four different clades were isolated, but these cells were only detected by flow cytometry in a few samples over the time series, suggesting they are rare at this site. Within clade I, we identified four distinct subclades. The relative abundances of each subclade varied over the seasonal cycle, and the high Synechococcus cell concentration at MVCO may be maintained by the diversity found within this clade. This study highlights the need to understand how temporal aspects of the environment affect Synechococcus community structure and cell abundance.

Shifts in Cyanobacterial Strain Dominance during the Onset of Harmful Algal Blooms in Florida Bay, USA

Cyanobacteria are fundamental components of aquatic phytoplankton communities and some taxa can cause harmful blooms in coastal ecosystems. Harmful cyanobacterial blooms are typically comprised of multiple strains of a single genus or species that cannot be resolved microscopically. Florida Bay, USA, has experienced harmful cyanobacterial blooms that have been associated with the loss of eelgrass, spiny lobsters, and general food web disruption for more than two decades. To identify the strain or strains of cyanobacteria forming blooms in Florida Bay, samples were collected across the system over an annual cycle and analyzed via DNA sequencing using cyanobacterial-specific 16S rRNA gene primers, flow cytometry, and scanning electron microscopy. Analyses demonstrated that the onset of blooms in Florida Bay was coincident with a transformation of the cyanobacterial populations. When blooms were absent, the cyanobacterial population in Florida Bay was dominated by phycoerythrin-containing Synechococcus cells that were most similar to strains within Clade III. As blooms developed, the cyanobacterial community transitioned to dominance by phycocyanin-containing Synechococcus cells that were coated with mucilage, chain-forming, and genetically most similar to the coastal strains within Clade VIII. Clade VIII strains of Synechococcus are known to grow rapidly, utilize organic nutrients, and resist top-down control by protozoan grazers and viruses, all characteristics consistent with observations of cyanobacterial blooms in Florida Bay. Further, the strains of Synechococcus blooming in this system are genetically distinct from the species previously thought to cause blooms in Florida Bay, Synechococcus elongatus. Collectively, this study identified the causative organism of harmful cyanobacterial blooms in Florida Bay, demonstrates the dynamic nature of cyanobacterial stains within genera in an estuary, and affirms factors promoting Synechococcus blooms.

Lifestyle evolution in cyanobacterial symbionts of sponges

The "Candidatus Synechococcus spongiarum" group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a "Ca. Synechococcus spongiarum" group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, "Ca. Synechococcus spongiarum" includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of "Ca. Synechococcus spongiarum," each from a different clade. By comparing all four symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of "Ca. Synechococcus spongiarum" members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the "Ca. Synechococcus spongiarum" group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack.

IMPORTANCE

While the Synechococcus/Prochlorococcus-type cyanobacteria are widely distributed in the world's oceans, a subgroup has established its niche within marine sponge tissues. Recently, the first genome of sponge-associated cyanobacteria, "Candidatus Synechococcus spongiarum," was described. The sequencing of three representatives of different clades within this cyanobacterial group has enabled us to investigate intraspecies diversity, as well as to give a more comprehensive understanding of the common symbiotic features that adapt "Ca. Synechococcus spongiarum" to its life within the sponge host.

Co-occurrence of phycocyanin- and phycoerythrin-rich Synechococcus in subtropical estuarine and coastal waters of Hong Kong

