Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer

Background

S-PM2 is a phage capable of infecting strains of unicellular cyanobacteria belonging to the genus Synechococcus. S-PM2, like other myoviruses infecting marine cyanobacteria, encodes a number of bacterial-like genes. Amongst these genes is one encoding a MazG homologue that is hypothesized to be involved in the adaption of the infected host for production of progeny phage.

Methodology/Principal Findings

This study focuses on establishing the occurrence of mazG homologues in other cyanophages isolated from different oceanic locations. Degenerate PCR primers were designed using the mazG gene of S-PM2. The mazG gene was found to be widely distributed and highly conserved among Synechococcus myoviruses and podoviruses from diverse oceanic provinces.

Conclusions/Significance

This study provides evidence of a globally connected cyanophage gene pool, the cyanophage mazG gene having a small effective population size indicative of rapid lateral gene transfer despite being present in a substantial fraction of cyanophage. The Prochlorococcus and Synechococcus phage mazG genes do not cluster with the host mazG gene, suggesting that their primary hosts are not the source of the mazG gene.     

Gene Order Phylogeny of the Genus Prochlorococcus

Background

Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria.

Methodology/Principal Findings

Orthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based trees. Also, a previously unresolved clade was resolved, that of MIT9211 and SS120.

Conclusions/Significance

This is the first study to use gene order data to resolve a bacterial phylogeny at the genus level. It suggests that the technique is useful in resolving the Tree of Life.     

Resolution of Prochlorococcus and Synechococcus Ecotypes by Using 16S-23S Ribosomal DNA Internal Transcribed Spacer Sequences

Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S-23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary-structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low-B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high-B/A ecotype into four genetically distinct clades. ITS-based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin). The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world's oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.     

Ecological Genomics of Marine Picocyanobacteria

Summary: Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.     

Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions

Regulatory small RNAs (sRNAs) have crucial roles in the adaptive responses of bacteria to changes in the environment. Thus far, potential regulatory RNAs have been studied mainly in marine picocyanobacteria in genetically intractable Prochlorococcus, rendering their molecular analysis difficult. Synechococcus sp. WH7803 is a model cyanobacterium, representative of the picocyanobacteria from the mesotrophic areas of the ocean. Similar to the closely related Prochlorococcus it possesses a relatively streamlined genome and a small number of genes, but is genetically tractable. Here, a comparative genome analysis was performed for this and four additional marine Synechococcus to identify the suite of possible sRNAs and other RNA elements. Based on the prediction and on complementary microarray profiling, we have identified several known as well as 32 novel sRNAs. Some sRNAs overlap adjacent coding regions, for instance for the central photosynthetic gene psbA. Several of these novel sRNAs responded specifically to environmentally relevant stress conditions. Among them are six sRNAs changing their accumulation level under cold stress, six responding to high light and two to iron limitation. Target predictions suggested genes encoding components of the light-harvesting apparatus as targets of sRNAs originating from genomic islands and that one of the iron-regulated sRNAs might be a functional homolog of RyhB. These data suggest that marine Synechococcus mount adaptive responses to these different stresses involving regulatory sRNAs.     

Comparative Genomic and Phylogenomic Analyses Reveal a Conserved Core Genome Shared by Estuarine and Oceanic Cyanopodoviruses

Podoviruses are among the major viral groups that infect marine picocyanobacteria Prochlorococcus and Synechococcus. Here, we reported the genome sequences of five Synechococcus podoviruses isolated from the estuarine environment, and performed comparative genomic and phylogenomic analyses based on a total of 20 cyanopodovirus genomes. The genomes of all the known marine cyanopodoviruses are highly syntenic. A pan-genome of 349 clustered orthologous groups was determined, among which 15 were core genes. These core genes make up nearly half of each genome in length, reflecting the high level of genome conservation among this cyanophage type. The whole genome phylogenies based on concatenated core genes and gene content were highly consistent and confirmed the separation of two discrete marine cyanopodovirus clusters MPP-A and MPP-B. The genomes within cluster MPP-B grouped into subclusters mainly corresponding to Prochlorococcus or Synechococcus host types. Auxiliary metabolic genes tend to occur in a specific phylogenetic group of these cyanopodoviruses. All the MPP-B phages analyzed here encode the photosynthesis gene psbA, which are absent in all the MPP-A genomes thus far. Interestingly, all the MPP-B and two MPP-A Synechococcus podoviruses encode the thymidylate synthase gene thyX, while at the same genome locus all the MPP-B Prochlorococcus podoviruses encode the transaldolase gene talC. Both genes are hypothesized to have the potential to facilitate the biosynthesis of deoxynucleotide for phage replication. Inheritance of specific functional genes could be important to the evolution and ecological fitness of certain cyanophage genotypes. Our analyses demonstrate that cyanopodoviruses of estuarine and oceanic origins share a conserved core genome and suggest that accessory genes may be related to environmental adaptation.     

