Relative stability of ploidy in a marine Synechococcus across various growth conditions

Marine picocyanobacteria of the genus Synechococcus are ubiquitous phototrophs in oceanic systems. Consistent with these organisms occupying vast tracts of the nutrient impoverished ocean, most marine Synechococcus so far studied are monoploid, i.e., contain a single chromosome copy. The exception is the oligoploid strain Synechococcus sp. WH7803, which on average possesses around 4 chromosome copies. Here, we set out to understand the role of resource availability (through nutrient deplete growth) and physical stressors (UV, exposure to low and high temperature) in regulating ploidy level in this strain. Using qPCR to assay ploidy status we demonstrate the relative stability of chromosome copy number in Synechococcus sp. WH7803. Such robustness in maintaining an oligoploid status even under nutrient and physical stress is indicative of a fundamental role, perhaps facilitating recombination of damaged DNA regions as a result of prolonged exposure to oxidative stress, or allowing added flexibility in gene expression via possessing multiple alleles

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

Marine picocyanobacteria are globally important primary producers, a facet facilitated via their ability to proliferate in nutrient impoverished regions of the sunlit ocean including oligotrophic gyres that are expected to expand due to climate change. Phosphorus is a major macronutrient potentially limiting growth and CO2 fixation capacity in such systems. Here, we identify a unique high-affinity phosphatase which in picocyanobacteria is present only in populations that occupy these P-deplete systems. This phosphatase is abundant and highly expressed in these regions, suggesting that genetic capacity exists within these populations to provide resilience to long-term P depletion. Moreover, this phosphatase is widely distributed in both heterotrophic bacteria and eukaryotic algae hinting that such a trait is broadly utilized to access such environments

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

Global phylogeography of marine synechococcus in coastal areas reveals strong community shifts

Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide

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

Functional characterisation of the pst1 and pst2 gene clusters in Synechocystis sp. PCC6803

Cyanobacteria are common components of the bacterioplankton in freshwater environments, where they play a key role as primary producers. Growth is limited by the availability of nutrients, particularly phosphate (Pi), and yet many species persist and flourish in environments with an unpredictable and constantly fluctuating supply of Pi. Genome analysis of the freshwater cyanobacterium Synechocystis sp. PCC6803 has identified that the membrane-bound transporter components of its Pho regulon consist of two high affinity (Pi) ABC transporters with multiple associated phosphate binding proteins (PBP), features in contrast to virtually all other known bacteria. Whilst the occurrence of duplicate ABC transporter mechanisms has been widely reported in freshwater cyanobacteria there are still very few reports that demonstrate the functional significance of individual, and apparently redundant, components of these ABC transporter systems. In previous work, disruption of one of the PBPs in Synechocystis sp. PCC6803, pstS1 (sll0680) led to an impairment in the expression of specific genes of the Pho regulon during Pi-deplete growth. This phenotype was not observed when the PBP from the second transporter was disrupted suggesting that each transporter could be functionally distinct. In this study 32Pi radiotracer uptake experiments using pst1 and pst2 deletion mutants showed Pst1 acts as a low affinity, high velocity transporter (Ks 3.7 ± 0.7 μM, Vmax 31.18 ± 3.96 fmol cell-1 min-1) and Pst2 a high affinity, low velocity system (Ks 0.07± 0.01 μM, Vmax 0.88 ± 0.11 fmol cell-1 min-1). Analysis of (qPCR) gene expression profiles and alkaline phosphatase activity also revealed how regulation of transporter abundance controls the nature of the Pi stress signal transduced by the SphS-SphR two component system. These Pi ABC transporters thus exhibit key differences in both their kinetic and regulatory properties, revealing a new strategy for the acquisition of phosphate that has potential implications for our understanding of the ecological success of this key microbial group.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Functional characterisation of the pst1 and pst2 gene clusters in Synechocystis sp. PCC6803

