Investigating the interactions between marine cyanobacteria and their viruses (phages) is important towards understanding the dynamic of ocean's primary productivity. Genome sequencing of marine cyanophages has greatly advanced our understanding about their ecology and evolution. Among 24 reported genomes of cyanophages that infect marine picocyanobacteria, 17 are from cyanomyoviruses and six from cyanopodoviruses, and only one from cyanosiphovirus (Prochlorococcus phage P-SS2). Here we present four complete genome sequences of siphoviruses (S-CBS1, S-CBS2, S-CBS3 and S-CBS4) that infect four different marine Synechococcus strains. Three distinct subtypes were recognized among the five known marine siphoviruses (including P-SS2) in terms of morphology, genome architecture, gene content and sequence similarity. Our study revealed that cyanosiphoviruses are genetically diverse with polyphyletic origin. No core genes were found across these five cyanosiphovirus genomes, and this is in contrast to the fact that many core genes have been found in cyanomyovirus or cyanopodovirus genomes. Interestingly, genes encoding three structural proteins and a lysozyme of S-CBS1 and S-CBS3 showed homology to a prophage-like genetic element in two freshwater Synechococcus elongatus genomes. Re-annotation of the prophage-like genomic region suggests that S. elongatus may contain an intact prophage. Cyanosiphovirus genes involved in DNA metabolism and replication share high sequence homology with those in cyanobacteria, and further phylogenetic analysis based on these genes suggests that ancient and selective genetic exchanges occurred, possibly due to past prophage integration. Metagenomic analysis based on the Global Ocean Sampling database showed that cyanosiphoviruses are present in relatively low abundance in the ocean surface water compared to cyanomyoviruses and cyanopodoviruses.

The VERtical Transport In the Global Ocean (VERTIGO) study examined particle sources and fluxes through the ocean's "twilight zone" (defined here as depths below the euphotic zone to 1000 m). Interdisciplinary process studies were conducted at contrasting sites off Hawaii (ALOHA) and in the NW Pacific (K2) during 3 week occupations in 2004 and 2005, respectively. We examine in this overview paper the contrasting physical, chemical and biological settings and how these conditions impact the source characteristics of the sinking material and the transport efficiency through the twilight zone. A major finding in VERTIGO is the considerably lower transfer efficiency (T eff ) of particulate organic carbon (POC), POC flux 500 / 150 m, at ALOHA (20%) vs. K2 (50%). This efficiency is higher in the diatom-dominated setting at K2 where silica-rich particles dominate the flux at the end of a diatom bloom, and where zooplankton and their pellets are larger. At K2, the drawdown of macronutrients is used to assess export and suggests that shallow remineralization above our 150 m trap is significant, especially for N relative to Si. We explore here also surface export ratios (POC flux/primary production) and possible reasons why this ratio is higher at K2, especially during the first trap deployment. When we compare the 500 m fluxes to deep moored traps, both sites lose about half of the sinking POC by >4000 m, but this comparison is limited in that fluxes at depth may have both a local and distant component.Certainly, the greatest difference in particle flux attenuation is in the mesopelagic, and we highlight other VERTIGO papers that provide a more detailed examination of the particle sources, flux and processes that attenuate the flux of sinking particles. Ultimately, we contend that at least three types of processes need to be considered: heterotrophic degradation of sinking particles, zooplankton migration and surface feeding, and lateral sources of suspended and sinking materials. We have evidence that all of these processes impacted the net attenuation of particle flux vs. depth measured in VERTIGO and would therefore need to be considered and quantified in order to understand the magnitude and efficiency of the ocean's biological pump.

Marine chromophoric dissolved organic matter (CDOM) and its related fluorescent components (FDOM), which are widely distributed but highly photobleached in the surface ocean, are critical in regulating light attenuation in the ocean. However, the origins of marine FDOM are still under investigation. Here we show that cultured picocyanobacteria, Synechococcus and Prochlorococcus, release FDOM that closely match the typical fluorescent signals found in oceanic environments. Picocyanobacterial FDOM also shows comparable apparent fluorescent quantum yields and undergoes similar photo-degradation behaviour when compared with deep-ocean FDOM, further strengthening the similarity between them. Ultrahigh-resolution mass spectrometry (MS) and nuclear magnetic resonance spectroscopy reveal abundant nitrogen-containing compounds in Synechococcus DOM, which may originate from degradation products of the fluorescent phycobilin pigments. Given the importance of picocyanobacteria in the global carbon cycle, our results indicate that picocyanobacteria are likely to be important sources of marine autochthonous FDOM, which may accumulate in the deep ocean.