Phylogenetic diversity of Synechococcus with different pigmentation in subtropical estuarine and coastal waters of Hong Kong was revealed by the phylogeny of cpcBA and cpeBA operons encoding for phycocyanin (PC) and phycoerythrin (PE). Synechococcus containing only PC (PC-rich Synechococcus) dominated at the estuarine station in summer, whereas PE-rich marine Synechococcus containing both PC and PE (PE-rich Synechococcus) dominated in the coastal waters. Our PC sequences are closely related to freshwater strains but differed from Baltic Sea strains, implying that they were from river discharge. Among PE-rich Synechococcus, clones grouping with strains containing only phycoerythrobilin (PEB-only) were abundant in July, while clones grouping with strains possessing a low content of phycourobilin (PUB) in addition to PEB (low PUB/PEB) were more abundant in January at both stations. Clones of high PUB/PEB types were only presented at the coastal station, but were not detected at the estuarine station. The much higher diversity of both PC-rich and PE-rich Synechococcus, as compared with the Baltic Sea, and the occurrence of the high PUB/PEB strains indicate the high dynamic nature of this subtropical estuarine-coastal environment with strong mixing of water masses ranging from Pearl River plume to oceanic South China Sea water. Our results of phylogenetic study agreed well with flow cytometric counts, which revealed the coexistence of PC-rich and PE-rich Synechococcus in the subtropical coastal waters and the dominance of the former type in the estuarine waters during summer high freshwater discharge. These results indicate that picocyanobacteria, particularly PC-rich Synechococcus, which has long been overlooked, are an important part of the primary production, and they could play an important role in the microbial food web in estuarine ecosystems.

Influence of the Changjiang River flood on Synechococcus ecology in the surface waters of the East China Sea

Synechococcus spp. have been suggested as the primary component of picophytoplankton in the East China Sea (ECS). However, the influences of sudden environmental changes on Synechococcus assemblage composition have not yet been investigated. In the summer of 2010, a disastrous flood occurred in the Changjiang River basin. To improve our understanding of how this flood affected the Synechococcus ecology on the ECS surface, their assemblages and distributions have been described using two-laser flow cytometry and phylogenetic analysis of the phycocyanin operon. During the nonflooding summer of 2009, phycoerythrin-rich (PE-rich) Synechococcus thrived near the outer boundary of the Changjiang River diluted water (CDW) coverage, while phycocyanin-rich (PC-rich) Synechococcus predominated inside the turbid CDW with a transparency of <80%. During the 2010 summer, flooding expanded the CDW coverage area to over half of the ECS. PE-rich cells showed a homogeneous distribution and a decline in abundance, while the spatial pattern of the PC-rich Synechococcus resembled the pattern from 2009. Based on the phycocyanin operon phylogeny, the Synechococcus in the ECS were categorized into five groups, ECS-1 to ECS-4 and ECS-PE, comprising a total of 19 operational taxonomic units. In the summer of 2009, ECS-2 dominated in the coast, and the ECS-3 and ECS-PE clades prevailed in the offshore waters. However, during the summer of 2010, ECS-4 and ECS-PE became the dominant strains. The injection of abundant anthropogenic pollutants and the enhancement of transparency within the CDW expansion area appear to be the factors needed to transiently alter the ecology of Synechococcus after flooding.

The first isolation of a cyanophage-Synechococcus system from the East China Sea

A cyanophage strain and its host Synechococcus were isolated from the East China Sea. The host Synechococcus sp. SJ01 was characterized by its 16S rRNA, ITS, and psbA gene sequences as well as by its morphological appearance and pigmentation. The cyanophage, strain S-SJ2, was able to cause a lytic infection of the coastal Synechococcus. TEM of negative-stained specimens showed that the phage isolate has an isometric head with a diameter of 68 nm and a long tail with a length of 280 nm. The cyanophage-Synechococcus system from the East China Sea shares many properties with other marine cyanophage-Synechococcus systems worldwide.

Detection and identification of potentially toxic cyanobacteria in Polish water bodies