Environmental shaping of sponge associated archaeal communities

Background

Archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood.

Methodology/Principal Findings

We compared the diversity and composition of archaea associated with seawater and with the sponges Hymeniacidon heliophila, Paraleucilla magna and Petromica citrina in two distinct environments: Guanabara Bay, a highly impacted estuary in Rio de Janeiro, Brazil, and the nearby Cagarras Archipelago. For this we used metagenomic analyses of 16S rRNA and ammonia monooxygenase (amoA) gene libraries. Hymeniacidon heliophila was more abundant inside the bay, while P. magna was more abundant outside and P. citrina was only recorded at the Cagarras Archipelago. Principal Component Analysis plots (PCA) generated using pairwise unweighted UniFrac distances showed that the archaeal community structure of inner bay seawater and sponges was different from that of coastal Cagarras Archipelago. Rarefaction analyses showed that inner bay archaeaoplankton were more diverse than those from the Cagarras Archipelago. Only members of Crenarchaeota were found in sponge libraries, while in seawater both Crenarchaeota and Euryarchaeota were observed. Although most amoA archaeal genes detected in this study seem to be novel, some clones were affiliated to known ammonia oxidizers such as Nitrosopumilus maritimus and Cenarchaeum symbiosum.

Conclusion/Significance

The composition and diversity of archaeal communities associated with pollution-tolerant sponge species can change in a range of few kilometers, probably influenced by eutrophication. The presence of archaeal amoA genes in Porifera suggests that Archaea are involved in the nitrogen cycle within the sponge holobiont, possibly increasing its resistance to anthropogenic impacts. The higher diversity of Crenarchaeota in the polluted area suggests that some marine sponges are able to change the composition of their associated archaeal communities, thereby improving their fitness in impacted environments.     

Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and Prochlorococcus

Marine unicellular cyanobacteria, represented by Synechococcus and Prochlorococcus, dominate the total phytoplankton biomass and production in oligotrophic ocean. In this study, we employed comparative genomics approaches to extensively investigate synonymous codon usage bias and evolutionary rates in a large number of closely related species of marine unicellular cyanobacteria. Although these two groups of marine cyanobacteria have a close phylogenetic relationship, we find that they are highly divergent not only in codon usage patterns but also in the driving forces behind the diversification. It is revealed that in Prochlorococcus, mutation and genome compositional constraints are the main forces contributing to codon usage bias, whereas in Synechococcus, translational selection. In addition, nucleotide substitution rate analysis indicates that they are not evolving at a constant rate after the divergence and that the average d_N/d_S values of core genes in Synechococcus are significantly higher than those in Prochlorococcus. Our evolutionary genomic analysis provides the first insight into codon usage, evolutionary genetic mechanisms and environmental adaptation of Synechococcus and Prochlorococcus after divergence.     

Monophyly,Distance and Character–Based Multigene Barcoding Reveal Extraordinary Cryptic Diversity in Nassarius: A Complex and Dangerous Community

Background

Correct identification and cryptic biodiversity revelation for marine organisms are pressing since the marine life is important in maintaining the balance of ecological system and is facing the problem of biodiversity crisis or food safety. DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Nassarius, the common mudsnail, plays an important role in marine environment and has problem in food safety, but the classification of it is quite confused because of the complex morphological diversity.

Methodology/Principal Findings

Here we report a comprehensive barcoding analysis of 22 Nassarius species. We integrated the mitochondrial and nuclear sequences and the morphological characters to determine 13 Nassarius species studied and reveal four cryptic species and one pair synonyms. Distance, monophyly, and character–based barcoding methods were employed.