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Picocyanobacteria make up half of the ocean’s primary production, and they are subjected to frequent viral infection. Viral lysis of picocyanobacteria is a major driving force converting biologically fixed carbon into dissolved organic carbon (DOC). Viral-induced dissolved organic matter (vDOM) released from picocyanobacteria provides complex organic matter to bacterioplankton in the marine ecosystem. In order to understand how picocyanobacterial vDOM are transformed by bacteria and the impact of this process on bacterial community structure, viral lysate of picocyanobacteria was incubated with coastal seawater for 90 days. The transformation of vDOM was analyzed by ultrahigh-resolution mass spectrometry and the shift of bacterial populations analyzed using high-throughput sequencing technology. Addition of picocyanobacterial vDOM introduced abundant nitrogen components into the coastal water, which were largely degraded during the 90 days’ incubation period. However, some DOM signatures were accumulated and the total assigned formulae number increased over time. In contrast to the control (no addition of vDOM), bacterial community enriched with vDOM changed markedly with increased biodiversity indices. The network analysis showed that key bacterial species formed complex relationship with vDOM components, suggesting the potential correspondence between bacterial populations and DOM molecules. We demonstrate that coastal bacterioplankton are able to quickly utilize and transform lysis products of picocyanobacteria, meanwhile, bacterial community varies with changing chemodiverisity of DOM. vDOM released from picocyanobacteria generated a complex labile DOM pool, which was converted to a rather stable DOM pool after microbial processing in the time frame of days to weeks.

Two bacteriophages, DSS3Φ2 and EE36Φ1, which infect marine roseobacters Silicibacter pomeroyi DSS-3 and Sulfitobacter sp. EE-36, respectively, were isolated from Baltimore Inner Harbor water. These two roseophages resemble bacteriophage N4, a large, short-tailed phage infecting Escherichia coli K12, in terms of their morphology and genomic structure. The full genome sequences of DSS3Φ2 and EE36Φ1 reveal that their genome sizes are 74.6 and 73.3 kb, respectively, and they both contain a highly conserved N4-like DNA replication and transcription system. Both roseophages contain a large virion-encapsidated RNA polymerase gene (> 10 kb), which was first discovered in N4. DSS3Φ2 and EE36Φ1 also possess several genes (i.e. ribonucleotide reductase and thioredoxin) that are most similar to the genes in roseobacters. Overall, the two roseophages are highly closely related, and share 80–94% nucleotide sequence identity over 85% of their ORFs. This is the first report of N4-like phages infecting marine bacteria and the second report of N4-like phage since the discovery of phage N4 40 years ago. The finding of these two N4-like roseophages will allow us to further explore the specific phage–host interaction and evolution for this unique group of bacteriophages.

Among the environmental stresses experienced by bacteria, temperature shifts are one of the most important. In this study, we discovered a novel cold adaptation mechanism in Shewanella oneidensis that occurs at the DNA level and is regulated by cryptic prophage excision. Previous studies on bacterial cold tolerance mainly focus on the structural change of cell membrane and changes at the RNA and protein levels. Whether or not genomic change can also contribute to this process has not been explored. Here we employed a whole-genome deep-sequencing method to probe the changes at DNA level in a model psychrotrophic bacteria strain. We found that temperature downshift induced a 10 000-fold increase of the excision of a novel P4-like cryptic prophage. Importantly, although prophage excision only occurred in a relatively small population of bacteria, it was able to facilitate biofilm formation and promote the survival of the entire population. This prophage excision affected cell physiology by disrupting a critical gene encoding transfer-messenger RNA (tmRNA). In addition, we found that the histone-like nucleoid-structuring protein (H-NS) could silence prophage excision via binding to the promoter of the putative excisionase gene at warm temperatures. H-NS level was reduced at cold temperatures, leading to de-repression of prophage excision. Collectively, our results reveal that cryptic prophage excision acts as a regulatory switch to enable the survival of the host at low temperature by controlling the activity of tmRNA and biofilm formation.

The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox) bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named “Ca. Scalindua pacifica”. Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds), alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these bacteria were active for the in situ N transforming process and maintained a versatile life style well adapted to the varying environmental conditions of the studied coastal ocean.