The main goal of this study was to determine the distribution of potentially toxic cyanobacteria in 39 selected Polish water bodies. From the water bodies with blooms and also from those in which blooms were not visible 87 samples were investigated. For the first time samples from ponds localized in villages with high agricultural activities were included. Lakes for which microcystin concentrations had been determined before were included as a reference for the research. The detection of cyanobacteria was conducted by microscopic observation as well as by PCR amplification of the rpoC1 gene fragment. Cyanobacteria were present in 75 out of 87 samples. The presence of potentially toxic cyanobacteria was detected by amplification of the mcyB and mcyE genes, which are involved in the biosynthesis of microcystins. Both genes were detected in 7 out of 9 blooms investigated. In the case of samples collected from water bodies in which blooms were not observed, the mcyB and mcyE genes were detected in 20 out of 36. In order to identify the cyanobacteria occurring in selected reservoirs, 16S plus ITS clone libraries were constructed. The method allowed distinguishing 18 different genotypes. After sequence analysis, cyanobacteria belonging to genera Microcystis, Planktothrix, Anabaena, Pseudanabaena, Synechocystis, Synechococcus and Woronichinia were identified. Results confirmed the usefulness of the rpoC1 and mcy genes for monitoring water bodies and detection of potentially toxic cyanobacteria. Application of molecular markers allowed detecting potentially toxic cyanobacteria before the bloom was visible. This is the first comprehensive study concerning cyanobacteria present in different types of Polish water bodies performed using molecular markers.

Influence of molecular resolution on sequence-based discovery of ecological diversity among Synechococcus populations in an alkaline siliceous hot spring microbial mat

Previous research has shown that sequences of 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions may not have enough genetic resolution to define all ecologically distinct Synechococcus populations (ecotypes) inhabiting alkaline, siliceous hot spring microbial mats. To achieve higher molecular resolution, we studied sequence variation in three protein-encoding loci sampled by PCR from 60°C and 65°C sites in the Mushroom Spring mat (Yellowstone National Park, WY). Sequences were analyzed using the ecotype simulation (ES) and AdaptML algorithms to identify putative ecotypes. Between 4 and 14 times more putative ecotypes were predicted from variation in protein-encoding locus sequences than from variation in 16S rRNA and 16S-23S rRNA internal transcribed spacer sequences. The number of putative ecotypes predicted depended on the number of sequences sampled and the molecular resolution of the locus. Chao estimates of diversity indicated that few rare ecotypes were missed. Many ecotypes hypothesized by sequence analyses were different in their habitat specificities, suggesting different adaptations to temperature or other parameters that vary along the flow channel.

Characterization of hydrocortisone bioconversion and 16S RNA gene in Synechococcus nidulans cultures

A unicellular cyanobacterium, Synechococcus nidulans (Pringsheim) Komárek, was isolated from paddy-fields and applied in the biotransformation experiment of hydrocortisone (1). This strain has not been previously tested for steroid bioconversion. Fermentation was carried out in BG-11 medium supplemented with 0.05% substrate at 25 degrees C for 14 days of incubation. The obtained products were chromatographically purified followed by their characterization using spectroscopic methods. 11beta,17beta-dihydroxyandrost-4-en-3-one (2), 11beta-hydroxyandrost-4-en-3,17-dione (3), and androst-4-ene-3,17-dione (4) were the main bioproducts in the hydrocortisone bioconversion. The observed bioreaction characteristics were the side chain degradation of the substrate to prepare compounds (2) and (3) following the 11beta-dehydroxylation for accumulation of the compound (4). Time course study showed the accumulation of the product (2) from the second day of the fermentation and compounds (3) and (4) from the third day. All the metabolites reached their maximum concentration in seven days. Cyanobacterial 16S rRNA gene was also amplified by PCR. Sequences were amplified using the universal prokaryotic primers which amplify a approximately 400-bp region of the 16S rRNA gene. PCR products were sequenced to confirm their authenticity as 16S rRNA gene of cyanobacteria. The result of PCR blasted with other sequenced cyanobacteria in NCBI showed 99% identity to the 16S small subunit rRNA of seven Synechococcus species.

[Identification of two cyanobacterial strains isolated from the Kotel'nikovskii hot spring of the Baikal rift]

Two cyanobacterial strains, Pseudanabaena sp. 0411 and Synechococcus sp. 0431, were isolated from a sample collected in the Kotel'nikovskii hot spring of the Baikal rift. According to the results of light and transmission electron microscopy, as well as of the phylogenetic analysis of the 16S rRNA gene, these cyanobacteria were classified as Pseudanabaena sp. nov. and Synechococcus bigranulatus Skuja. The constructed phylogenetic tree shows that the studied strains are positioned in the clades of cyanobacteria isolated from hydrothermal vents of Asia and New Zealand, separately from marine and freshwater members of these genera, including those isolated from Lake Baikal.