Conclusions/Significance

Such successful identification and unexpected cryptic discovery is significant for Nassarius in food safety and species conversation and remind us to pay more attention to the hidden cryptic biodiversity ignored in marine life. Distance, monophyly, and character–based barcoding methods are all very helpful in identification but the character-based method shows some advantages.     

Molecular Genetics of the Usher Syndrome in Lebanon: Identification of 11 Novel Protein Truncating Mutations by Whole Exome Sequencing

Background

Usher syndrome (USH) is a genetically heterogeneous condition with ten disease-causing genes. The spectrum of genes and mutations causing USH in the Lebanese and Middle Eastern populations has not been described. Consequently, diagnostic approaches designed to screen for previously reported mutations were unlikely to identify the mutations in 11 unrelated families, eight of Lebanese and three of Middle Eastern origins. In addition, six of the ten USH genes consist of more than 20 exons, each, which made mutational analysis by Sanger sequencing of PCR-amplified exons from genomic DNA tedious and costly. The study was aimed at the identification of USH causing genes and mutations in 11 unrelated families with USH type I or II.

Methods

Whole exome sequencing followed by expanded familial validation by Sanger sequencing.

Results

We identified disease-causing mutations in all the analyzed patients in four USH genes, MYO7A, USH2A, GPR98 and CDH23. Eleven of the mutations were novel and protein truncating, including a complex rearrangement in GPR98.

Conclusion

Our data highlight the genetic diversity of Usher syndrome in the Lebanese population and the time and cost-effectiveness of whole exome sequencing approach for mutation analysis of genetically heterogeneous conditions caused by large genes.     

Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone

Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological information from several isolates. Currently, all available Prochlorococcus genomes show their incapacity for nitrate utilization. However, environmental sequence data suggest that some uncultivated lineages may have acquired this capacity. Here we report that uncultivated low-light-adapted Prochlorococcus from the nutrient-rich, low-light, anoxic marine zone (AMZ) of the eastern tropical South Pacific have the genetic potential for nitrate uptake and assimilation. All genes involved in this trait were found syntenic with those present in marine Synechococcus. Genomic and phylogenetic analyses also suggest that these genes have not been aquired recently, but perhaps were retained from a common ancestor, highlighting the basal characteristics of the AMZ lineages within Prochlorococcus.Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic microorganisms inhabiting the oceans, key factors in the carbon cycle and a model organism in environmental microbiology (Partensky and Garczarek, 2010). They can be broadly classified into high-light and low-light (LL)-adapted ecotypes (Rocap et al., 2002). These ecotypes exhibit distinct distributions both vertically in the water column and geographically across oligotrophic tropical and subtropical waters (Bouman et al., 2006; Johnson et al., 2006; Zwirglmaier et al., 2008).In past years, the genomes of over a dozen isolates of Prochlorocococus have been fully sequenced (for example, Kettler et al., 2007) and over a hundred single-cell-amplified partial genomes have been described (Malmstrom et al., 2013; Kashtan et al., 2014). All of them have revealed that they cannot use nitrate as a nitrogen source. However, new uncultivated lineages of Prochlorocococus have been identified in the environment using culture-independent techniques based on the sequencing of the 16S rRNA gene and related genomic regions (Lavin et al., 2010; West et al., 2011; Mühling, 2012; Malmstrom et al., 2013). On the other hand, nitrate assimilation rates were reported for uncultivated deep populations of Prochlorococcus in the Western Atlantic Ocean (Casey et al., 2007). In adition, genes necessary for nitrate assimilation associated to Prochlorococcus were identified in the global ocean sampling metagenomic database (Martiny et al., 2009) and in metagenomes of flow-cytometry-sorted Prochlorococcus populations (Batmalle et al., 2014).Important uncultivated Prochlorococcus lineages include those thriving in anoxic marine zones (AMZs), where oxygen concentrations fall below the detection limit of modern sensors, light is scarce, but inorganic nutrients are plentiful (Goericke et al., 2000; Ulloa et al., 2012). Phylogenetic analysis using the 16S–23S rRNA internal transcribed spacer region revealed that the AMZ-associated Prochlorococcus assemblages are mainly composed of two novel LL ecotypes (termed LL-V and LL-VI), which correspond to basal groups linking Prochlorococcus with marine Synechococcus (Lavin et al., 2010), the other dominant marine picocyanobacterium. However, no genomic or physiological information exists for these AMZ lineages.Here we report results from a metagenomic analysis carried out on environmental genomic sequences retrieved from a sample collected at 60 m depth within the AMZ of the eastern tropical South Pacific (Supplementary Figure S1), where dissolved oxygen was undetectable and inorganic nutrients were abundant (Supplementary Figure S2a; Thamdrup et al., 2012). The microbial community was enriched in Prochlorococcus, shown to comprise ~10% of cell abundance, versus ~0.7% of Synechococcus, assessed by flow cytometry (Supplementary Figure S2b). Blast analysis of the taxonomic affiliation of sequences matching the rpoC region 1, a taxonomic marker for cyanobacteria based on a single-copy gene (Palenik, 1994), showed an rpoC gene relative abundance of 86% for Prochlorococcus and 14% for Synechococcus (Supplementary Table S1), supporting the flow cytometry results. Moreover, of the 15% protein-coding sequences assigned to cyanobacteria, 10% binned with Prochlorococcus and 5% with Synechococcus (Supplementary Figure S3). Of those assigned to Prochlorococcus, 90% were related to the LL ecotypes MIT9313 and MIT9303, the closest reported relatives to the AMZ lineages with genomes fully sequenced (Lavin et al., 2010). General statistics of this AMZ metagenome are shown in Supplementary Tables S2 and S3.Analysis of de novo-assembled contigs revealed the presence of several large contigs that binned with Prochlorocococus. In particular, a single contig was found to encode genes related to urea and nitrate uptake and assimilation (contig 51148, GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"KM282015","term_id":"729772065","term_text":"KM282015"}}KM282015; 10 300 bp; Figure 1), in synteny with those in Synechococcus WH8102. The genes in the urease gene cluster (ureABCD) presented high identity to those described for Prochlorococcus MIT9313 and MIT9303 (Rocap et al., 2003; Supplementary Figure S4). Notably, the nitrate/nitrite transporter napA and assimilatory nitrate reductase narB were also found within the same contig (Figure 1a), as well as the genes moeA and mobA (Supplementary Figure S5) involved in the biosynthesis of the Mo-cofactor and necessary for the narB function (Flores et al., 2005). None of these genes have been found in any of the genomes of Prochlorococcus sequenced and described so far. However, homologues that presumably come from uncultivated relatives of Prochlorococcus have been found in the global ocean sampling database (Martiny et al., 2009) and in metagenomes of uncultured, sorted Prochlorococcus populations (Batmalle et al., 2014).Open in a separate windowFigure 1Genomic characteristics of the nitrogen assimilation operon found in contig 51148. (a) Schematic representation of syntenies among contig 51148, Prochlorococcus MIT9313 and MIT9303 genomes, and Synechococcus WH7803 and WH8102 genomes centered on nitrate and urea assimilation genes. Identities (%) among sequences are shown in gray. (b) GC content. (c) Contig coverage. (d) Proximity matrix (Euclidean distance) of the difference in codon usage pattern for the genomes of Prochlorococcus (Pro) and Synechococcus (Syn), and of contig 51148. The shortest distance (dark blue) indicates the highest proximity. (e) Spearman rank-order correlation between tetranucleotide frequency of contig 51148 and those of genomes of marine Prochlorococcus (Pro) and marine Synechococcus (Syn). The highest correlation is shown in dark green.The GC content of contig 51148 was ~51.1% (Figure 1b) and similar to that of LL Prochlorococcus and some marine Synechococcus (Kettler et al., 2007). Likewise, the narB gene had a GC content of 52%, which is less than the ~60% of those in the marine Synechococcus strains WH8102 and WH7803 (to which it presented the highest nucleotide identity), but significantly higher than the ~40% GC of the global ocean sampling high-light Prochlorococcus narB (Supplementary Figure S6). Analysis of codon usage patterns (Yu et al., 2012) and tetranucleotide frequencies (see Supplementary Material and Methods) showed that the cyanobacterial portion of the metagenome and contig 51148 exhibit the highest similarity with LL Prochlorococcus MIT9303 (Figures 1d and e). Additionally, nucleotide identities and phylogenetic analysis confirmed that the urease genes of contig 51148 were associated more closely with Prochlorococcus than Synechococcus (Supplementary Table S4 and Supplementary Figure S4).The homogeneous GC content of contig 51148, the differences in codon usage bias with Synechococcus and phylogenetic analyses of AMZ narB and napA (Figures 2a and b) all suggest that the genetic potential for nitrate uptake and assimilation was not obtained recently by horizontal gene transfer, but instead potentially were retained from a common ancestor with Synechococcus. Mapping the presence/absence of the different nitrate utilization genes onto the cyanobacteria 16S rRNA phylogenetic tree is consistent with this hypothesis (Supplementary Figure S7).Open in a separate windowFigure 2Phylogenetic trees for nitrate assimilation and uptake genes. Maximum-likelihood phylogenetic trees of (a) narB- and (b) napA-predicted amino acid sequences found in contig 51148. Evolutionary history was inferred using neighbour joining (NJ), maximum parsimony (MP) and maximum likelihood (ML). Bootstrap support values for 100 replications are shown at the nodes (NJ/MP/ML).In summary, our results indicate that AMZ Prochlorococcus lineages have the genetic potential for urea and nitrate assimilation, likely an adaptation to the unique nutrient-rich environment where they thrive. Additional genomic characteristics that could explain their high abundance in the oxygen-deficient and very-LL waters of AMZs remain to be assessed.     