Cyanobacteria are common components of the bacterioplankton in freshwater environments, where they play a key role as primary producers. Growth is limited by the availability of nutrients, particularly phosphate (Pi), and yet many species persist and flourish in environments with an unpredictable and constantly fluctuating supply of Pi. Genome analysis of the freshwater cyanobacterium Synechocystis sp. PCC6803 has identified that the membrane-bound transporter components of its Pho regulon consist of two high affinity (Pi) ABC transporters with multiple associated phosphate binding proteins (PBP), features in contrast to virtually all other known bacteria. Whilst the occurrence of duplicate ABC transporter mechanisms has been widely reported in freshwater cyanobacteria there are still very few reports that demonstrate the functional significance of individual, and apparently redundant, components of these ABC transporter systems. In previous work, disruption of one of the PBPs in Synechocystis sp. PCC6803, pstS1 (sll0680) led to an impairment in the expression of specific genes of the Pho regulon during Pi-deplete growth. This phenotype was not observed when the PBP from the second transporter was disrupted suggesting that each transporter could be functionally distinct. In this study 32Pi radiotracer uptake experiments using pst1 and pst2 deletion mutants showed Pst1 acts as a low affinity, high velocity transporter (Ks 3.7 ± 0.7 μM, Vmax 31.18 ± 3.96 fmol cell-1 min-1) and Pst2 a high affinity, low velocity system (Ks 0.07± 0.01 μM, Vmax 0.88 ± 0.11 fmol cell-1 min-1). Analysis of (qPCR) gene expression profiles and alkaline phosphatase activity also revealed how regulation of transporter abundance controls the nature of the Pi stress signal transduced by the SphS-SphR two component system. These Pi ABC transporters thus exhibit key differences in both their kinetic and regulatory properties, revealing a new strategy for the acquisition of phosphate that has potential implications for our understanding of the ecological success of this key microbial group

Functional characterization of synechocystis sp strain PCC 6803 pst1 and pst2 gene clusters reveals a novel strategy for phosphate uptake in a freshwater cyanobacterium

Synechocystis sp. strain PCC 6803 possesses two putative ABC-type inorganic phosphate (P-i) transporters with three associated P-i-binding proteins (PBPs), SphX (encoded by sll0679), PstS1 (encoded by sll0680), and PstS2 (encoded by slr1247), organized in two spatially discrete gene clusters, pst1 and pst2. We used a combination of mutagenesis, gene expression, and radiotracer uptake analyses to functionally characterize the role of these PBPs and associated gene clusters. Quantitative PCR (qPCR) demonstrated that pstS1 was expressed at a high level in P-i-replete conditions compared to sphX or pstS2. However, a P-i stress shift increased expression of pstS2 318-fold after 48 h, compared to 43-fold for pstS1 and 37-fold for sphX. A shift to high-light conditions caused a transient increase of all PBPs, whereas N stress primarily increased expression of sphX. Interposon mutagenesis of each PBP demonstrated that disruption of pstS1 alone caused constitutive expression of pho regulon genes, implicating PstS1 as a major component of the P-i sensing machinery. The pstS1 mutant was also transformation incompetent. P-32(i) radiotracer uptake experiments using pst1 and pst2 deletion mutants showed that Pst1 acts as a low-affinity, high-velocity transporter (K-s, 3.7 +/- 0.7 mu M; V-max, 31.18 +/- 3.96 fmol cell(-1) min(-1)) and Pst2 acts as a high-affinity, low-velocity system (K-s, 0.07 +/- 0.01 mu M; V-max, 0.88 +/- 0.11 fmol cell(-1) min(-1)). These P-i ABC transporters thus exhibit differences in both kinetic and regulatory properties, the former trait potentially dramatically increasing the dynamic range of P-i transport into the cell, which has potential implications for our understanding of the ecological success of this key microbial group

Marine phage genomics: the tip of the iceberg

Marine viruses are the most abundant biological entity in the oceans, the majority of which infect bacteria and are known as bacteriophages. Yet, the bulk of bacteriophages form part of the vast uncultured dark matter of the microbial biosphere. In spite of the paucity of cultured marine bacteriophages, it is known that marine bacteriophages have major impacts on microbial population structure and the biogeochemical cycling of key elements. Despite the ecological relevance of marine bacteriophages, there are relatively few isolates with complete genome sequences. This minireview focuses on knowledge gathered from these genomes put in the context of viral metagenomic data and highlights key advances in the field, particularly focusing on genome structure and auxiliary metabolic genes