Seasonal and habitat-related distribution pattern of Synechococcus genotypes in Lake Constance

The abundance and distribution of Synechococcus spp. in the autotrophic picoplankton of Lake Constance, were followed in the pelagic and littoral habitat by qPCR over 2 years. One genotype, represented by isolated phycoerythrin-rich strain BO 8807, showed a seasonal distribution pattern in both habitats. Before a stable thermal stratification, the maximum of both the Synechococcus population and genotype BO 8807 occurred at 15 or 20 m water depth in the pelagic habitat. During the summer stratification, when the absolute abundance of all Synechococcus spp. was highest above 15 m, the absolute and relative abundance of genotype BO 8807 was maximal at 20 m. These results indicate that Synechococcus spp. or single genotypes are present in deep maxima in Lake Constance. The in situ dynamics of genotype BO 8807 is consistent with the observation that isolated strain BO 8807 requires higher phosphate concentrations for maximum growth rates than a strain from the same phylogenetic cluster that dominates the pelagic summer population. In contrast to these findings, low genome numbers of phycocyanin-rich genotype BO 8805 were found temporarily only in both the littoral and pelagic plankton. Microscopy revealed that PC-rich cells in general occurred preferentially in the littoral habitat. We discuss our results with respect to the versatility of picocyanobacteria of the evolutionary lineage VI of cyanobacteria, and a habitat-related distribution pattern of Synechococcus genotypes.

The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography

Carboxysomes are organelle-like polyhedral bodies found in cyanobacteria and many chemoautotrophic bacteria that are thought to facilitate carbon fixation. Carboxysomes are bounded by a proteinaceous outer shell and filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the first enzyme in the CO(2) fixation pathway, but exactly how they enhance carbon fixation is unclear. Here we report the three-dimensional structure of purified carboxysomes from Synechococcus species strain WH8102 as revealed by electron cryotomography. We found that while the sizes of individual carboxysomes in this organism varied from 114 nm to 137 nm, surprisingly, all were approximately icosahedral. There were on average approximately 250 RuBisCOs per carboxysome, organized into three to four concentric layers. Some models of carboxysome function depend on specific contacts between individual RuBisCOs and the shell, but no evidence of such contacts was found: no systematic patterns of connecting densities or RuBisCO positions against the shell's presumed hexagonal lattice could be discerned, and simulations showed that packing forces alone could account for the layered organization of RuBisCOs.

Responses of a thermophilic Synechococcus isolate from the microbial mat of Octopus Spring to light

Thermophilic cyanobacteria of the genus Synechococcus are major contributors to photosynthetic carbon fixation in the photic zone of microbial mats in Octopus Spring, Yellowstone National Park. Synechococcus OS-B' was characterized with regard to the ability to acclimate to a range of different light irradiances; it grows well at 25 to 200 micromol photons m(-2) s(-1) but dies when the irradiance is increased to 400 micromol photons m(-2) s(-1). At 200 micromol photons m(-2) s(-1) (high light [HL]), we noted several responses that had previously been associated with HL acclimation of cyanobacteria, including cell bleaching, reduced levels of phycobilisomes and chlorophyll, and elevated levels of a specific carotenoid. Synechococcus OS-B' synthesizes the carotenoids zeaxanthin and beta,beta-carotene and a novel myxol-anhydrohexoside. Interestingly, 77-K fluorescence emission spectra suggest that Synechococcus OS-B' accumulates very small amounts of photosystem II relative to that of photosystem I. This ratio further decreased at higher growth irradiances, which may reflect potential photodamage following exposure to HL. We also noted that HL caused reduced levels of transcripts encoding phycobilisome components, particularly that for CpcH, a 20.5-kDa rod linker polypeptide. There was enhanced transcript abundance of genes encoding terminal oxidases, superoxide dismutase, tocopherol cyclase, and phytoene desaturase. Genes encoding the photosystem II D1:1 and D1:2 isoforms (psbAI and psbAII/psbAIII, respectively) were also regulated according to the light regimen. The results are discussed in the context of how Synechococcus OS-B' may cope with high light irradiances in the high-temperature environment of the microbial mat.