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

Background

Single-cell genome sequencing has the potential to allow the in-depth exploration of the vast genetic diversity found in uncultured microbes. We used the marine cyanobacterium Prochlorococcus as a model system for addressing important challenges facing high-throughput whole genome amplification (WGA) and complete genome sequencing of individual cells.

Methodology/Principal Findings

We describe a pipeline that enables single-cell WGA on hundreds of cells at a time while virtually eliminating non-target DNA from the reactions. We further developed a post-amplification normalization procedure that mitigates extreme variations in sequencing coverage associated with multiple displacement amplification (MDA), and demonstrated that the procedure increased sequencing efficiency and facilitated genome assembly. We report genome recovery as high as 99.6% with reference-guided assembly, and 95% with de novo assembly starting from a single cell. We also analyzed the impact of chimera formation during MDA on de novo assembly, and discuss strategies to minimize the presence of incorrectly joined regions in contigs.

Conclusions/Significance

The methods describe in this paper will be useful for sequencing genomes of individual cells from a variety of samples.     

Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions

Background

Vibrio cholerae is a globally dispersed pathogen that has evolved with humans for centuries, but also includes non-pathogenic environmental strains. Here, we identify the genomic variability underlying this remarkable persistence across the three major niche dimensions space, time, and habitat.

Results

Taking an innovative approach of genome-wide association applicable to microbial genomes (GWAS-M), we classify 274 complete V. cholerae genomes by niche, including 39 newly sequenced for this study with the Ion Torrent DNA-sequencing platform. Niche metadata were collected for each strain and analyzed together with comprehensive annotations of genetic and genomic attributes, including point mutations (single-nucleotide polymorphisms, SNPs), protein families, functions and prophages.

Conclusions

Our analysis revealed that genomic variations, in particular mobile functions including phages, prophages, transposable elements, and plasmids underlie the metadata structuring in each of the three niche dimensions. This underscores the role of phages and mobile elements as the most rapidly evolving elements in bacterial genomes, creating local endemicity (space), leading to temporal divergence (time), and allowing the invasion of new habitats. Together, we take a data-driven approach for comparative functional genomics that exploits high-volume genome sequencing and annotation, in conjunction with novel statistical and machine learning analyses to identify connections between genotype and phenotype on a genome-wide scale.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-654) contains supplementary material, which is available to authorized users.     

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities

Background

Environmental shotgun sequencing (metagenomics) provides a new way to study communities in microbial ecology. We here use sequence data from the Global Ocean Sampling (GOS) expedition to investigate toxicant selection pressures revealed by the presence of detoxification genes in marine bacteria. To capture a broad range of potential toxicants we selected detoxification protein families representing systems protecting microorganisms from a variety of stressors, such as metals, organic compounds, antibiotics and oxygen radicals.

Results

Using a bioinformatics procedure based on comparative analysis to finished bacterial genomes we found that the amount of detoxification genes present in marine microorganisms seems surprisingly small. The underrepresentation is particularly evident for toxicant transporters and proteins involved in detoxifying metals. Exceptions are enzymes involved in oxidative stress defense where peroxidase enzymes are more abundant in marine bacteria compared to bacteria in general. In contrast, catalases are almost completely absent from the open ocean environment, suggesting that peroxidases and peroxiredoxins constitute a core line of defense against reactive oxygen species (ROS) in the marine milieu.