Identification and characterization of thermophilicSynechococcusspp. isolates from Asian geothermal springs

Two thermophilic cyanobacterial strains, Ts and Bs, collected from Asian geothermal springs were identified morphologically and phylogenetically as Synechococcus in the order Chroococcales and were isolated into axenic cultures. In addition to the high similarities between their full 16S rRNA gene sequences, both strains also shared similar pigment profiles and fatty acid compositions but with varied ratios. Strain Ts had elevated levels of photoprotective pigments such as carotenoid and scytonemin even after prolonged culture under identical laboratory conditions, whereas strain Bs produced more chlorophyll a per unit cell volume, perhaps resulting from UV adaptation in the natural habitats. In addition, strain Ts had more content than strain Bs in terms of the total fatty acids and the proportion of unsaturated fatty acids. Neither isolate was able to fix nitrogen, and they had zero susceptibility to ampicillin and streptomycin.

Microbial diversity in natural environments: focusing on fundamental questions

Interactions with Gijs Kuenen and other Dutch scientists have led my lab to fundamental insights into the composition, structure and function of a hot spring cyanobacterial mat community that should influence our thinking about all microbial communities. By focusing on the distribution of molecular sequence variants of predominant mat phototrophs, we have discovered that small-scale sequence variation can be ecologically meaningful. By applying novel cultivation approaches, we have been able to obtain genetically relevant community members and thus to test the hypothesis that closely related sequence variants arose via adaptive evolutionary radiation. By applying the analytical tools of organic geochemistry we have gained insight into the metabolisms of major phototrophic members of the mat community as well as interactions between phototrophic guilds. These observations challenge traditional paradigms about prokaryotic species and cause us to consider evolutionary ecology theory as we develop genome-based methods for high-resolution analysis of the species-like fundamental units comprising microbial communities, and for investigating how such units coordinate the physiological activities within guilds of the community.

Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies

Marine microbial communities often contain multiple closely related phylogenetic clades, but in many cases, it is still unclear what physiological traits differentiate these putative ecotypes. The numerically abundant marine cyanobacterium Synechococcus can be divided into at least 14 clades. In order to better understand ecotype differentiation in this genus, we assessed the diversity of a Synechococcus community from a well-mixed water column in the Sargasso Sea during March 2002, a time of year when this genus typically reaches its annual peak in abundance. Diversity was estimated from water sampled at three depths (approximately 5, 70, and 170 m) using both culture isolation and construction of cyanobacterial 16S-23S rRNA internal transcribed sequence clone libraries. Clonal isolates were obtained by enrichment with ammonium, nitrite, or nitrate as the sole N source, followed by pour plating. Each method sampled the in situ diversity differently. The combined methods revealed a total of seven Synechococcus phylotypes including two new putative ecotypes, labeled XV and XVI. Although most other isolates grow on nitrate, clade XV exhibited a reduced efficiency in nitrate utilization, and both clade XV and XVI are capable of chromatic adaptation, demonstrating that this trait is more widely distributed among Synechococcus strains than previously known. Thus, as in its sister genus Prochlorococcus, light and nitrogen utilization are important factors in ecotype differentiation in the marine Synechococcus lineage.

A suppression subtractive hybridization approach reveals niche-specific genes that may be involved in predator avoidance in marine Synechococcus isolates

Picocyanobacteria of the genus Synechococcus are important contributors to marine primary production and are ubiquitous in the world's oceans. This genus is genetically diverse, and at least 10 discrete lineages or clades have been identified phylogenetically. However, little if anything is known about the genetic attributes which characterize particular lineages or are unique to specific strains. Here, we used a suppression subtractive hybridization (SSH) approach to identify strain- and clade-specific genes in two well-characterized laboratory strains, Synechococcus sp. strain WH8103 (clade III) and Synechococcus sp. strain WH7803 (clade V). Among the genes that were identified as potentially unique to each strain were genes encoding proteins that may be involved in specific predator avoidance, including a glycosyltransferase in strain WH8103 and a permease component of an ABC-type polysaccharide/polyol phosphate export system in WH7803. During this work the genome of one of these strains, WH7803, became available. This allowed assessment of the number of false-positive sequences (i.e., sequences present in the tester genome) present among the SSH-enriched sequences. We found that approximately 9% of the WH8103 sequences were potential false-positive sequences, which demonstrated that caution should be used when this technology is used to assess genomic differences in genetically similar bacterial strains.

Diverse and unique picocyanobacteria in Chesapeake Bay, revealed by 16S-23S rRNA internal transcribed spacer sequences

rRNA internal transcribed spacer phylogeny showed that Chesapeake Bay is populated with diverse Synechococcus strains, including members of the poorly studied marine cluster B. Marine cluster B prevailed in the upper bay, while marine cluster A was common in the lower bay. Interestingly, marine cluster B Synechococcus included phycocyanin- and phycoerythrin-rich strains.

Toxic Microcystis is widespread in Lake Erie: PCR detection of toxin genes and molecular characterization of associated cyanobacterial communities

During the past decade, algae blooms, which include the toxic cyanobacterium Microcystis, have reoccurred in the Laurentian Great Lakes, most commonly in the western basin of Lake Erie. Whereas the western basin is the most impacted by toxic Microcystis in Lake Erie, there has historically been little effort focused on identifying the spatial distribution of Microcystis throughout this lake. To address this lack of knowledge, we have employed a polymerase-chain-reaction-based detection of genes required for synthesis of the toxin microcystin (mcyD and mcyB), as well as 16S rDNA fragments specific to either all Microcystis or all cyanobacteria. Using a multiplex approach, we tested 21 samples from 13 field stations and found that toxigenic Microcystis were present in the western and eastern basins in the summers of 1999, 2000, and 2002 and the central basin in 1999 and 2002. This is the most extensive distribution of Microcystis reported in Lake Erie. Clone libraries (16S rDNA) of these cyanobacterial communities were generated from 7 of the 13 field stations (representing all three basins) to partially characterize this microbial community. These libraries were shown to be dominated by sequences assigned to the Synechococcus and Cyanobium phylogenetic cluster, indicating the importance of picoplankton in this large lake system.

Time series observation based InfraRed Epifluorescence Microscopic (TIREM) approach for accurate enumeration of bacteriochlorophyll-containing microbes in marine environments

Bacteriochlorophyll a Containing Microbes (BCM) are a unique group of microorganisms in the marine environment. Accurate determination of their abundance is critical for understanding their role in energy flow and carbon cycle in the ecosystem. The InfraRed Epifluorescence Microscopy (IREM) method, using infrared fluorescence as the diagnostic signal of BCM, is the most convenient means to date for enumeration of BCM in seawater, but IREM methodology suffers from serious errors introduced by cyanobacteria, which also can emit infrared fluorescence and whose abundance is of the same order of magnitude as BCM. In the present study, an advanced "Time-series observation based cyanobacteria-calibrated InfraRed Epifluorescence Microscopy (TIREM)" approach is established for accurate enumeration of BCM in marine environments. The protocol is distinguished by its use of time series observation, auto-imaging and digital analysis. In principle, the correct count of BCM can be obtained by subtracting the cyanobacterial count from the total infrared positive count. The challenge, however, is that Prochlorococcus, the most abundant cyanobacterium in the sea, is readily visible in infrared images but not visible in the initial cyanobacterial images obtained by epifluorescence microscopy because its emission signals are masked by brighter fluorescence from larger cells like Synechococcus coexisting in seawater samples. Prochlorococcus cells become gradually visible when the fluorescence from Synechococcus cells declines after a period of exposure to excitation light. Therefore the plateau (maximum) count of the cyanobacterial cells in time series images rather than in the initial ones, as previously believed, represents the correct count for the total number of cyanobacteria (Synechococcus plus Prochlorococcus cells). Thus, the accurate estimation of BCM abundance can only be calculated from the formula: [BCM cells] = [plateau count of infrared positive cells]-[plateau count of cyanobacterial cells]. The conceptual advance of the TIREM protocol is that in classical epifluorescence microscopy or in IREM protocols, quick observation is recommended to avoid quenching the fluorescence, but in the TIREM protocol, instead, time series observation is the key for obtaining reliable data. The TIREM protocol is validated by studies using BCM and cyanobacterial pure cultures as well as by examination of samples from various marine environments.