Conclusions

We found no indication that detoxification systems would be generally more abundant close to the coast compared to the open ocean. On the contrary, for several of the protein families that displayed a significant geographical distribution, like peroxidase, penicillin binding transpeptidase and divalent ion transport protein, the open ocean samples showed the highest abundance. Along the same lines, the abundance of most detoxification proteins did not increase with estimated pollution. The low level of detoxification systems in marine bacteria indicate that the majority of marine bacteria have a low capacity to adapt to increased pollution. Our study exemplifies the use of metagenomics data in ecotoxicology, and in particular how anthropogenic consequences on life in the sea can be examined.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-749) contains supplementary material, which is available to authorized users.     

Vertical distribution of epibenthic freshwater cyanobacterial Synechococcus spp. strains depends on their ability for photoprotection

Background

Epibenthic cyanobacteria often grow in environments where the fluctuation of light intensity and quality is extreme and frequent. Different strategies have been developed to cope with this problem depending on the distribution of cyanobacteria in the water column.

Principal Findings

Here we provide an experimental proof that the light intensity plays an important role in the vertical distribution of seven, closely related, epibenthic Synechococcus spp. strains isolated from various water depths from the littoral zone of Lake Constance in Germany and cultivated under laboratory conditions. Pigment analysis revealed that the amount of chlorophyll a and total carotenoids decreased with the time of light stress exposure in three phycoerythrin-rich strains collected from 7.0 m water depth and remained low during the recovery phase. In contrast, a constant level of chlorophyll a and either constant or enhanced levels of carotenoids were assayed in phycocyanin-rich strains collected from 1.0 and 0.5 m water depths. Protein analysis revealed that while the amount of biliproteins remained constant in all strains during light stress and recovery, the amount of D1 protein from photosystem II reaction centre was strongly reduced under light stress conditions in strains from 7.0 m and 1.0 m water depth, but not in strains collected from 0.5 m depth.

Conclusion

Based on these data we propose that light intensity, in addition to light quality, is an important selective force in the vertical distribution of Synechococcus spp. strains, depending on their genetically fixed mechanisms for photoprotection.     

Modeling Selective Pressures on Phytoplankton in the Global Ocean

Our view of marine microbes is transforming, as culture-independent methods facilitate rapid characterization of microbial diversity. It is difficult to assimilate this information into our understanding of marine microbe ecology and evolution, because their distributions, traits, and genomes are shaped by forces that are complex and dynamic. Here we incorporate diverse forces—physical, biogeochemical, ecological, and mutational—into a global ocean model to study selective pressures on a simple trait in a widely distributed lineage of picophytoplankton: the nitrogen use abilities of Synechococcus and Prochlorococcus cyanobacteria. Some Prochlorococcus ecotypes have lost the ability to use nitrate, whereas their close relatives, marine Synechococcus, typically retain it. We impose mutations for the loss of nitrogen use abilities in modeled picophytoplankton, and ask: in which parts of the ocean are mutants most disadvantaged by losing the ability to use nitrate, and in which parts are they least disadvantaged? Our model predicts that this selective disadvantage is smallest for picophytoplankton that live in tropical regions where Prochlorococcus are abundant in the real ocean. Conversely, the selective disadvantage of losing the ability to use nitrate is larger for modeled picophytoplankton that live at higher latitudes, where Synechococcus are abundant. In regions where we expect Prochlorococcus and Synechococcus populations to cycle seasonally in the real ocean, we find that model ecotypes with seasonal population dynamics similar to Prochlorococcus are less disadvantaged by losing the ability to use nitrate than model ecotypes with seasonal population dynamics similar to Synechococcus. The model predictions for the selective advantage associated with nitrate use are broadly consistent with the distribution of this ability among marine picocyanobacteria, and at finer scales, can provide insights into interactions between temporally varying ocean processes and selective pressures that may be difficult or impossible to study by other means. More generally, and perhaps more importantly, this study introduces an approach for testing hypotheses about the processes that underlie genetic variation among marine microbes, embedded in the dynamic physical, chemical, and biological forces that generate and shape this diversity.