Nitrate and phosphate affect cultivability of cyanobacteria from environments with low nutrient levels

Nitrate and phosphate concentrations higher than those found in the natural environment slowed down growth of two strains of non-bloom-forming, phycoerythrin-rich Synechococcus spp. isolated from mesotrophic subalpine lakes. The results make clear why isolation of these picocyanobacteria in standard cultivation media was difficult. At low concentrations, closely related strains exhibited distinct growth characteristics with respect to these two nutrients, possibly explaining differences in their seasonal appearance in the natural environment.

The distribution of cyanobacteria across physical and chemical gradients in hot springs in northern Thailand

We mapped the distribution of mat forming cyanobacteria along the thermal gradient from 30 to 80 degrees C, in nine hot spring districts in northern Thailand. Nineteen genera and 36 species were identified by morphometric analysis. Water temperature was the predominant determinant of community structure in the springs. The diversity of cyanobacterial morphotypes fell as temperature increased. Water chemistry (pH, alkalinity and ammonia concentration) was a much weaker descriptor of the floral similarity between the springs. The morphotypes which dominated all springs were Synechococcus lividus and Synechococcus sp. (>40 and <80 degrees C) and Phormidium boryanum (>30 and <60 degrees C). The occurrence of Synechococcus lividus and Synechococcus sp. in every spring at 70 degrees C or more, implied there was no regional barrier to the distribution of these highly thermophilic taxa. Conversely, there were regional differences in the diversity of mat communities growing below 60 degrees C. The most depauperate flora were in the northernmost springs (SKP, TPN, PD, JS) and the springs further south around Chiang Mai had more diverse flora, suggestive of barriers to the dispersal of some taxa. More discriminating analyses using molecular tools will be required to determine whether the ubiquitous distribution Synechoccoccus morphotypes above 60 degrees C masks a genotypic diversity, comparable to the morphotype diversity observed below 60 degrees C.

Screening of Cyanobacterial Species for Calcification

Species of cyanobacteria in the genera Synechococcus and Synechocystis are known to be the catalysts of a phenomenon called "whitings", which is the formation and precipitation of fine-grained CaCO3 particles. Whitings occur when the cyanobacteria fix atmospheric CO2 through the formation of CaCO3 on their cell surfaces, which leads to precipitation to the ocean floor and subsequent entombment in mud. Whitings represent one potential mechanism for CO2 sequestration. Research was performed to determine the ability of various strains of Synechocystis and Synechococcus to calcify when grown in microcosms amended with 2.5 mM HCO(3-) and 3.4 mM Ca2+. Results indicated that although all strains tested have the ability to calcify, only two Synechococcus species, strains PCC 8806 and PCC 8807, were able to calcify to the extent that a CaCO3 precipitate was formed. Enumeration of the cyanobacterial cultures during testing indicated that cell density did not appear to have a direct effect on calcification. Factors that had the greatest effect on calcification were CO2 removal and subsequent generation of alkaline pH. Whereas cell density was similar for all strains tested, differences in maximum pH were demonstrated. As CO2 was removed, growth medium pH increased and soluble Ca2+ was removed from solution. The largest increases in growth medium pH occurred when CO2 levels dropped below 400 ppmv. Research presented demonstrates that, under the conditions tested, many species of cyanobacteria in the genera Synechocystis and Synechococcus are able to calcify but only two species of Synechococcus were able to calcify to an extent that led to the precipitation of calcium carbonate.